WorldWideScience

Sample records for modeling workflow including

  1. Reporting workflow modeling

    Science.gov (United States)

    Noumeir, Rita

    2004-04-01

    The radiology diagnostic reporting is a process that results in generating a diagnostic report to be made available outside the radiology department. The report captures the radiologist"s interpretations and impressions. It is an element of the patient healthcare record and represents important clinical information to assist in healthcare decisions. The reporting process is initiated by the existence of images or other radiology evidences to be interpreted. The work of individuals is controlled by systems that manage workflow. These systems may introduce delays or constraints on how and when tasks are performed. In order to design and implement efficient information systems that manage the reporting workflow, an accurate workflow modeling is needed. Workflow modeling consists in describing what is done by whom and in what sequence, that is the roles, tasks and sequences of tasks. The workflow model is very important and has major consequences. An inaccurate model introduces inefficiencies, frustrations and may result in a useless information system. In this paper, we will model several common reporting workflows by describing the roles, tasks and information flows involved.

  2. Data Workflow - A Workflow Model for Continuous Data Processing

    NARCIS (Netherlands)

    Wombacher, Andreas

    2010-01-01

    Online data or streaming data are getting more and more important for enterprise information systems, e.g. by integrating sensor data and workflows. The continuous flow of data provided e.g. by sensors requires new workflow models addressing the data perspective of these applications, since

  3. UML based modeling of medical applications workflow in maxillofacial surgery

    OpenAIRE

    Toma, M; Busam, A; Ortmaier, T; Raczkowsky, J; Höpner, C; Marmulla, R

    2007-01-01

    This paper presents our research in medical workflow modeling for computer- and robot-based surgical intervention in maxillofacial surgery. Our goal is to provide a method for clinical workflow modeling including workflow definition for pre- and intra-operative steps, analysis of new methods for combining conventional surgical procedures with robot- and computer-assisted procedures and facilitate an easy implementation of hard- and software systems.

  4. A Multi-Dimensional Classification Model for Scientific Workflow Characteristics

    Energy Technology Data Exchange (ETDEWEB)

    Ramakrishnan, Lavanya; Plale, Beth

    2010-04-05

    Workflows have been used to model repeatable tasks or operations in manufacturing, business process, and software. In recent years, workflows are increasingly used for orchestration of science discovery tasks that use distributed resources and web services environments through resource models such as grid and cloud computing. Workflows have disparate re uirements and constraints that affects how they might be managed in distributed environments. In this paper, we present a multi-dimensional classification model illustrated by workflow examples obtained through a survey of scientists from different domains including bioinformatics and biomedical, weather and ocean modeling, astronomy detailing their data and computational requirements. The survey results and classification model contribute to the high level understandingof scientific workflows.

  5. Rapid Energy Modeling Workflow Demonstration Project

    Science.gov (United States)

    2014-01-01

    Conditioning Engineers BIM Building Information Model BLCC building life cycle costs BPA Building Performance Analysis CAD computer assisted...utilizes information on operations, geometry, orientation, weather, and materials, generating Three-Dimensional (3D) Building Information Models ( BIM ...executed a demonstration of Rapid Energy Modeling (REM) workflows that employed building information modeling ( BIM ) approaches and conceptual energy

  6. Patient-centered care requires a patient-oriented workflow model.

    Science.gov (United States)

    Ozkaynak, Mustafa; Brennan, Patricia Flatley; Hanauer, David A; Johnson, Sharon; Aarts, Jos; Zheng, Kai; Haque, Saira N

    2013-06-01

    Effective design of health information technology (HIT) for patient-centered care requires consideration of workflow from the patient's perspective, termed 'patient-oriented workflow.' This approach organizes the building blocks of work around the patients who are moving through the care system. Patient-oriented workflow complements the more familiar clinician-oriented workflow approaches, and offers several advantages, including the ability to capture simultaneous, cooperative work, which is essential in care delivery. Patient-oriented workflow models can also provide an understanding of healthcare work taking place in various formal and informal health settings in an integrated manner. We present two cases demonstrating the potential value of patient-oriented workflow models. Significant theoretical, methodological, and practical challenges must be met to ensure adoption of patient-oriented workflow models. Patient-oriented workflow models define meaningful system boundaries and can lead to HIT implementations that are more consistent with cooperative work and its emergent features.

  7. Workflow Fault Tree Generation Through Model Checking

    DEFF Research Database (Denmark)

    Herbert, Luke Thomas; Sharp, Robin

    2014-01-01

    We present a framework for the automated generation of fault trees from models of realworld process workflows, expressed in a formalised subset of the popular Business Process Modelling and Notation (BPMN) language. To capture uncertainty and unreliability in workflows, we extend this formalism...... to calculate the probabilities of reaching each non-error system state. Each generated error state is assigned a variable indicating its individual probability of occurrence. Our method can determine the probability of combined faults occurring, while accounting for the basic probabilistic structure...... of the system being modelled. From these calculations, a comprehensive fault tree is generated. Further, we show that annotating the model with rewards (data) allows the expected mean values of reward structures to be calculated at points of failure....

  8. Ship Repair Workflow Cost Model

    National Research Council Canada - National Science Library

    McDevitt, Mike

    2003-01-01

    The effects of intermittent work patterns and funding on the costs of ship repair and maintenance were modeled for the San Diego region in 2002 for Supervisor of Shipbuilding and Repair (SUPSHIP) San Diego...

  9. A Formal Model For Declarative Workflows

    DEFF Research Database (Denmark)

    Mukkamala, Raghava Rao

    the declarative nature of the projected graphs (which are also DCR graphs). We have also provided semantics for distributed executions based on synchronous communication among network of projected graphs and proved that global and distributed executions are equivalent. Further, to support modeling of processes...... using DCR Graphs and to make the formal model available to a wider audience, we have developed prototype tools for specification and a workflow engine for the execution of DCR Graphs. We have also developed tools interfacing SPIN model checker to formally verify safety and liveness properties on the DCR...

  10. Evaluation of Workflow Management Systems - A Meta Model Approach

    Directory of Open Access Journals (Sweden)

    Michael Rosemann

    1998-11-01

    Full Text Available The automated enactment of processes through the use of workflow management systems enables the outsourcing of the control flow from application systems. By now a large number of systems, that follow different workflow paradigms, are available. This leads to the problem of selecting the appropriate workflow management system for a given situation. In this paper we outline the benefits of a meta model approach for the evaluation and comparison of different workflow management systems. After a general introduction on the topic of meta modeling the meta models of the workflow management systems WorkParty (Siemens Nixdorf and FlowMark (IBM are compared as an example. These product specific meta models can be generalized to meta reference models, which helps to specify a workflow methodology. Exemplary, an organisational reference meta model is presented, which helps users in specifying their requirements for a workflow management system.

  11. A Model of Workflow Composition for Emergency Management

    Science.gov (United States)

    Xin, Chen; Bin-ge, Cui; Feng, Zhang; Xue-hui, Xu; Shan-shan, Fu

    The common-used workflow technology is not flexible enough in dealing with concurrent emergency situations. The paper proposes a novel model for defining emergency plans, in which workflow segments appear as a constituent part. A formal abstraction, which contains four operations, is defined to compose workflow segments under constraint rule. The software system of the business process resources construction and composition is implemented and integrated into Emergency Plan Management Application System.

  12. A workflow learning model to improve geovisual analytics utility.

    Science.gov (United States)

    Roth, Robert E; Maceachren, Alan M; McCabe, Craig A

    2009-01-01

    INTRODUCTION: This paper describes the design and implementation of the G-EX Portal Learn Module, a web-based, geocollaborative application for organizing and distributing digital learning artifacts. G-EX falls into the broader context of geovisual analytics, a new research area with the goal of supporting visually-mediated reasoning about large, multivariate, spatiotemporal information. Because this information is unprecedented in amount and complexity, GIScientists are tasked with the development of new tools and techniques to make sense of it. Our research addresses the challenge of implementing these geovisual analytics tools and techniques in a useful manner. OBJECTIVES: The objective of this paper is to develop and implement a method for improving the utility of geovisual analytics software. The success of software is measured by its usability (i.e., how easy the software is to use?) and utility (i.e., how useful the software is). The usability and utility of software can be improved by refining the software, increasing user knowledge about the software, or both. It is difficult to achieve transparent usability (i.e., software that is immediately usable without training) of geovisual analytics software because of the inherent complexity of the included tools and techniques. In these situations, improving user knowledge about the software through the provision of learning artifacts is as important, if not more so, than iterative refinement of the software itself. Therefore, our approach to improving utility is focused on educating the user. METHODOLOGY: The research reported here was completed in two steps. First, we developed a model for learning about geovisual analytics software. Many existing digital learning models assist only with use of the software to complete a specific task and provide limited assistance with its actual application. To move beyond task-oriented learning about software use, we propose a process-oriented approach to learning based on

  13. Automated evolutionary restructuring of workflows to minimise errors via stochastic model checking

    DEFF Research Database (Denmark)

    Herbert, Luke Thomas; Hansen, Zaza Nadja Lee; Jacobsen, Peter

    2014-01-01

    This paper presents a framework for the automated restructuring of workflows that allows one to minimise the impact of errors on a production workflow. The framework allows for the modelling of workflows by means of a formalised subset of the Business Process Modelling and Notation (BPMN) language......, a well-established visual language for modelling workflows in a business context. The framework’s modelling language is extended to include the tracking of real-valued quantities associated with the process (such as time, cost, temperature). In addition, this language also allows for an intention...... by means of a case study from the food industry. Through this case study we explore the extent to which the risk of production faults can be reduced and the impact of these can be minimised, primarily through restructuring of the production workflows. This approach is fully automated and only the modelling...

  14. Design, Modelling and Analysis of a Workflow Reconfiguration

    DEFF Research Database (Denmark)

    Mazzara, Manuel; Abouzaid, Faisal; Dragoni, Nicola

    2011-01-01

    This paper describes a case study involving the reconfiguration of an office workflow. We state the requirements on a system implementing the workflow and its reconfiguration, and describe the system’s design in BPMN. We then use an asynchronous pi-calculus and Web.1 to model the design...

  15. Modelling and analysis of workflow for lean supply chains

    Science.gov (United States)

    Ma, Jinping; Wang, Kanliang; Xu, Lida

    2011-11-01

    Cross-organisational workflow systems are a component of enterprise information systems which support collaborative business process among organisations in supply chain. Currently, the majority of workflow systems is developed in perspectives of information modelling without considering actual requirements of supply chain management. In this article, we focus on the modelling and analysis of the cross-organisational workflow systems in the context of lean supply chain (LSC) using Petri nets. First, the article describes the assumed conditions of cross-organisation workflow net according to the idea of LSC and then discusses the standardisation of collaborating business process between organisations in the context of LSC. Second, the concept of labelled time Petri nets (LTPNs) is defined through combining labelled Petri nets with time Petri nets, and the concept of labelled time workflow nets (LTWNs) is also defined based on LTPNs. Cross-organisational labelled time workflow nets (CLTWNs) is then defined based on LTWNs. Third, the article proposes the notion of OR-silent CLTWNS and a verifying approach to the soundness of LTWNs and CLTWNs. Finally, this article illustrates how to use the proposed method by a simple example. The purpose of this research is to establish a formal method of modelling and analysis of workflow systems for LSC. This study initiates a new perspective of research on cross-organisational workflow management and promotes operation management of LSC in real world settings.

  16. Multi-perspective workflow modeling for online surgical situation models.

    Science.gov (United States)

    Franke, Stefan; Meixensberger, Jürgen; Neumuth, Thomas

    2015-04-01

    Surgical workflow management is expected to enable situation-aware adaptation and intelligent systems behavior in an integrated operating room (OR). The overall aim is to unburden the surgeon and OR staff from both manual maintenance and information seeking tasks. A major step toward intelligent systems behavior is a stable classification of the surgical situation from multiple perspectives based on performed low-level tasks. The present work proposes a method for the classification of surgical situations based on multi-perspective workflow modeling. A model network that interconnects different types of surgical process models is described. Various aspects of a surgical situation description were considered: low-level tasks, high-level tasks, patient status, and the use of medical devices. A study with sixty neurosurgical interventions was conducted to evaluate the performance of our approach and its robustness against incomplete workflow recognition input. A correct classification rate of over 90% was measured for high-level tasks and patient status. The device usage models for navigation and neurophysiology classified over 95% of the situations correctly, whereas the ultrasound usage was more difficult to predict. Overall, the classification rate decreased with an increasing level of input distortion. Autonomous adaptation of medical devices and intelligent systems behavior do not currently depend solely on low-level tasks. Instead, they require a more general type of understanding of the surgical condition. The integration of various surgical process models in a network provided a comprehensive representation of the interventions and allowed for the generation of extensive situation descriptions. Multi-perspective surgical workflow modeling and online situation models will be a significant pre-requisite for reliable and intelligent systems behavior. Hence, they will contribute to a cooperative OR environment. Copyright © 2015 Elsevier Inc. All rights reserved.

  17. Web-video-mining-supported workflow modeling for laparoscopic surgeries.

    Science.gov (United States)

    Liu, Rui; Zhang, Xiaoli; Zhang, Hao

    2016-11-01

    As quality assurance is of strong concern in advanced surgeries, intelligent surgical systems are expected to have knowledge such as the knowledge of the surgical workflow model (SWM) to support their intuitive cooperation with surgeons. For generating a robust and reliable SWM, a large amount of training data is required. However, training data collected by physically recording surgery operations is often limited and data collection is time-consuming and labor-intensive, severely influencing knowledge scalability of the surgical systems. The objective of this research is to solve the knowledge scalability problem in surgical workflow modeling with a low cost and labor efficient way. A novel web-video-mining-supported surgical workflow modeling (webSWM) method is developed. A novel video quality analysis method based on topic analysis and sentiment analysis techniques is developed to select high-quality videos from abundant and noisy web videos. A statistical learning method is then used to build the workflow model based on the selected videos. To test the effectiveness of the webSWM method, 250 web videos were mined to generate a surgical workflow for the robotic cholecystectomy surgery. The generated workflow was evaluated by 4 web-retrieved videos and 4 operation-room-recorded videos, respectively. The evaluation results (video selection consistency n-index ≥0.60; surgical workflow matching degree ≥0.84) proved the effectiveness of the webSWM method in generating robust and reliable SWM knowledge by mining web videos. With the webSWM method, abundant web videos were selected and a reliable SWM was modeled in a short time with low labor cost. Satisfied performances in mining web videos and learning surgery-related knowledge show that the webSWM method is promising in scaling knowledge for intelligent surgical systems. Copyright © 2016 Elsevier B.V. All rights reserved.

  18. LQCD workflow execution framework: Models, provenance and fault-tolerance

    International Nuclear Information System (INIS)

    Piccoli, Luciano; Simone, James N; Kowalkowlski, James B; Dubey, Abhishek

    2010-01-01

    Large computing clusters used for scientific processing suffer from systemic failures when operated over long continuous periods for executing workflows. Diagnosing job problems and faults leading to eventual failures in this complex environment is difficult, specifically when the success of an entire workflow might be affected by a single job failure. In this paper, we introduce a model-based, hierarchical, reliable execution framework that encompass workflow specification, data provenance, execution tracking and online monitoring of each workflow task, also referred to as participants. The sequence of participants is described in an abstract parameterized view, which is translated into a concrete data dependency based sequence of participants with defined arguments. As participants belonging to a workflow are mapped onto machines and executed, periodic and on-demand monitoring of vital health parameters on allocated nodes is enabled according to pre-specified rules. These rules specify conditions that must be true pre-execution, during execution and post-execution. Monitoring information for each participant is propagated upwards through the reflex and healing architecture, which consists of a hierarchical network of decentralized fault management entities, called reflex engines. They are instantiated as state machines or timed automatons that change state and initiate reflexive mitigation action(s) upon occurrence of certain faults. We describe how this cluster reliability framework is combined with the workflow execution framework using formal rules and actions specified within a structure of first order predicate logic that enables a dynamic management design that reduces manual administrative workload, and increases cluster-productivity.

  19. Design and development of a workflow for microbial spray formulations including decision criteria.

    Science.gov (United States)

    Bejarano, Ana; Sauer, Ursula; Preininger, Claudia

    2017-10-01

    Herein, we present a workflow for the development of talc-based microbial inoculants for foliar spray consisting of four steps. These include together with decision-making criteria (1) the selection of additives based on their capability to wet juvenile maize leaves, (2) their adhesion on the plant, (3) their interaction with the biological systems, and (4) the choice of thickener for good dispersion stability. In total, 29 additives including polysaccharides and proteins, polyols, glycosides, oils, waxes, and surfactants (e.g., chitosan, gelatin, glycerol, saponin, castor oil, polyethylene, rhamnolipid) were evaluated. Contact angle and spreading index measurements revealed that the use of 5% Geloil, 1% rhamnolipid, or suitable combinations of Geloil + rhamnolipid and Nurture Yield S 2002 + rhamnolipid enhanced wetting of hydrophobic maize leaves and adherence, similarly to the commercial wetting agents recommended for plant protection 1% Prev B2 and 1% Trifolio S Forte. Interaction of additives with biological systems was based on biocompatibility and phytotoxicity assays, and cell viability monitoring using the endophytic Gram-negative bacterium Paraburkholderia phytofirmans PsJN. Results from biocompatibility assays indicated that in contrast to rhamnolipid and Prev B2 Geloil, Nurture Yield S 2002 and Trifolio S Forte fully supported bacterial growth within a concentration range of 1 to 5%. Dose-dependent phytotoxicity was observed in plants treated with rhamnolipid. Most efficient formulation was composed of PsJN, talc, xanthan, and Geloil. Beyond that, the proposed workflow is expected to generally provide guidance for the development of spray formulations and help other researchers to optimize their choices in this area.

  20. A Workflow for Global Sensitivity Analysis of PBPK Models

    Directory of Open Access Journals (Sweden)

    Kevin eMcNally

    2011-06-01

    Full Text Available Physiologically based pharmacokinetic models have a potentially significant role in the development of a reliable predictive toxicity testing strategy. The structure of PBPK models are ideal frameworks into which disparate in vitro and in vivo data can be integrated and utilised to translate information generated, using alternative to animal measures of toxicity and human biological monitoring data, into plausible corresponding exposures. However, these models invariably include the description of well known non-linear biological processes such as, enzyme saturation and interactions between parameters such as, organ mass and body mass. Therefore, an appropriate sensitivity analysis technique is required which can quantify the influences associated with individual parameters, interactions between parameters and any non-linear processes. In this report we have defined a workflow for sensitivity analysis of PBPK models that is computationally feasible, accounts for interactions between parameters, and can be displayed in the form of a bar chart and cumulative sum line (Lowry plot, which we believe is intuitive and appropriate for toxicologists, risk assessors and regulators.

  1. Towards an integrated workflow for structural reservoir model updating and history matching

    NARCIS (Netherlands)

    Leeuwenburgh, O.; Peters, E.; Wilschut, F.

    2011-01-01

    A history matching workflow, as typically used for updating of petrophysical reservoir model properties, is modified to include structural parameters including the top reservoir and several fault properties: position, slope, throw and transmissibility. A simple 2D synthetic oil reservoir produced by

  2. A STRUCTURAL MODEL OF AN EXCAVATOR WORKFLOW CONTROL SYSTEM

    Directory of Open Access Journals (Sweden)

    A. Gurko

    2016-12-01

    Full Text Available Earthwork improving is connected with excavators automation. In this paper, on the basis of the analysis of problems that a hydraulic excavator control system have to solve, the hierarchical structure of a control system have been proposed. The decomposition of the control process had been executed that allowed to develop the structural model which reflects the characteristics of a multilevel space-distributed control system of an excavator workflow.

  3. CSPBuilder - CSP based Scientific Workflow Modelling

    DEFF Research Database (Denmark)

    Friborg, Rune Møllegaard; Vinter, Brian

    2008-01-01

    This paper introduces a framework for building CSP based applications, targeted for clusters and next generation CPU designs. CPUs are produced with several cores today and every future CPU generation will feature increasingly more cores, resulting in a requirement for concurrency that has...... not previously been called for. The framework is CSP presented as a scienti¿c work¿ow model, specialized for scienti¿c computing applications. The purpose of the framework is to enable scientists to exploit large parallel computation resources, which has previously been hard due of the dif¿culty of concurrent...

  4. Coupling of a continuum ice sheet model and a discrete element calving model using a scientific workflow system

    Science.gov (United States)

    Memon, Shahbaz; Vallot, Dorothée; Zwinger, Thomas; Neukirchen, Helmut

    2017-04-01

    Scientific communities generate complex simulations through orchestration of semi-structured analysis pipelines which involves execution of large workflows on multiple, distributed and heterogeneous computing and data resources. Modeling ice dynamics of glaciers requires workflows consisting of many non-trivial, computationally expensive processing tasks which are coupled to each other. From this domain, we present an e-Science use case, a workflow, which requires the execution of a continuum ice flow model and a discrete element based calving model in an iterative manner. Apart from the execution, this workflow also contains data format conversion tasks that support the execution of ice flow and calving by means of transition through sequential, nested and iterative steps. Thus, the management and monitoring of all the processing tasks including data management and transfer of the workflow model becomes more complex. From the implementation perspective, this workflow model was initially developed on a set of scripts using static data input and output references. In the course of application usage when more scripts or modifications introduced as per user requirements, the debugging and validation of results were more cumbersome to achieve. To address these problems, we identified a need to have a high-level scientific workflow tool through which all the above mentioned processes can be achieved in an efficient and usable manner. We decided to make use of the e-Science middleware UNICORE (Uniform Interface to Computing Resources) that allows seamless and automated access to different heterogenous and distributed resources which is supported by a scientific workflow engine. Based on this, we developed a high-level scientific workflow model for coupling of massively parallel High-Performance Computing (HPC) jobs: a continuum ice sheet model (Elmer/Ice) and a discrete element calving and crevassing model (HiDEM). In our talk we present how the use of a high

  5. Integrate Data into Scientific Workflows for Terrestrial Biosphere Model Evaluation through Brokers

    Science.gov (United States)

    Wei, Y.; Cook, R. B.; Du, F.; Dasgupta, A.; Poco, J.; Huntzinger, D. N.; Schwalm, C. R.; Boldrini, E.; Santoro, M.; Pearlman, J.; Pearlman, F.; Nativi, S.; Khalsa, S.

    2013-12-01

    Terrestrial biosphere models (TBMs) have become integral tools for extrapolating local observations and process-level understanding of land-atmosphere carbon exchange to larger regions. Model-model and model-observation intercomparisons are critical to understand the uncertainties within model outputs, to improve model skill, and to improve our understanding of land-atmosphere carbon exchange. The DataONE Exploration, Visualization, and Analysis (EVA) working group is evaluating TBMs using scientific workflows in UV-CDAT/VisTrails. This workflow-based approach promotes collaboration and improved tracking of evaluation provenance. But challenges still remain. The multi-scale and multi-discipline nature of TBMs makes it necessary to include diverse and distributed data resources in model evaluation. These include, among others, remote sensing data from NASA, flux tower observations from various organizations including DOE, and inventory data from US Forest Service. A key challenge is to make heterogeneous data from different organizations and disciplines discoverable and readily integrated for use in scientific workflows. This presentation introduces the brokering approach taken by the DataONE EVA to fill the gap between TBMs' evaluation scientific workflows and cross-organization and cross-discipline data resources. The DataONE EVA started the development of an Integrated Model Intercomparison Framework (IMIF) that leverages standards-based discovery and access brokers to dynamically discover, access, and transform (e.g. subset and resampling) diverse data products from DataONE, Earth System Grid (ESG), and other data repositories into a format that can be readily used by scientific workflows in UV-CDAT/VisTrails. The discovery and access brokers serve as an independent middleware that bridge existing data repositories and TBMs evaluation scientific workflows but introduce little overhead to either component. In the initial work, an OpenSearch-based discovery broker

  6. Modernizing Earth and Space Science Modeling Workflows in the Big Data Era

    Science.gov (United States)

    Kinter, J. L.; Feigelson, E.; Walker, R. J.; Tino, C.

    2017-12-01

    Modeling is a major aspect of the Earth and space science research. The development of numerical models of the Earth system, planetary systems or astrophysical systems is essential to linking theory with observations. Optimal use of observations that are quite expensive to obtain and maintain typically requires data assimilation that involves numerical models. In the Earth sciences, models of the physical climate system are typically used for data assimilation, climate projection, and inter-disciplinary research, spanning applications from analysis of multi-sensor data sets to decision-making in climate-sensitive sectors with applications to ecosystems, hazards, and various biogeochemical processes. In space physics, most models are from first principles, require considerable expertise to run and are frequently modified significantly for each case study. The volume and variety of model output data from modeling Earth and space systems are rapidly increasing and have reached a scale where human interaction with data is prohibitively inefficient. A major barrier to progress is that modeling workflows isn't deemed by practitioners to be a design problem. Existing workflows have been created by a slow accretion of software, typically based on undocumented, inflexible scripts haphazardly modified by a succession of scientists and students not trained in modern software engineering methods. As a result, existing modeling workflows suffer from an inability to onboard new datasets into models; an inability to keep pace with accelerating data production rates; and irreproducibility, among other problems. These factors are creating an untenable situation for those conducting and supporting Earth system and space science. Improving modeling workflows requires investments in hardware, software and human resources. This paper describes the critical path issues that must be targeted to accelerate modeling workflows, including script modularization, parallelization, and

  7. Open innovation: Towards sharing of data, models and workflows.

    Science.gov (United States)

    Conrado, Daniela J; Karlsson, Mats O; Romero, Klaus; Sarr, Céline; Wilkins, Justin J

    2017-11-15

    Sharing of resources across organisations to support open innovation is an old idea, but which is being taken up by the scientific community at increasing speed, concerning public sharing in particular. The ability to address new questions or provide more precise answers to old questions through merged information is among the attractive features of sharing. Increased efficiency through reuse, and increased reliability of scientific findings through enhanced transparency, are expected outcomes from sharing. In the field of pharmacometrics, efforts to publicly share data, models and workflow have recently started. Sharing of individual-level longitudinal data for modelling requires solving legal, ethical and proprietary issues similar to many other fields, but there are also pharmacometric-specific aspects regarding data formats, exchange standards, and database properties. Several organisations (CDISC, C-Path, IMI, ISoP) are working to solve these issues and propose standards. There are also a number of initiatives aimed at collecting disease-specific databases - Alzheimer's Disease (ADNI, CAMD), malaria (WWARN), oncology (PDS), Parkinson's Disease (PPMI), tuberculosis (CPTR, TB-PACTS, ReSeqTB) - suitable for drug-disease modelling. Organized sharing of pharmacometric executable model code and associated information has in the past been sparse, but a model repository (DDMoRe Model Repository) intended for the purpose has recently been launched. In addition several other services can facilitate model sharing more generally. Pharmacometric workflows have matured over the last decades and initiatives to more fully capture those applied to analyses are ongoing. In order to maximize both the impact of pharmacometrics and the knowledge extracted from clinical data, the scientific community needs to take ownership of and create opportunities for open innovation. Copyright © 2017 Elsevier B.V. All rights reserved.

  8. Restructuring of workflows to minimise errors via stochastic model checking: An automated evolutionary approach

    DEFF Research Database (Denmark)

    Herbert, Luke Thomas; Hansen, Zaza Nadja Lee

    2016-01-01

    This article presents a framework for the automated restructuring of stochastic workflows to reduce the impact of faults. The framework allows for the modelling of workflows by means of a formalised subset of the BPMN workflow language. We extend this modelling formalism to describe faults...... and incorporate an intention preserving stochastic semantics able to model both probabilistic- and non-deterministic behaviour. Stochastic model checking techniques are employed to generate the state-space of a given workflow. Possible improvements obtained by restructuring are measured by employing the framework......'s capacity for tracking real-valued quantities associated with states and transitions of the workflow. The space of possible restructurings of a workflow are explored by means of an evolutionary algorithm, where the goals for improvement are defined in terms of optimising quantities, typically employed...

  9. Declarative Modelling and Safe Distribution of Healthcare Workflows

    DEFF Research Database (Denmark)

    Hildebrandt, Thomas; Mukkamala, Raghava Rao; Slaats, Tijs

    2012-01-01

    We present a formal technique for safe distribution of workflow processes described declaratively as Nested Condition Response (NCR) Graphs and apply the technique to a distributed healthcare workflow. Concretely, we provide a method to synthesize from a NCR Graph and any distribution of its events......-organizational case management. The contributions of this paper is to adapt the technique to allow for nested processes and milestones and to apply it to a healthcare workflow identified in a previous field study at danish hospitals....

  10. An ontology-based hierarchical semantic modeling approach to clinical pathway workflows.

    Science.gov (United States)

    Ye, Yan; Jiang, Zhibin; Diao, Xiaodi; Yang, Dong; Du, Gang

    2009-08-01

    This paper proposes an ontology-based approach of modeling clinical pathway workflows at the semantic level for facilitating computerized clinical pathway implementation and efficient delivery of high-quality healthcare services. A clinical pathway ontology (CPO) is formally defined in OWL web ontology language (OWL) to provide common semantic foundation for meaningful representation and exchange of pathway-related knowledge. A CPO-based semantic modeling method is then presented to describe clinical pathways as interconnected hierarchical models including the top-level outcome flow and intervention workflow level along a care timeline. Furthermore, relevant temporal knowledge can be fully represented by combing temporal entities in CPO and temporal rules based on semantic web rule language (SWRL). An illustrative example about a clinical pathway for cesarean section shows the applicability of the proposed methodology in enabling structured semantic descriptions of any real clinical pathway.

  11. VisTrails SAHM: visualization and workflow management for species habitat modeling

    Science.gov (United States)

    Morisette, Jeffrey T.; Jarnevich, Catherine S.; Holcombe, Tracy R.; Talbert, Colin B.; Ignizio, Drew A.; Talbert, Marian; Silva, Claudio; Koop, David; Swanson, Alan; Young, Nicholas E.

    2013-01-01

    The Software for Assisted Habitat Modeling (SAHM) has been created to both expedite habitat modeling and help maintain a record of the various input data, pre- and post-processing steps and modeling options incorporated in the construction of a species distribution model through the established workflow management and visualization VisTrails software. This paper provides an overview of the VisTrails:SAHM software including a link to the open source code, a table detailing the current SAHM modules, and a simple example modeling an invasive weed species in Rocky Mountain National Park, USA.

  12. Next-Generation Climate Modeling Science Challenges for Simulation, Workflow and Analysis Systems

    Science.gov (United States)

    Koch, D. M.; Anantharaj, V. G.; Bader, D. C.; Krishnan, H.; Leung, L. R.; Ringler, T.; Taylor, M.; Wehner, M. F.; Williams, D. N.

    2016-12-01

    We will present two examples of current and future high-resolution climate-modeling research that are challenging existing simulation run-time I/O, model-data movement, storage and publishing, and analysis. In each case, we will consider lessons learned as current workflow systems are broken by these large-data science challenges, as well as strategies to repair or rebuild the systems. First we consider the science and workflow challenges to be posed by the CMIP6 multi-model HighResMIP, involving around a dozen modeling groups performing quarter-degree simulations, in 3-member ensembles for 100 years, with high-frequency (1-6 hourly) diagnostics, which is expected to generate over 4PB of data. An example of science derived from these experiments will be to study how resolution affects the ability of models to capture extreme-events such as hurricanes or atmospheric rivers. Expected methods to transfer (using parallel Globus) and analyze (using parallel "TECA" software tools) HighResMIP data for such feature-tracking by the DOE CASCADE project will be presented. A second example will be from the Accelerated Climate Modeling for Energy (ACME) project, which is currently addressing challenges involving multiple century-scale coupled high resolution (quarter-degree) climate simulations on DOE Leadership Class computers. ACME is anticipating production of over 5PB of data during the next 2 years of simulations, in order to investigate the drivers of water cycle changes, sea-level-rise, and carbon cycle evolution. The ACME workflow, from simulation to data transfer, storage, analysis and publication will be presented. Current and planned methods to accelerate the workflow, including implementing run-time diagnostics, and implementing server-side analysis to avoid moving large datasets will be presented.

  13. Conceptual-level workflow modeling of scientific experiments using NMR as a case study

    Directory of Open Access Journals (Sweden)

    Gryk Michael R

    2007-01-01

    Full Text Available Abstract Background Scientific workflows improve the process of scientific experiments by making computations explicit, underscoring data flow, and emphasizing the participation of humans in the process when intuition and human reasoning are required. Workflows for experiments also highlight transitions among experimental phases, allowing intermediate results to be verified and supporting the proper handling of semantic mismatches and different file formats among the various tools used in the scientific process. Thus, scientific workflows are important for the modeling and subsequent capture of bioinformatics-related data. While much research has been conducted on the implementation of scientific workflows, the initial process of actually designing and generating the workflow at the conceptual level has received little consideration. Results We propose a structured process to capture scientific workflows at the conceptual level that allows workflows to be documented efficiently, results in concise models of the workflow and more-correct workflow implementations, and provides insight into the scientific process itself. The approach uses three modeling techniques to model the structural, data flow, and control flow aspects of the workflow. The domain of biomolecular structure determination using Nuclear Magnetic Resonance spectroscopy is used to demonstrate the process. Specifically, we show the application of the approach to capture the workflow for the process of conducting biomolecular analysis using Nuclear Magnetic Resonance (NMR spectroscopy. Conclusion Using the approach, we were able to accurately document, in a short amount of time, numerous steps in the process of conducting an experiment using NMR spectroscopy. The resulting models are correct and precise, as outside validation of the models identified only minor omissions in the models. In addition, the models provide an accurate visual description of the control flow for conducting

  14. Transactional Workflows or Workflow Transactions?

    NARCIS (Netherlands)

    Symes, W.W.; Cicchetti, R.; Grefen, P.W.P.J.

    Workflows have generally been accepted as a means to model and support processes in complex organizations. The fact that these processes re-quire robustness and clear semantics has generally been observed and has lead to the combination of workflow and transaction concepts. Many variations on this

  15. Metadata Standards and Workflow Systems

    Science.gov (United States)

    Habermann, T.

    2012-12-01

    All modern workflow systems include mechanisms for recording inputs, outputs and processes. These descriptions can include details required to reproduce the workflows exactly and, in some cases, can include virtual images of the hardware and operating system. There are several on-going and emerging standards for representing these detailed workflows including the Open Provenance Model (OPM) and the W3C PROV. At the same time, ISO metadata standards include a simple provenance or lineage model that includes many important elements of workflows. The ISO model could play a critical role in sharing and discovering workflow information for collections and perhaps in recording some details in granules. In order for this goal to be reached, connections between the detailed standards and ISO must be understood and conventions for using them must be developed.

  16. A workflow model to analyse pediatric emergency overcrowding.

    Science.gov (United States)

    Zgaya, Hayfa; Ajmi, Ines; Gammoudi, Lotfi; Hammadi, Slim; Martinot, Alain; Beuscart, Régis; Renard, Jean-Marie

    2014-01-01

    The greatest source of delay in patient flow is the waiting time from the health care request, and especially the bed request to exit from the Pediatric Emergency Department (PED) for hospital admission. It represents 70% of the time that these patients occupied in the PED waiting rooms. Our objective in this study is to identify tension indicators and bottlenecks that contribute to overcrowding. Patient flow mapping through the PED was carried out in a continuous 2 years period from January 2011 to December 2012. Our method is to use the collected real data, basing on accurate visits made in the PED of the Regional University Hospital Center (CHRU) of Lille (France), in order to construct an accurate and complete representation of the PED processes. The result of this representation is a Workflow model of the patient journey in the PED representing most faithfully possible the reality of the PED of CHRU of Lille. This model allowed us to identify sources of delay in patient flow and aspects of the PED activity that could be improved. It must be enough retailed to produce an analysis allowing to identify the dysfunctions of the PED and also to propose and to estimate prevention indicators of tensions. Our survey is integrated into the French National Research Agency project, titled: "Hospital: optimization, simulation and avoidance of strain" (ANR HOST).

  17. Advanced computational workflow for the multi-scale modeling of the bone metabolic processes.

    Science.gov (United States)

    Dao, Tien Tuan

    2017-06-01

    Multi-scale modeling of the musculoskeletal system plays an essential role in the deep understanding of complex mechanisms underlying the biological phenomena and processes such as bone metabolic processes. Current multi-scale models suffer from the isolation of sub-models at each anatomical scale. The objective of this present work was to develop a new fully integrated computational workflow for simulating bone metabolic processes at multi-scale levels. Organ-level model employs multi-body dynamics to estimate body boundary and loading conditions from body kinematics. Tissue-level model uses finite element method to estimate the tissue deformation and mechanical loading under body loading conditions. Finally, cell-level model includes bone remodeling mechanism through an agent-based simulation under tissue loading. A case study on the bone remodeling process located on the human jaw was performed and presented. The developed multi-scale model of the human jaw was validated using the literature-based data at each anatomical level. Simulation outcomes fall within the literature-based ranges of values for estimated muscle force, tissue loading and cell dynamics during bone remodeling process. This study opens perspectives for accurately simulating bone metabolic processes using a fully integrated computational workflow leading to a better understanding of the musculoskeletal system function from multiple length scales as well as to provide new informative data for clinical decision support and industrial applications.

  18. Gocad2OGS: Workflow to Integrate Geo-structural Information into Numerical Simulation Models

    Science.gov (United States)

    Fischer, Thomas; Walther, Marc; Naumov, Dmitri; Sattler, Sabine; Kolditz, Olaf

    2015-04-01

    The investigation of fluid circulation in the Thuringian syncline is one of the INFLUINS project's targets. A 3D geo-structural model including 12 stratigraphic layers and 54 fault zones is created by geologists in the first step using the Gocad software. Within the INFLUINS project a ground-water flow simulation is used to check existing hypotheses and to gain new ideas of the underground fluid flow behaviour. We used the scientific, platform independent, open source software OpenGeoSys that implements the finite element method to solve the governing equations describing fluid flow in porous media. The geo-structural Gocad model is not suitable for the FEM numerical analysis. Therefore it is converted into an unstructured grid satisfying all mesh quality criteria required for the ground-water flow simulation. The resulting grid is stored in an open data format given by the Visualization Toolkit (vtk). In this work we present a workflow to convert geological structural models, created using the Gocad software, into a simulation model that is easy to use from numerical simulation software. We tested our workflow with the 3D geo-structural model of the Thuringian syncline and were able to setup and to evaluate a hydrogeological simulation model successfully.

  19. POPULATING A LIBRARY OF REUSABLE H-BOMS: ASSESSMENT OF A FEASIBLE IMAGE BASED MODELING WORKFLOW

    Directory of Open Access Journals (Sweden)

    C. Santagati

    2017-08-01

    Full Text Available The paper shows the intermediate results of a research activity aimed at populating a library of reusable Historical Building Object Models (H-BOMs by testing a full digital workflow that takes advantages from using Structure from Motion (SfM models and is centered on the geometrical/stylistic/materic analysis of the architectural element (portal, window, altar. The aim is to find common (invariant and uncommon (variant features in terms of identification of architectural parts and their relationships, geometrical rules, dimensions and proportions, construction materials and measure units, in order to model archetypal shapes from which it is possible to derive all the style variations. At this regard, a set of 14th - 16th century gothic portals of the catalan-aragonese architecture in Etnean area of Eastern Sicily has been studied and used to assess the feasibility of the identified workflow. This approach tries to answer the increasingly demand for guidelines and standards in the field of Cultural Heritage Conservation to create and manage semantic-aware 3D models able to include all the information (both geometrical and alphanumerical ones concerning historical buildings and able to be reused in several projects.

  20. Populating a Library of Reusable H-Boms Assessment of a Feasible Image Based Modeling Workflow

    Science.gov (United States)

    Santagati, C.; Lo Turco, M.; D'Agostino, G.

    2017-08-01

    The paper shows the intermediate results of a research activity aimed at populating a library of reusable Historical Building Object Models (H-BOMs) by testing a full digital workflow that takes advantages from using Structure from Motion (SfM) models and is centered on the geometrical/stylistic/materic analysis of the architectural element (portal, window, altar). The aim is to find common (invariant) and uncommon (variant) features in terms of identification of architectural parts and their relationships, geometrical rules, dimensions and proportions, construction materials and measure units, in order to model archetypal shapes from which it is possible to derive all the style variations. At this regard, a set of 14th - 16th century gothic portals of the catalan-aragonese architecture in Etnean area of Eastern Sicily has been studied and used to assess the feasibility of the identified workflow. This approach tries to answer the increasingly demand for guidelines and standards in the field of Cultural Heritage Conservation to create and manage semantic-aware 3D models able to include all the information (both geometrical and alphanumerical ones) concerning historical buildings and able to be reused in several projects.

  1. Designing Collaborative Developmental Standards by Refactoring of the Earth Science Models, Libraries, Workflows and Frameworks.

    Science.gov (United States)

    Mirvis, E.; Iredell, M.

    2015-12-01

    The operational (OPS) NOAA National Centers for Environmental Prediction (NCEP) suite, traditionally, consist of a large set of multi- scale HPC models, workflows, scripts, tools and utilities, which are very much depending on the variety of the additional components. Namely, this suite utilizes a unique collection of the in-house developed 20+ shared libraries (NCEPLIBS), certain versions of the 3-rd party libraries (like netcdf, HDF, ESMF, jasper, xml etc.), HPC workflow tool within dedicated (sometimes even vendors' customized) HPC system homogeneous environment. This domain and site specific, accompanied with NCEP's product- driven large scale real-time data operations complicates NCEP collaborative development tremendously by reducing chances to replicate this OPS environment anywhere else. The NOAA/NCEP's Environmental Modeling Center (EMC) missions to develop and improve numerical weather, climate, hydrological and ocean prediction through the partnership with the research community. Realizing said difficulties, lately, EMC has been taken an innovative approach to improve flexibility of the HPC environment by building the elements and a foundation for NCEP OPS functionally equivalent environment (FEE), which can be used to ease the external interface constructs as well. Aiming to reduce turnaround time of the community code enhancements via Research-to-Operations (R2O) cycle, EMC developed and deployed several project sub-set standards that already paved the road to NCEP OPS implementation standards. In this topic we will discuss the EMC FEE for O2R requirements and approaches in collaborative standardization, including NCEPLIBS FEE and models code version control paired with the models' derived customized HPC modules and FEE footprints. We will share NCEP/EMC experience and potential in the refactoring of EMC development processes, legacy codes and in securing model source code quality standards by using combination of the Eclipse IDE, integrated with the

  2. A priori modeling of chemical reactions on computational grid platforms: Workflows and data models

    International Nuclear Information System (INIS)

    Rampino, S.; Monari, A.; Rossi, E.; Evangelisti, S.; Laganà, A.

    2012-01-01

    Graphical abstract: The quantum framework of the Grid Empowered Molecular Simulator GEMS assembled on the European Grid allows the ab initio evaluation of the dynamics of small systems starting from the calculation of the electronic properties. Highlights: ► The grid based GEMS simulator accurately models small chemical systems. ► Q5Cost and D5Cost file formats provide interoperability in the workflow. ► Benchmark runs on H + H 2 highlight the Grid empowering. ► O + O 2 and N + N 2 calculated k (T)’s fall within the error bars of the experiment. - Abstract: The quantum framework of the Grid Empowered Molecular Simulator GEMS has been assembled on the segment of the European Grid devoted to the Computational Chemistry Virtual Organization. The related grid based workflow allows the ab initio evaluation of the dynamics of small systems starting from the calculation of the electronic properties. Interoperability between computational codes across the different stages of the workflow was made possible by the use of the common data formats Q5Cost and D5Cost. Illustrative benchmark runs have been performed on the prototype H + H 2 , N + N 2 and O + O 2 gas phase exchange reactions and thermal rate coefficients have been calculated for the last two. Results are discussed in terms of the modeling of the interaction and advantages of using the Grid is highlighted.

  3. Load Composition Model Workflow (BPA TIP-371 Deliverable 1A)

    Energy Technology Data Exchange (ETDEWEB)

    Chassin, David P.; Cezar, Gustavo V.; /SLAC

    2017-07-17

    This project is funded under Bonneville Power Administration (BPA) Strategic Partnership Project (SPP) 17-005 between BPA and SLAC National Accelerator Laboratory. The project in a BPA Technology Improvement Project (TIP) that builds on and validates the Composite Load Model developed by the Western Electric Coordinating Council's (WECC) Load Modeling Task Force (LMTF). The composite load model is used by the WECC Modeling and Validation Work Group to study the stability and security of the western electricity interconnection. The work includes development of load composition data sets, collection of load disturbance data, and model development and validation. This work supports reliable and economic operation of the power system. This report was produced for Deliverable 1A of the BPA TIP-371 Project entitled \\TIP 371: Advancing the Load Composition Model". The deliverable documents the proposed work ow for the Composite Load Model, which provides the basis for the instrumentation, data acquisition, analysis and data dissemination activities addressed by later phases of the project.

  4. Dynamic Chemical Model for $\\text {H} _2 $/$\\text {O} _2 $ Combustion Developed Through a Community Workflow

    KAUST Repository

    Oreluk, James

    2018-01-30

    Elementary-reaction models for $\\\\text{H}_2$/$\\\\text{O}_2$ combustion were evaluated and optimized through a collaborative workflow, establishing accuracy and characterizing uncertainties. Quantitative findings were the optimized model, the importance of $\\\\text{H}_2 + \\\\text{O}_2(1\\\\Delta) = \\\\text{H} + \\\\text{HO}_2$ in high-pressure flames, and the inconsistency of certain low-temperature shock-tube data. The workflow described here is proposed to be even more important because the approach and publicly available cyberinfrastructure allows future community development of evolving improvements. The workflow steps applied here were to develop an initial reaction set using Burke et al. [2012], Burke et al. [2013], Sellevag et al. [2009], and Konnov [2015]; test it for thermodynamic and kinetics consistency and plausibility against other sets in the literature; assign estimated uncertainties where not stated in the sources; select key data targets (

  5. Precise Quantitative Analysis of Probabilistic Business Process Model and Notation Workflows

    DEFF Research Database (Denmark)

    Herbert, Luke Thomas; Sharp, Robin

    2013-01-01

    We present a framework for modeling and analysis of real-world business workflows. We present a formalized core subset of the business process modeling and notation (BPMN) and then proceed to extend this language with probabilistic nondeterministic branching and general-purpose reward annotations......, occurrence and ordering of events, reward-based properties, and best- and worst- case scenarios. We develop a simple example of medical workflow and demonstrate the utility of this analysis in accurate provisioning of drug stocks. Finally, we suggest a path to building upon these techniques to cover...... the entire BPMN language, allow for more complex annotations and ultimately to automatically synthesize workflows by composing predefined subprocesses, in order to achieve a configuration that is optimal for parameters of interest....

  6. Model-based Vestibular Afferent Stimulation: Modular Workflow for Analyzing Stimulation Scenarios in Patient Specific and Statistical Vestibular Anatomy

    Directory of Open Access Journals (Sweden)

    Michael Handler

    2017-12-01

    Full Text Available Our sense of balance and spatial orientation strongly depends on the correct functionality of our vestibular system. Vestibular dysfunction can lead to blurred vision and impaired balance and spatial orientation, causing a significant decrease in quality of life. Recent studies have shown that vestibular implants offer a possible treatment for patients with vestibular dysfunction. The close proximity of the vestibular nerve bundles, the facial nerve and the cochlear nerve poses a major challenge to targeted stimulation of the vestibular system. Modeling the electrical stimulation of the vestibular system allows for an efficient analysis of stimulation scenarios previous to time and cost intensive in vivo experiments. Current models are based on animal data or CAD models of human anatomy. In this work, a (semi-automatic modular workflow is presented for the stepwise transformation of segmented vestibular anatomy data of human vestibular specimens to an electrical model and subsequently analyzed. The steps of this workflow include (i the transformation of labeled datasets to a tetrahedra mesh, (ii nerve fiber anisotropy and fiber computation as a basis for neuron models, (iii inclusion of arbitrary electrode designs, (iv simulation of quasistationary potential distributions, and (v analysis of stimulus waveforms on the stimulation outcome. Results obtained by the workflow based on human datasets and the average shape of a statistical model revealed a high qualitative agreement and a quantitatively comparable range compared to data from literature, respectively. Based on our workflow, a detailed analysis of intra- and extra-labyrinthine electrode configurations with various stimulation waveforms and electrode designs can be performed on patient specific anatomy, making this framework a valuable tool for current optimization questions concerning vestibular implants in humans.

  7. A system for deduction-based formal verification of workflow-oriented software models

    Directory of Open Access Journals (Sweden)

    Klimek Radosław

    2014-12-01

    Full Text Available The work concerns formal verification of workflow-oriented software models using the deductive approach. The formal correctness of a model’s behaviour is considered. Manually building logical specifications, which are regarded as a set of temporal logic formulas, seems to be a significant obstacle for an inexperienced user when applying the deductive approach. A system, along with its architecture, for deduction-based verification of workflow-oriented models is proposed. The process inference is based on the semantic tableaux method, which has some advantages when compared with traditional deduction strategies. The algorithm for automatic generation of logical specifications is proposed. The generation procedure is based on predefined workflow patterns for BPMN, which is a standard and dominant notation for the modeling of business processes. The main idea behind the approach is to consider patterns, defined in terms of temporal logic, as a kind of (logical primitives which enable the transformation of models to temporal logic formulas constituting a logical specification. Automation of the generation process is crucial for bridging the gap between the intuitiveness of deductive reasoning and the difficulty of its practical application when logical specifications are built manually. This approach has gone some way towards supporting, hopefully enhancing, our understanding of deduction-based formal verification of workflow-oriented models.

  8. An organizational model to support the flexible workflow based on ontology

    International Nuclear Information System (INIS)

    Yuan Feng; Li Xudong; Zhu Guangying; Zhang Xiankun

    2012-01-01

    Based on ontology theory, the paper addresses an organizational model for flexible workflow. Firstly, the paper describes the conceptual model of the organizational model on ontology chart, which provides a consistent semantic framework of organization. Secondly, the paper gives the formalization of the model and describes the six key ontology elements of the mode in detail. Finally, the paper discusses deeply how the model supports the flexible workflow and indicates that the model has the advantages of cross-area, cross-organization and cross-domain, multi-process support and scalability. Especially, because the model is represented by ontology, the paper produces the conclusion that the model has covered the defect of unshared feature in traditional models, at the same time, it is more capable and flexible. (authors)

  9. Workflow analysis of laparoscopic Nissen fundoplication in infant pigs- a model for surgical feedback and training.

    Science.gov (United States)

    Krauss, Alexandra; Muensterer, Oliver J; Neumuth, Thomas; Wachowiak, Robin; Donaubauer, Bernd; Korb, Werner; Burgert, Oliver

    2009-04-01

    Many fields use workflow analysis to assess and improve performance of complex tasks. In pediatric endosurgery, workflow analysis may help optimize operative planning and motor skills by breaking down the procedure into particular phases, evaluating these steps individually, and supplying feedback to the surgeon. To develop a module of computer-based surgical workflow analysis for laparoscopic Nissen fundoplication(LNF) and to evaluate its applicability in an infant pig model. LNF was performed in 12 pigs (weight, 7-10 kg) by a single surgeon. Based on synchronized intra and extracorporal movie recordings, the surgical workflow was segmented into temporal operative phases(preparation, dissection, reconstruction and conclusion). During each stage, all actions were recorded in a virtual timeline using a customized workflow editor. Specific tasks, such as knot-tying, were evaluated in detail.Time necessary to perform these actions was compared throughout the study. While time required for the preparation decreased by more than 70% from 4577 to 1379 seconds,and the dissection phase decreased from 2359 to 399 seconds (pig 1 and 12, respectively), the other two phases remained relatively stable. Mean time to perform the entire suture and a 5-throw knot remained constant as well. Our workflow analysis model allows the quantitative evaluation of dynamic actions related to LNF.This data can be used to define average benchmark criteria for the procedures that comprise this operation. It thereby permits task-oriented refinement of surgical technique as well as monitoring the efficacy of training.Although preoperative preparation time decreased substantially, and dissection became faster, time required for the reconstruction and conclusion phases remained relatively constant for a surgeon with moderate experience.Likewise, knot-tying did not accelerate in this setting.S-117

  10. Developing a Collection of Composable Data Translation Software Units to Improve Efficiency and Reproducibility in Ecohydrologic Modeling Workflows

    Science.gov (United States)

    Olschanowsky, C.; Flores, A. N.; FitzGerald, K.; Masarik, M. T.; Rudisill, W. J.; Aguayo, M.

    2017-12-01

    Dynamic models of the spatiotemporal evolution of water, energy, and nutrient cycling are important tools to assess impacts of climate and other environmental changes on ecohydrologic systems. These models require spatiotemporally varying environmental forcings like precipitation, temperature, humidity, windspeed, and solar radiation. These input data originate from a variety of sources, including global and regional weather and climate models, global and regional reanalysis products, and geostatistically interpolated surface observations. Data translation measures, often subsetting in space and/or time and transforming and converting variable units, represent a seemingly mundane, but critical step in the application workflows. Translation steps can introduce errors, misrepresentations of data, slow execution time, and interrupt data provenance. We leverage a workflow that subsets a large regional dataset derived from the Weather Research and Forecasting (WRF) model and prepares inputs to the Parflow integrated hydrologic model to demonstrate the impact translation tool software quality on scientific workflow results and performance. We propose that such workflows will benefit from a community approved collection of data transformation components. The components should be self-contained composable units of code. This design pattern enables automated parallelization and software verification, improving performance and reliability. Ensuring that individual translation components are self-contained and target minute tasks increases reliability. The small code size of each component enables effective unit and regression testing. The components can be automatically composed for efficient execution. An efficient data translation framework should be written to minimize data movement. Composing components within a single streaming process reduces data movement. Each component will typically have a low arithmetic intensity, meaning that it requires about the same number of

  11. Modeling workflow to design machine translation applications for public health practice.

    Science.gov (United States)

    Turner, Anne M; Brownstein, Megumu K; Cole, Kate; Karasz, Hilary; Kirchhoff, Katrin

    2015-02-01

    Provide a detailed understanding of the information workflow processes related to translating health promotion materials for limited English proficiency individuals in order to inform the design of context-driven machine translation (MT) tools for public health (PH). We applied a cognitive work analysis framework to investigate the translation information workflow processes of two large health departments in Washington State. Researchers conducted interviews, performed a task analysis, and validated results with PH professionals to model translation workflow and identify functional requirements for a translation system for PH. The study resulted in a detailed description of work related to translation of PH materials, an information workflow diagram, and a description of attitudes towards MT technology. We identified a number of themes that hold design implications for incorporating MT in PH translation practice. A PH translation tool prototype was designed based on these findings. This study underscores the importance of understanding the work context and information workflow for which systems will be designed. Based on themes and translation information workflow processes, we identified key design guidelines for incorporating MT into PH translation work. Primary amongst these is that MT should be followed by human review for translations to be of high quality and for the technology to be adopted into practice. The time and costs of creating multilingual health promotion materials are barriers to translation. PH personnel were interested in MT's potential to improve access to low-cost translated PH materials, but expressed concerns about ensuring quality. We outline design considerations and a potential machine translation tool to best fit MT systems into PH practice. Copyright © 2014 Elsevier Inc. All rights reserved.

  12. Unified Geomorphological Analysis Workflows with Benthic Terrain Modeler

    Directory of Open Access Journals (Sweden)

    Shaun Walbridge

    2018-03-01

    Full Text Available High resolution remotely sensed bathymetric data is rapidly increasing in volume, but analyzing this data requires a mastery of a complex toolchain of disparate software, including computing derived measurements of the environment. Bathymetric gradients play a fundamental role in energy transport through the seascape. Benthic Terrain Modeler (BTM uses bathymetric data to enable simple characterization of benthic biotic communities and geologic types, and produces a collection of key geomorphological variables known to affect marine ecosystems and processes. BTM has received continual improvements since its 2008 release; here we describe the tools and morphometrics BTM can produce, the research context which this enables, and we conclude with an example application using data from a protected reef in St. Croix, US Virgin Islands.

  13. Design Tools and Workflows for Braided Structures

    DEFF Research Database (Denmark)

    Vestartas, Petras; Heinrich, Mary Katherine; Zwierzycki, Mateusz

    2017-01-01

    This paper presents design workflows for the representation, analysis and fabrication of braided structures. The workflows employ a braid pattern and simulation method which extends the state-of-the-art in the following ways: by supporting the braid design of both pre-determined target shapes...... and merits of our method, demonstrated though four example design and analysis workflows. The workflows frame specific aspects of enquiry for the ongoing research project flora robotica. These include modelling target geometries, automatically producing instructions for fabrication, conducting structural...

  14. Optimize Internal Workflow Management

    Directory of Open Access Journals (Sweden)

    Lucia RUSU

    2010-01-01

    Full Text Available Workflow Management has the role of creating andmaintaining an efficient flow of information and tasks inside anorganization. The major benefit of workflows is the solutions tothe growing needs of organizations. The external and theinternal processes associated with a business need to be carefullyorganized in order to provide a strong foundation for the dailywork. This paper focuses internal workflow within a company,attempts to provide some basic principles related to workflows,and a workflows solution for modeling and deploying usingVisual Studio and SharePoint Server.

  15. Workflow Generation from the Two-Hemisphere Model

    Directory of Open Access Journals (Sweden)

    Gusarovs Konstantīns

    2017-12-01

    Full Text Available Model-Driven Software Development (MDSD is a trend in Software Development that focuses on code generation from various kinds of models. To perform such a task, it is necessary to develop an algorithm that performs source model transformation into the target model, which ideally is an actual software code written in some kind of a programming language. However, at present a lot of methods focus on Unified Modelling Language (UML diagram generation. The present paper describes a result of authors’ research on Two-Hemisphere Model (2HM processing for easier code generation.

  16. On Lifecycle Constraints of Artifact-Centric Workflows

    Science.gov (United States)

    Kucukoguz, Esra; Su, Jianwen

    Data plays a fundamental role in modeling and management of business processes and workflows. Among the recent "data-aware" workflow models, artifact-centric models are particularly interesting. (Business) artifacts are the key data entities that are used in workflows and can reflect both the business logic and the execution states of a running workflow. The notion of artifacts succinctly captures the fluidity aspect of data during workflow executions. However, much of the technical dimension concerning artifacts in workflows is not well understood. In this paper, we study a key concept of an artifact "lifecycle". In particular, we allow declarative specifications/constraints of artifact lifecycle in the spirit of DecSerFlow, and formulate the notion of lifecycle as the set of all possible paths an artifact can navigate through. We investigate two technical problems: (Compliance) does a given workflow (schema) contain only lifecycle allowed by a constraint? And (automated construction) from a given lifecycle specification (constraint), is it possible to construct a "compliant" workflow? The study is based on a new formal variant of artifact-centric workflow model called "ArtiNets" and two classes of lifecycle constraints named "regular" and "counting" constraints. We present a range of technical results concerning compliance and automated construction, including: (1) compliance is decidable when workflow is atomic or constraints are regular, (2) for each constraint, we can always construct a workflow that satisfies the constraint, and (3) sufficient conditions where atomic workflows can be constructed.

  17. Enabling Structured Exploration of Workflow Performance Variability in Extreme-Scale Environments

    Energy Technology Data Exchange (ETDEWEB)

    Kleese van Dam, Kerstin; Stephan, Eric G.; Raju, Bibi; Altintas, Ilkay; Elsethagen, Todd O.; Krishnamoorthy, Sriram

    2015-11-15

    Workflows are taking an Workflows are taking an increasingly important role in orchestrating complex scientific processes in extreme scale and highly heterogeneous environments. However, to date we cannot reliably predict, understand, and optimize workflow performance. Sources of performance variability and in particular the interdependencies of workflow design, execution environment and system architecture are not well understood. While there is a rich portfolio of tools for performance analysis, modeling and prediction for single applications in homogenous computing environments, these are not applicable to workflows, due to the number and heterogeneity of the involved workflow and system components and their strong interdependencies. In this paper, we investigate workflow performance goals and identify factors that could have a relevant impact. Based on our analysis, we propose a new workflow performance provenance ontology, the Open Provenance Model-based WorkFlow Performance Provenance, or OPM-WFPP, that will enable the empirical study of workflow performance characteristics and variability including complex source attribution.

  18. Development of a Sampling-Based Global Sensitivity Analysis Workflow for Multiscale Computational Cancer Models

    Science.gov (United States)

    Wang, Zhihui; Deisboeck, Thomas S.; Cristini, Vittorio

    2014-01-01

    There are two challenges that researchers face when performing global sensitivity analysis (GSA) on multiscale in silico cancer models. The first is increased computational intensity, since a multiscale cancer model generally takes longer to run than does a scale-specific model. The second problem is the lack of a best GSA method that fits all types of models, which implies that multiple methods and their sequence need to be taken into account. In this article, we therefore propose a sampling-based GSA workflow consisting of three phases – pre-analysis, analysis, and post-analysis – by integrating Monte Carlo and resampling methods with the repeated use of analysis of variance (ANOVA); we then exemplify this workflow using a two-dimensional multiscale lung cancer model. By accounting for all parameter rankings produced by multiple GSA methods, a summarized ranking is created at the end of the workflow based on the weighted mean of the rankings for each input parameter. For the cancer model investigated here, this analysis reveals that ERK, a downstream molecule of the EGFR signaling pathway, has the most important impact on regulating both the tumor volume and expansion rate in the algorithm used. PMID:25257020

  19. Automated workflows for modelling chemical fate, kinetics and toxicity.

    Science.gov (United States)

    Sala Benito, J V; Paini, Alicia; Richarz, Andrea-Nicole; Meinl, Thorsten; Berthold, Michael R; Cronin, Mark T D; Worth, Andrew P

    2017-12-01

    Automation is universal in today's society, from operating equipment such as machinery, in factory processes, to self-parking automobile systems. While these examples show the efficiency and effectiveness of automated mechanical processes, automated procedures that support the chemical risk assessment process are still in their infancy. Future human safety assessments will rely increasingly on the use of automated models, such as physiologically based kinetic (PBK) and dynamic models and the virtual cell based assay (VCBA). These biologically-based models will be coupled with chemistry-based prediction models that also automate the generation of key input parameters such as physicochemical properties. The development of automated software tools is an important step in harmonising and expediting the chemical safety assessment process. In this study, we illustrate how the KNIME Analytics Platform can be used to provide a user-friendly graphical interface for these biokinetic models, such as PBK models and VCBA, which simulates the fate of chemicals in vivo within the body and in vitro test systems respectively. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  20. Efficient Workflows for Curation of Heterogeneous Data Supporting Modeling of U-Nb Alloy Aging

    International Nuclear Information System (INIS)

    Ward, Logan Timothy; Hackenberg, Robert Errol

    2016-01-01

    These are slides from a presentation summarizing a graduate research associate's summer project. The following topics are covered in these slides: data challenges in materials, aging in U-Nb Alloys, Building an Aging Model, Different Phase Trans. in U-Nb, the Challenge, Storing Materials Data, Example Data Source, Organizing Data: What is a Schema?, What does a 'XML Schema' look like?, Our Data Schema: Nice and Simple, Storing Data: Materials Data Curation System (MDCS), Problem with MDCS: Slow Data Entry, Getting Literature into MDCS, Staging Data in Excel Document, Final Result: MDCS Records, Analyzing Image Data, Process for Making TTT Diagram, Bottleneck Number 1: Image Analysis, Fitting a TTP Boundary, Fitting a TTP Curve: Comparable Results, How Does it Compare to Our Data?, Image Analysis Workflow, Curating Hardness Records, Hardness Data: Two Key Decisions, Before Peak Age? - Automation, Interactive Viz, Which Transformation?, Microstructure-Informed Model, Tracking the Entire Process, General Problem with Property Models, Pinyon: Toolkit for Managing Model Creation, Tracking Individual Decisions, Jupyter: Docs and Code in One File, Hardness Analysis Workflow, Workflow for Aging Models, and conclusions.

  1. Efficient Workflows for Curation of Heterogeneous Data Supporting Modeling of U-Nb Alloy Aging

    Energy Technology Data Exchange (ETDEWEB)

    Ward, Logan Timothy [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Hackenberg, Robert Errol [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2016-08-31

    These are slides from a presentation summarizing a graduate research associate's summer project. The following topics are covered in these slides: data challenges in materials, aging in U-Nb Alloys, Building an Aging Model, Different Phase Trans. in U-Nb, the Challenge, Storing Materials Data, Example Data Source, Organizing Data: What is a Schema?, What does a "XML Schema" look like?, Our Data Schema: Nice and Simple, Storing Data: Materials Data Curation System (MDCS), Problem with MDCS: Slow Data Entry, Getting Literature into MDCS, Staging Data in Excel Document, Final Result: MDCS Records, Analyzing Image Data, Process for Making TTT Diagram, Bottleneck Number 1: Image Analysis, Fitting a TTP Boundary, Fitting a TTP Curve: Comparable Results, How Does it Compare to Our Data?, Image Analysis Workflow, Curating Hardness Records, Hardness Data: Two Key Decisions, Before Peak Age? - Automation, Interactive Viz, Which Transformation?, Microstructure-Informed Model, Tracking the Entire Process, General Problem with Property Models, Pinyon: Toolkit for Managing Model Creation, Tracking Individual Decisions, Jupyter: Docs and Code in One File, Hardness Analysis Workflow, Workflow for Aging Models, and conclusions.

  2. A Workflow to Model Microbial Loadings in Watersheds

    Science.gov (United States)

    Many watershed models simulate overland and instream microbial fate and transport, but few actually provide loading rates on land surfaces and point sources to the water body network. This paper describes the underlying general equations for microbial loading rates associated wit...

  3. A Workflow to Model Microbial Loadings in Watersheds (proceedings)

    Science.gov (United States)

    Many watershed models simulate overland and instream microbial fate and transport, but few actually provide loading rates on land surfaces and point sources to the water body network. This paper describes the underlying general equations for microbial loading rates associated wit...

  4. modeling workflow management in a distributed computing system

    African Journals Online (AJOL)

    Dr Obe

    extension in colour, time etc, have been applied successfully to model and ... The general characteristics are: (i) The absence of' shared memory;. (ii) Unpredictable inter-node communication delays; and. (iii) Practically no global system state observable by component machines. Due to the lack of shared memory, inter-site.

  5. PROBADO3D – Towards an automatic multimedia indexing workflow for architectural 3D models

    OpenAIRE

    R. Berndt; I. Blümel; R. Wessel

    2010-01-01

    In this paper, we describe a repository for architectural 3D-CAD models which is currently set up at the German National Library of Science and Technology (TIB), Hannover, as part of the larger German PROBADO digital library initiative: The proposed PROBADO-framework is integrating different types of multimedia content-repositories and adding features available in text-based digital libraries. A workflow for automated content-based data analysis and indexing is proposed.

  6. High‐resolution trench photomosaics from image‐based modeling: Workflow and error analysis

    Science.gov (United States)

    Reitman, Nadine G.; Bennett, Scott E. K.; Gold, Ryan D.; Briggs, Richard; Duross, Christopher

    2015-01-01

    Photomosaics are commonly used to construct maps of paleoseismic trench exposures, but the conventional process of manually using image‐editing software is time consuming and produces undesirable artifacts and distortions. Herein, we document and evaluate the application of image‐based modeling (IBM) for creating photomosaics and 3D models of paleoseismic trench exposures, illustrated with a case‐study trench across the Wasatch fault in Alpine, Utah. Our results include a structure‐from‐motion workflow for the semiautomated creation of seamless, high‐resolution photomosaics designed for rapid implementation in a field setting. Compared with conventional manual methods, the IBM photomosaic method provides a more accurate, continuous, and detailed record of paleoseismic trench exposures in approximately half the processing time and 15%–20% of the user input time. Our error analysis quantifies the effect of the number and spatial distribution of control points on model accuracy. For this case study, an ∼87  m2 exposure of a benched trench photographed at viewing distances of 1.5–7 m yields a model with <2  cm root mean square error (rmse) with as few as six control points. Rmse decreases as more control points are implemented, but the gains in accuracy are minimal beyond 12 control points. Spreading control points throughout the target area helps to minimize error. We propose that 3D digital models and corresponding photomosaics should be standard practice in paleoseismic exposure archiving. The error analysis serves as a guide for future investigations that seek balance between speed and accuracy during photomosaic and 3D model construction.

  7. Web-based workflow planning platform supporting the design and execution of complex multiscale cancer models.

    Science.gov (United States)

    Sakkalis, Vangelis; Sfakianakis, Stelios; Tzamali, Eleftheria; Marias, Kostas; Stamatakos, Georgios; Misichroni, Fay; Ouzounoglou, Eleftherios; Kolokotroni, Eleni; Dionysiou, Dimitra; Johnson, David; McKeever, Steve; Graf, Norbert

    2014-05-01

    Significant Virtual Physiological Human efforts and projects have been concerned with cancer modeling, especially in the European Commission Seventh Framework research program, with the ambitious goal to approach personalized cancer simulation based on patient-specific data and thereby optimize therapy decisions in the clinical setting. However, building realistic in silico predictive models targeting the clinical practice requires interactive, synergetic approaches to integrate the currently fragmented efforts emanating from the systems biology and computational oncology communities all around the globe. To further this goal, we propose an intelligent graphical workflow planning system that exploits the multiscale and modular nature of cancer and allows building complex cancer models by intuitively linking/interchanging highly specialized models. The system adopts and extends current standardization efforts, key tools, and infrastructure in view of building a pool of reliable and reproducible models capable of improving current therapies and demonstrating the potential for clinical translation of these technologies.

  8. Integrating prediction, provenance, and optimization into high energy workflows

    Energy Technology Data Exchange (ETDEWEB)

    Schram, M.; Bansal, V.; Friese, R. D.; Tallent, N. R.; Yin, J.; Barker, K. J.; Stephan, E.; Halappanavar, M.; Kerbyson, D. J.

    2017-10-01

    We propose a novel approach for efficient execution of workflows on distributed resources. The key components of this framework include: performance modeling to quantitatively predict workflow component behavior; optimization-based scheduling such as choosing an optimal subset of resources to meet demand and assignment of tasks to resources; distributed I/O optimizations such as prefetching; and provenance methods for collecting performance data. In preliminary results, these techniques improve throughput on a small Belle II workflow by 20%.

  9. Dual-use tools and systematics-aware analysis workflows in the ATLAS Run-2 analysis model

    CERN Document Server

    FARRELL, Steven; The ATLAS collaboration; Calafiura, Paolo; Delsart, Pierre-Antoine; Elsing, Markus; Koeneke, Karsten; Krasznahorkay, Attila; Krumnack, Nils; Lancon, Eric; Lavrijsen, Wim; Laycock, Paul; Lei, Xiaowen; Strandberg, Sara Kristina; Verkerke, Wouter; Vivarelli, Iacopo; Woudstra, Martin

    2015-01-01

    The ATLAS analysis model has been overhauled for the upcoming run of data collection in 2015 at 13 TeV. One key component of this upgrade was the Event Data Model (EDM), which now allows for greater flexibility in the choice of analysis software framework and provides powerful new features that can be exploited by analysis software tools. A second key component of the upgrade is the introduction of a dual-use tool technology, which provides abstract interfaces for analysis software tools to run in either the Athena framework or a ROOT-based framework. The tool interfaces, including a new interface for handling systematic uncertainties, have been standardized for the development of improved analysis workflows and consolidation of high-level analysis tools. This paper will cover the details of the dual-use tool functionality, the systematics interface, and how these features fit into a centrally supported analysis environment.

  10. Dual-use tools and systematics-aware analysis workflows in the ATLAS Run-II analysis model

    CERN Document Server

    FARRELL, Steven; The ATLAS collaboration

    2015-01-01

    The ATLAS analysis model has been overhauled for the upcoming run of data collection in 2015 at 13 TeV. One key component of this upgrade was the Event Data Model (EDM), which now allows for greater flexibility in the choice of analysis software framework and provides powerful new features that can be exploited by analysis software tools. A second key component of the upgrade is the introduction of a dual-use tool technology, which provides abstract interfaces for analysis software tools to run in either the Athena framework or a ROOT-based framework. The tool interfaces, including a new interface for handling systematic uncertainties, have been standardized for the development of improved analysis workflows and consolidation of high-level analysis tools. This presentation will cover the details of the dual-use tool functionality, the systematics interface, and how these features fit into a centrally supported analysis environment.

  11. An integrated workflow for stress and flow modelling using outcrop-derived discrete fracture networks

    DEFF Research Database (Denmark)

    Bisdom, Kevin; Nick, Hamid; Bertotti, Giovanni

    2017-01-01

    Fluid flow in naturally fractured reservoirs is often controlled by subseismic-scale fracture networks. Although the fracture network can be partly sampled in the direct vicinity of wells, the inter-well scale network is poorly constrained in fractured reservoir models. Outcrop analogues can...... provide data for populating domains of the reservoir model where no direct measurements are available. However, extracting relevant statistics from large outcrops representative of inter-well scale fracture networks remains challenging. Recent advances in outcrop imaging provide high-resolution datasets...... that can cover areas of several hundred by several hundred meters, i.e. the domain between adjacent wells, but even then, data from the high-resolution models is often upscaled to reservoir flow grids, resulting in loss of accuracy. We present a workflow that uses photorealistic georeferenced outcrop...

  12. A comprehensive workflow for general-purpose neural modeling with highly configurable neuromorphic hardware systems.

    Science.gov (United States)

    Brüderle, Daniel; Petrovici, Mihai A; Vogginger, Bernhard; Ehrlich, Matthias; Pfeil, Thomas; Millner, Sebastian; Grübl, Andreas; Wendt, Karsten; Müller, Eric; Schwartz, Marc-Olivier; de Oliveira, Dan Husmann; Jeltsch, Sebastian; Fieres, Johannes; Schilling, Moritz; Müller, Paul; Breitwieser, Oliver; Petkov, Venelin; Muller, Lyle; Davison, Andrew P; Krishnamurthy, Pradeep; Kremkow, Jens; Lundqvist, Mikael; Muller, Eilif; Partzsch, Johannes; Scholze, Stefan; Zühl, Lukas; Mayr, Christian; Destexhe, Alain; Diesmann, Markus; Potjans, Tobias C; Lansner, Anders; Schüffny, René; Schemmel, Johannes; Meier, Karlheinz

    2011-05-01

    In this article, we present a methodological framework that meets novel requirements emerging from upcoming types of accelerated and highly configurable neuromorphic hardware systems. We describe in detail a device with 45 million programmable and dynamic synapses that is currently under development, and we sketch the conceptual challenges that arise from taking this platform into operation. More specifically, we aim at the establishment of this neuromorphic system as a flexible and neuroscientifically valuable modeling tool that can be used by non-hardware experts. We consider various functional aspects to be crucial for this purpose, and we introduce a consistent workflow with detailed descriptions of all involved modules that implement the suggested steps: The integration of the hardware interface into the simulator-independent model description language PyNN; a fully automated translation between the PyNN domain and appropriate hardware configurations; an executable specification of the future neuromorphic system that can be seamlessly integrated into this biology-to-hardware mapping process as a test bench for all software layers and possible hardware design modifications; an evaluation scheme that deploys models from a dedicated benchmark library, compares the results generated by virtual or prototype hardware devices with reference software simulations and analyzes the differences. The integration of these components into one hardware-software workflow provides an ecosystem for ongoing preparative studies that support the hardware design process and represents the basis for the maturity of the model-to-hardware mapping software. The functionality and flexibility of the latter is proven with a variety of experimental results.

  13. An enhancement of the role-based access control model to facilitate information access management in context of team collaboration and workflow.

    Science.gov (United States)

    Le, Xuan Hung; Doll, Terry; Barbosu, Monica; Luque, Amneris; Wang, Dongwen

    2012-12-01

    Although information access control models have been developed and applied to various applications, few of the previous works have addressed the issue of managing information access in the combined context of team collaboration and workflow. To facilitate this requirement, we have enhanced the Role-Based Access Control (RBAC) model through formulating universal constraints, defining bridging entities and contributing attributes, extending access permissions to include workflow contexts, synthesizing a role-based access delegation model to target on specific objects, and developing domain ontologies as instantiations of the general model to particular applications. We have successfully applied this model to the New York State HIV Clinical Education Initiative (CEI) project to address the specific needs of information management in collaborative processes. An initial evaluation has shown this model achieved a high level of agreement with an existing system when applied to 4576 cases (kappa=0.801). Comparing to a reference standard, the sensitivity and specificity of the enhanced RBAC model were at the level of 97-100%. These results indicate that the enhanced RBAC model can be effectively used for information access management in context of team collaboration and workflow to coordinate clinical education programs. Future research is required to incrementally develop additional types of universal constraints, to further investigate how the workflow context and access delegation can be enriched to support the various needs on information access management in collaborative processes, and to examine the generalizability of the enhanced RBAC model for other applications in clinical education, biomedical research, and patient care. Copyright © 2012 Elsevier Inc. All rights reserved.

  14. Modeling Boston: A workflow for the efficient generation and maintenance of urban building energy models from existing geospatial datasets

    International Nuclear Information System (INIS)

    Cerezo Davila, Carlos; Reinhart, Christoph F.; Bemis, Jamie L.

    2016-01-01

    City governments and energy utilities are increasingly focusing on the development of energy efficiency strategies for buildings as a key component in emission reduction plans and energy supply strategies. To support these diverse needs, a new generation of Urban Building Energy Models (UBEM) is currently being developed and validated to estimate citywide hourly energy demands at the building level. However, in order for cities to rely on UBEMs, effective model generation and maintenance workflows are needed based on existing urban data structures. Within this context, the authors collaborated with the Boston Redevelopment Authority to develop a citywide UBEM based on official GIS datasets and a custom building archetype library. Energy models for 83,541 buildings were generated and assigned one of 52 use/age archetypes, within the CAD modelling environment Rhinoceros3D. The buildings were then simulated using the US DOE EnergyPlus simulation program, and results for buildings of the same archetype were crosschecked against data from the US national energy consumption surveys. A district-level intervention combining photovoltaics with demand side management is presented to demonstrate the ability of UBEM to provide actionable information. Lack of widely available archetype templates and metered energy data, were identified as key barriers within existing workflows that may impede cities from effectively applying UBEM to guide energy policy. - Highlights: • Data requirements for Urban Building Energy Models are reviewed. • A workflow for UBEM generation from available GIS datasets is developed. • A citywide demand simulation model for Boston is generated and tested. • Limitations for UBEM in current urban data systems are identified and discussed. • Model application for energy management policy is shown in an urban PV scenario.

  15. Design Tools and Workflows for Braided Structures

    DEFF Research Database (Denmark)

    Vestartas, Petras; Heinrich, Mary Katherine; Zwierzycki, Mateusz

    2017-01-01

    This paper presents design workflows for the representation, analysis and fabrication of braided structures. The workflows employ a braid pattern and simulation method which extends the state-of-the-art in the following ways: by supporting the braid design of both pre-determined target shapes...... and exploratory, generative, or evolved designs; by incorporating material and fabrication constraints generalised for both hand and machine; by providing a greater degree of design agency and supporting real-time modification of braid topologies. The paper first introduces braid as a technique, stating...... and merits of our method, demonstrated though four example design and analysis workflows. The workflows frame specific aspects of enquiry for the ongoing research project flora robotica. These include modelling target geometries, automatically producing instructions for fabrication, conducting structural...

  16. Querying Workflow Logs

    Directory of Open Access Journals (Sweden)

    Yan Tang

    2018-01-01

    Full Text Available A business process or workflow is an assembly of tasks that accomplishes a business goal. Business process management is the study of the design, configuration/implementation, enactment and monitoring, analysis, and re-design of workflows. The traditional methodology for the re-design and improvement of workflows relies on the well-known sequence of extract, transform, and load (ETL, data/process warehousing, and online analytical processing (OLAP tools. In this paper, we study the ad hoc queryiny of process enactments for (data-centric business processes, bypassing the traditional methodology for more flexibility in querying. We develop an algebraic query language based on “incident patterns” with four operators inspired from Business Process Model and Notation (BPMN representation, allowing the user to formulate ad hoc queries directly over workflow logs. A formal semantics of this query language, a preliminary query evaluation algorithm, and a group of elementary properties of the operators are provided.

  17. Towards a High Reliable Enforcement of Safety Regulations - A Workflow Meta Data Model and Probabilistic Failure Management Approach

    Directory of Open Access Journals (Sweden)

    Heiko Henning Thimm

    2016-10-01

    Full Text Available Today’s companies are able to automate the enforcement of Environmental, Health and Safety (EH&S duties through the use of workflow management technology. This approach requires to specify activities that are combined to workflow models for EH&S enforcement duties. In order to meet given safety regulations these activities are to be completed correctly and within given deadlines. Otherwise, activity failures emerge which may lead to breaches against safety regulations. A novel domain-specific workflow meta data model is proposed. The model enables a system to detect and predict activity failures through the use of data about the company, failure statistics, and activity proxies. Since the detection and prediction methods are based on the evaluation of constraints specified on EH&S regulations, a system approach is proposed that builds on the integration of a Workflow Management System (WMS with an EH&S Compliance Information System. Main principles of the failure detection and prediction are described. For EH&S managers the system shall provide insights into the current failure situation. This can help to prevent and mitigate critical situations such as safety enforcement measures that are behind their deadlines. As a result a more reliable enforcement of safety regulations can be achieved.

  18. Information Management Workflow and Tools Enabling Multiscale Modeling Within ICME Paradigm

    Science.gov (United States)

    Arnold, Steven M.; Bednarcyk, Brett A.; Austin, Nic; Terentjev, Igor; Cebon, Dave; Marsden, Will

    2016-01-01

    With the increased emphasis on reducing the cost and time to market of new materials, the need for analytical tools that enable the virtual design and optimization of materials throughout their processing - internal structure - property - performance envelope, along with the capturing and storing of the associated material and model information across its lifecycle, has become critical. This need is also fueled by the demands for higher efficiency in material testing; consistency, quality and traceability of data; product design; engineering analysis; as well as control of access to proprietary or sensitive information. Fortunately, material information management systems and physics-based multiscale modeling methods have kept pace with the growing user demands. Herein, recent efforts to establish workflow for and demonstrate a unique set of web application tools for linking NASA GRC's Integrated Computational Materials Engineering (ICME) Granta MI database schema and NASA GRC's Integrated multiscale Micromechanics Analysis Code (ImMAC) software toolset are presented. The goal is to enable seamless coupling between both test data and simulation data, which is captured and tracked automatically within Granta MI®, with full model pedigree information. These tools, and this type of linkage, are foundational to realizing the full potential of ICME, in which materials processing, microstructure, properties, and performance are coupled to enable application-driven design and optimization of materials and structures.

  19. A data analysis workflow to enhance clay and organic carbon models using proximal Vis-NIR data

    DEFF Research Database (Denmark)

    Tabatabai, Salman; Knadel, Maria; Greve, Mogens Humlekrog

    Modelling proximal sensors data is becoming a norm in soil characterization and mapping. In many cases, these models still have low predictive capabilities and lack robustness due to the large amount of noise from several environmental factors. In this study we proposed a combination of extensive...... the importance of following a well-designed workflow of preprocessing survey and variable selection in producing reliable and robust models from proximally sensed Vis-NIRS data....

  20. 3d-modelling workflows for trans-nationally shared geological models - first approaches from the project GeoMol

    Science.gov (United States)

    Rupf, Isabel

    2013-04-01

    To meet the EU's ambitious targets for carbon emission reduction, renewable energy production has to be strongly upgraded and made more efficient for grid energy storage. Alpine Foreland Basins feature a unique geological inventory which can contribute substantially to tackle these challenges. They offer a geothermal potential and storage capacity for compressed air, as well as space for underground storage of CO2. Exploiting these natural subsurface resources will strongly compete with existing oil and gas claims and groundwater issues. The project GeoMol will provide consistent 3-dimensional subsurface information about the Alpine Foreland Basins based on a holistic and transnational approach. Core of the project GeoMol is a geological framework model for the entire Northern Molasse Basin, complemented by five detailed models in pilot areas, also in the Po Basin, which are dedicated to specific questions of subsurface use. The models will consist of up to 13 litho-stratigraphic horizons ranging from the Cenozoic basin fill down to Mesozoic and late Paleozoic sedimentary rocks and the crystalline basement. More than 5000 wells and 28 000 km seismic lines serve as input data sets for the geological subsurface model. The data have multiple sources and various acquisition dates, and their interpretations have gone through several paradigm changes. Therefore, it is necessary to standardize the data with regards to technical parameters and content prior to further analysis (cf. Capar et al. 2013, EGU2013-5349). Each partner will build its own geological subsurface model with different software solutions for seismic interpretation and 3d-modelling. Therefore, 3d-modelling follows different software- and partner-specific workflows. One of the main challenges of the project is to ensure a seamlessly fitting framework model. It is necessary to define several milestones for cross border checks during the whole modelling process. Hence, the main input data set of the

  1. Scientific Workflows: Business as Usual?

    Science.gov (United States)

    Ludäscher, Bertram; Weske, Mathias; McPhillips, Timothy; Bowers, Shawn

    Business workflow management and business process modeling are mature research areas, whose roots go far back to the early days of office automation systems. Scientific workflow management, on the other hand, is a much more recent phenomenon, triggered by (i) a shift towards data-intensive and computational methods in the natural sciences, and (ii) the resulting need for tools that can simplify and automate recurring computational tasks. In this paper, we provide an introduction and overview of scientific workflows, highlighting features and important concepts commonly found in scientific workflow applications. We illustrate these using simple workflow examples from a bioinformatics domain. We then discuss similarities and, more importantly, differences between scientific workflows and business workflows. While some concepts and solutions developed in one domain may be readily applicable to the other, there remain sufficiently many differences that warrant a new research effort at the intersection of scientific and business workflows. We close by proposing a number of research opportunities for cross-fertilization between the scientific workflow and business workflow communities.

  2. CMS distributed computing workflow experience

    International Nuclear Information System (INIS)

    Adelman-McCarthy, Jennifer; Gutsche, Oliver; Haas, Jeffrey D; Prosper, Harrison B; Dutta, Valentina; Gomez-Ceballos, Guillelmo; Hahn, Kristian; Klute, Markus; Mohapatra, Ajit; Spinoso, Vincenzo; Kcira, Dorian; Caudron, Julien; Liao Junhui; Pin, Arnaud; Schul, Nicolas; Lentdecker, Gilles De; McCartin, Joseph; Vanelderen, Lukas; Janssen, Xavier; Tsyganov, Andrey

    2011-01-01

    The vast majority of the CMS Computing capacity, which is organized in a tiered hierarchy, is located away from CERN. The 7 Tier-1 sites archive the LHC proton-proton collision data that is initially processed at CERN. These sites provide access to all recorded and simulated data for the Tier-2 sites, via wide-area network (WAN) transfers. All central data processing workflows are executed at the Tier-1 level, which contain re-reconstruction and skimming workflows of collision data as well as reprocessing of simulated data to adapt to changing detector conditions. This paper describes the operation of the CMS processing infrastructure at the Tier-1 level. The Tier-1 workflows are described in detail. The operational optimization of resource usage is described. In particular, the variation of different workflows during the data taking period of 2010, their efficiencies and latencies as well as their impact on the delivery of physics results is discussed and lessons are drawn from this experience. The simulation of proton-proton collisions for the CMS experiment is primarily carried out at the second tier of the CMS computing infrastructure. Half of the Tier-2 sites of CMS are reserved for central Monte Carlo (MC) production while the other half is available for user analysis. This paper summarizes the large throughput of the MC production operation during the data taking period of 2010 and discusses the latencies and efficiencies of the various types of MC production workflows. We present the operational procedures to optimize the usage of available resources and we the operational model of CMS for including opportunistic resources, such as the larger Tier-3 sites, into the central production operation.

  3. CMS distributed computing workflow experience

    Science.gov (United States)

    Adelman-McCarthy, Jennifer; Gutsche, Oliver; Haas, Jeffrey D.; Prosper, Harrison B.; Dutta, Valentina; Gomez-Ceballos, Guillelmo; Hahn, Kristian; Klute, Markus; Mohapatra, Ajit; Spinoso, Vincenzo; Kcira, Dorian; Caudron, Julien; Liao, Junhui; Pin, Arnaud; Schul, Nicolas; De Lentdecker, Gilles; McCartin, Joseph; Vanelderen, Lukas; Janssen, Xavier; Tsyganov, Andrey; Barge, Derek; Lahiff, Andrew

    2011-12-01

    The vast majority of the CMS Computing capacity, which is organized in a tiered hierarchy, is located away from CERN. The 7 Tier-1 sites archive the LHC proton-proton collision data that is initially processed at CERN. These sites provide access to all recorded and simulated data for the Tier-2 sites, via wide-area network (WAN) transfers. All central data processing workflows are executed at the Tier-1 level, which contain re-reconstruction and skimming workflows of collision data as well as reprocessing of simulated data to adapt to changing detector conditions. This paper describes the operation of the CMS processing infrastructure at the Tier-1 level. The Tier-1 workflows are described in detail. The operational optimization of resource usage is described. In particular, the variation of different workflows during the data taking period of 2010, their efficiencies and latencies as well as their impact on the delivery of physics results is discussed and lessons are drawn from this experience. The simulation of proton-proton collisions for the CMS experiment is primarily carried out at the second tier of the CMS computing infrastructure. Half of the Tier-2 sites of CMS are reserved for central Monte Carlo (MC) production while the other half is available for user analysis. This paper summarizes the large throughput of the MC production operation during the data taking period of 2010 and discusses the latencies and efficiencies of the various types of MC production workflows. We present the operational procedures to optimize the usage of available resources and we the operational model of CMS for including opportunistic resources, such as the larger Tier-3 sites, into the central production operation.

  4. SHARING ON WEB 3D MODELS OF ANCIENT THEATRES. A METHODOLOGICAL WORKFLOW

    Directory of Open Access Journals (Sweden)

    A. Scianna

    2016-06-01

    Full Text Available In the last few years, the need to share on the Web the knowledge of Cultural Heritage (CH through navigable 3D models has increased. This need requires the availability of Web-based virtual reality systems and 3D WEBGIS. In order to make the information available to all stakeholders, these instruments should be powerful and at the same time very user-friendly. However, research and experiments carried out so far show that a standardized methodology doesn’t exist. All this is due both to complexity and dimensions of geometric models to be published, on the one hand, and to excessive costs of hardware and software tools, on the other. In light of this background, the paper describes a methodological approach for creating 3D models of CH, freely exportable on the Web, based on HTML5 and free and open source software. HTML5, supporting the WebGL standard, allows the exploration of 3D spatial models using most used Web browsers like Chrome, Firefox, Safari, Internet Explorer. The methodological workflow here described has been tested for the construction of a multimedia geo-spatial platform developed for three-dimensional exploration and documentation of the ancient theatres of Segesta and of Carthage, and the surrounding landscapes. The experimental application has allowed us to explore the potential and limitations of sharing on the Web of 3D CH models based on WebGL standard. Sharing capabilities could be extended defining suitable geospatial Web-services based on capabilities of HTML5 and WebGL technology.

  5. Customized atomicity specification for transactional workflows

    NARCIS (Netherlands)

    Derks, W.L.A.; Dehnert, Juliane; Grefen, P.W.P.J.; Jonker, Willem

    2000-01-01

    This paper introduces a new approach for specifying transaction management requirements for workflow applications. We propose independent models for the specification of workflow and transaction properties. Although we distinguish multiple transaction properties in our approach, we focus on

  6. Customized Atomicity Specification for Transactional Workflows

    NARCIS (Netherlands)

    Derks, W.L.A.; Dehnert, Juliane; Grefen, P.W.P.J.; Jonker, Willem

    This paper introduces a new approach for specifying transaction management requirements for workflow applications. We propose independent models for the specification of workflow and transaction properties. Although we distinguish multiple transaction properties in our approach, we focus on

  7. Data intensive ATLAS workflows in the Cloud

    CERN Document Server

    Rzehorz, Gerhard Ferdinand; The ATLAS collaboration

    2018-01-01

    From 2025 onwards, the ATLAS collaboration at the Large Hadron Collider (LHC) at CERN will experience a massive increase in data quantity as well as complexity. Including mitigating factors, the prevalent computing power by that time will only fulfil one tenth of the requirement. This contribution will focus on Cloud computing as an approach to help overcome this challenge by providing flexible hardware that can be configured to the specific needs of a workflow. Experience with Cloud computing exists, but there is a large uncertainty if and to which degree it can be able to reduce the burden by 2025. In order to understand and quantify the benefits of Cloud computing, the "Workflow and Infrastructure Model" was created. It estimates the viability of Cloud computing by combining different inputs from the workflow side with infrastructure specifications. The model delivers metrics that enable the comparison of different Cloud configurations as well as different Cloud offerings with each other. A wide range of r...

  8. SEEPAGE MODEL FOR PA INCLUDING DRIFT COLLAPSE

    International Nuclear Information System (INIS)

    C. Tsang

    2004-01-01

    The purpose of this report is to document the predictions and analyses performed using the seepage model for performance assessment (SMPA) for both the Topopah Spring middle nonlithophysal (Tptpmn) and lower lithophysal (Tptpll) lithostratigraphic units at Yucca Mountain, Nevada. Look-up tables of seepage flow rates into a drift (and their uncertainty) are generated by performing numerical simulations with the seepage model for many combinations of the three most important seepage-relevant parameters: the fracture permeability, the capillary-strength parameter 1/a, and the percolation flux. The percolation flux values chosen take into account flow focusing effects, which are evaluated based on a flow-focusing model. Moreover, multiple realizations of the underlying stochastic permeability field are conducted. Selected sensitivity studies are performed, including the effects of an alternative drift geometry representing a partially collapsed drift from an independent drift-degradation analysis (BSC 2004 [DIRS 166107]). The intended purpose of the seepage model is to provide results of drift-scale seepage rates under a series of parameters and scenarios in support of the Total System Performance Assessment for License Application (TSPA-LA). The SMPA is intended for the evaluation of drift-scale seepage rates under the full range of parameter values for three parameters found to be key (fracture permeability, the van Genuchten 1/a parameter, and percolation flux) and drift degradation shape scenarios in support of the TSPA-LA during the period of compliance for postclosure performance [Technical Work Plan for: Performance Assessment Unsaturated Zone (BSC 2002 [DIRS 160819], Section I-4-2-1)]. The flow-focusing model in the Topopah Spring welded (TSw) unit is intended to provide an estimate of flow focusing factors (FFFs) that (1) bridge the gap between the mountain-scale and drift-scale models, and (2) account for variability in local percolation flux due to

  9. Grand unified models including extra Z bosons

    International Nuclear Information System (INIS)

    Li Tiezhong

    1989-01-01

    The grand unified theories (GUT) of the simple Lie groups including extra Z bosons are discussed. Under authors's hypothesis there are only SU 5+m SO 6+4n and E 6 groups. The general discussion of SU 5+m is given, then the SU 6 and SU 7 are considered. In SU 6 the 15+6 * +6 * fermion representations are used, which are not same as others in fermion content, Yukawa coupling and broken scales. A conception of clans of particles, which are not families, is suggested. These clans consist of extra Z bosons and the corresponding fermions of the scale. The all of fermions in the clans are down quarks except for the standard model which consists of Z bosons and 15 fermions, therefore, the spectrum of the hadrons which are composed of these down quarks are different from hadrons at present

  10. A Photogrammetric Workflow for the Creation of a Forest Canopy Height Model from Small Unmanned Aerial System Imagery

    Directory of Open Access Journals (Sweden)

    Philippe Lejeune

    2013-11-01

    Full Text Available The recent development of operational small unmanned aerial systems (UASs opens the door for their extensive use in forest mapping, as both the spatial and temporal resolution of UAS imagery better suit local-scale investigation than traditional remote sensing tools. This article focuses on the use of combined photogrammetry and “Structure from Motion” approaches in order to model the forest canopy surface from low-altitude aerial images. An original workflow, using the open source and free photogrammetric toolbox, MICMAC (acronym for Multi Image Matches for Auto Correlation Methods, was set up to create a digital canopy surface model of deciduous stands. In combination with a co-registered light detection and ranging (LiDAR digital terrain model, the elevation of vegetation was determined, and the resulting hybrid photo/LiDAR canopy height model was compared to data from a LiDAR canopy height model and from forest inventory data. Linear regressions predicting dominant height and individual height from plot metrics and crown metrics showed that the photogrammetric canopy height model was of good quality for deciduous stands. Although photogrammetric reconstruction significantly smooths the canopy surface, the use of this workflow has the potential to take full advantage of the flexible revisit period of drones in order to refresh the LiDAR canopy height model and to collect dense multitemporal canopy height series.

  11. Standardizing clinical trials workflow representation in UML for international site comparison.

    Science.gov (United States)

    de Carvalho, Elias Cesar Araujo; Jayanti, Madhav Kishore; Batilana, Adelia Portero; Kozan, Andreia M O; Rodrigues, Maria J; Shah, Jatin; Loures, Marco R; Patil, Sunita; Payne, Philip; Pietrobon, Ricardo

    2010-11-09

    With the globalization of clinical trials, a growing emphasis has been placed on the standardization of the workflow in order to ensure the reproducibility and reliability of the overall trial. Despite the importance of workflow evaluation, to our knowledge no previous studies have attempted to adapt existing modeling languages to standardize the representation of clinical trials. Unified Modeling Language (UML) is a computational language that can be used to model operational workflow, and a UML profile can be developed to standardize UML models within a given domain. This paper's objective is to develop a UML profile to extend the UML Activity Diagram schema into the clinical trials domain, defining a standard representation for clinical trial workflow diagrams in UML. Two Brazilian clinical trial sites in rheumatology and oncology were examined to model their workflow and collect time-motion data. UML modeling was conducted in Eclipse, and a UML profile was developed to incorporate information used in discrete event simulation software. Ethnographic observation revealed bottlenecks in workflow: these included tasks requiring full commitment of CRCs, transferring notes from paper to computers, deviations from standard operating procedures, and conflicts between different IT systems. Time-motion analysis revealed that nurses' activities took up the most time in the workflow and contained a high frequency of shorter duration activities. Administrative assistants performed more activities near the beginning and end of the workflow. Overall, clinical trial tasks had a greater frequency than clinic routines or other general activities. This paper describes a method for modeling clinical trial workflow in UML and standardizing these workflow diagrams through a UML profile. In the increasingly global environment of clinical trials, the standardization of workflow modeling is a necessary precursor to conducting a comparative analysis of international clinical trials

  12. Recommending audio mixing workflows

    OpenAIRE

    Sauer, Christian; Roth-Berghofer, Thomas; Auricchio, Nino; Proctor, Sam

    2013-01-01

    This paper describes our work on Audio Advisor, a workflow recommender for audio mixing. We examine the process of eliciting, formalising and modelling the domain knowledge and expert’s experience. We are also describing the effects and problems associated with the knowledge formalisation processes. We decided to employ structured case-based reasoning using the myCBR 3 to capture the vagueness encountered in the audio domain. We detail on how we used extensive similarity measure modelling to ...

  13. An Integrated Biochemistry Laboratory, Including Molecular Modeling

    Science.gov (United States)

    Hall, Adele J. Wolfson Mona L.; Branham, Thomas R.

    1996-11-01

    ) experience with methods of protein purification; (iii) incorporation of appropriate controls into experiments; (iv) use of basic statistics in data analysis; (v) writing papers and grant proposals in accepted scientific style; (vi) peer review; (vii) oral presentation of results and proposals; and (viii) introduction to molecular modeling. Figure 1 illustrates the modular nature of the lab curriculum. Elements from each of the exercises can be separated and treated as stand-alone exercises, or combined into short or long projects. We have been able to offer the opportunity to use sophisticated molecular modeling in the final module through funding from an NSF-ILI grant. However, many of the benefits of the research proposal can be achieved with other computer programs, or even by literature survey alone. Figure 1.Design of project-based biochemistry laboratory. Modules (projects, or portions of projects) are indicated as boxes. Each of these can be treated independently, or used as part of a larger project. Solid lines indicate some suggested paths from one module to the next. The skills and knowledge required for protein purification and design are developed in three units: (i) an introduction to critical assays needed to monitor degree of purification, including an evaluation of assay parameters; (ii) partial purification by ion-exchange techniques; and (iii) preparation of a grant proposal on protein design by mutagenesis. Brief descriptions of each of these units follow, with experimental details of each project at the end of this paper. Assays for Lysozyme Activity and Protein Concentration (4 weeks) The assays mastered during the first unit are a necessary tool for determining the purity of the enzyme during the second unit on purification by ion exchange. These assays allow an introduction to the concept of specific activity (units of enzyme activity per milligram of total protein) as a measure of purity. In this first sequence, students learn a turbidimetric assay

  14. A standard-enabled workflow for synthetic biology

    KAUST Repository

    Myers, Chris J.

    2017-06-15

    A synthetic biology workflow is composed of data repositories that provide information about genetic parts, sequence-level design tools to compose these parts into circuits, visualization tools to depict these designs, genetic design tools to select parts to create systems, and modeling and simulation tools to evaluate alternative design choices. Data standards enable the ready exchange of information within such a workflow, allowing repositories and tools to be connected from a diversity of sources. The present paper describes one such workflow that utilizes, among others, the Synthetic Biology Open Language (SBOL) to describe genetic designs, the Systems Biology Markup Language to model these designs, and SBOL Visual to visualize these designs. We describe how a standard-enabled workflow can be used to produce types of design information, including multiple repositories and software tools exchanging information using a variety of data standards. Recently, the ACS Synthetic Biology journal has recommended the use of SBOL in their publications.

  15. Towards an Intelligent Workflow Designer based on the Reuse of Workflow Patterns

    NARCIS (Netherlands)

    Iochpe, C.; Chiao, C.; Hess, G.; Nascimento, G.S.; Thom, L.H.; Reichert, M.U.

    2007-01-01

    In order to perform process-aware information systems we need sophisticated methods and concepts for designing and modeling processes. Recently, research on workflow patterns has emerged in order to increase the reuse of recurring workflow structures. However, current workflow modeling tools do not

  16. Structural and parametric models of the Zalezcze and Zuchlow gas field region, fore-Sudetic monocline, Poland - An example of a general static modeling work-flow in mature petroleum areas for CCS, EGR or EOR purposes

    International Nuclear Information System (INIS)

    Papiernik, Bartosz; Doligez, Brigitte; Klimkowski, Lukasz

    2015-01-01

    Zalecze and Zuchlow are strongly depleted natural gas fields in aeolian sandstones of the Rotliegend, located in the central part of the Fore-Sudetic Monocline. A set of three static 3D models was generated to check the possibility of CO 2 injection for Enhanced Gas Recovery (EGR) and to check the safety of storage by means of geomechanical modeling: one regional model (ZZA) and two local models - the first for Zalecze (ZA) gas field and the second for Zuchlow (ZU) gas field. The regional model is composed of 12 stratigraphic complexes (zones) from the base of the Rotliegend to the ground surface. The local models comprise only the three lowermost complexes: fluvial deposits of the Rotliegend, aeolian sandstones of the Rotliegend (Reservoir I) and basal Zechstein limestone, Ca1. The key elements of the modeling procedure include: Quality Control (QC) of the data, interpretation of missing parameters necessary for static modeling and their integration within a geo-model. The processing work-flow was elaborated to produce convergent regional and local models. The regional static model is a framework for a regional geomechanical model. The local models are the basis for dynamic simulations and local geomechanical modeling. The presented work-flow could be used with some changes for geo-modeling of many mature gas and oil fields. (authors)

  17. Seepage Model for PA Including Drift Collapse

    International Nuclear Information System (INIS)

    Li, G.; Tsang, C.

    2000-01-01

    The purpose of this Analysis/Model Report (AMR) is to document the predictions and analysis performed using the Seepage Model for Performance Assessment (PA) and the Disturbed Drift Seepage Submodel for both the Topopah Spring middle nonlithophysal and lower lithophysal lithostratigraphic units at Yucca Mountain. These results will be used by PA to develop the probability distribution of water seepage into waste-emplacement drifts at Yucca Mountain, Nevada, as part of the evaluation of the long term performance of the potential repository. This AMR is in accordance with the ''Technical Work Plan for Unsaturated Zone (UZ) Flow and Transport Process Model Report'' (CRWMS M andO 2000 [153447]). This purpose is accomplished by performing numerical simulations with stochastic representations of hydrological properties, using the Seepage Model for PA, and evaluating the effects of an alternative drift geometry representing a partially collapsed drift using the Disturbed Drift Seepage Submodel. Seepage of water into waste-emplacement drifts is considered one of the principal factors having the greatest impact of long-term safety of the repository system (CRWMS M andO 2000 [153225], Table 4-1). This AMR supports the analysis and simulation that are used by PA to develop the probability distribution of water seepage into drift, and is therefore a model of primary (Level 1) importance (AP-3.15Q, ''Managing Technical Product Inputs''). The intended purpose of the Seepage Model for PA is to support: (1) PA; (2) Abstraction of Drift-Scale Seepage; and (3) Unsaturated Zone (UZ) Flow and Transport Process Model Report (PMR). Seepage into drifts is evaluated by applying numerical models with stochastic representations of hydrological properties and performing flow simulations with multiple realizations of the permeability field around the drift. The Seepage Model for PA uses the distribution of permeabilities derived from air injection testing in niches and in the cross drift to

  18. Seepage Model for PA Including Dift Collapse

    Energy Technology Data Exchange (ETDEWEB)

    G. Li; C. Tsang

    2000-12-20

    The purpose of this Analysis/Model Report (AMR) is to document the predictions and analysis performed using the Seepage Model for Performance Assessment (PA) and the Disturbed Drift Seepage Submodel for both the Topopah Spring middle nonlithophysal and lower lithophysal lithostratigraphic units at Yucca Mountain. These results will be used by PA to develop the probability distribution of water seepage into waste-emplacement drifts at Yucca Mountain, Nevada, as part of the evaluation of the long term performance of the potential repository. This AMR is in accordance with the ''Technical Work Plan for Unsaturated Zone (UZ) Flow and Transport Process Model Report'' (CRWMS M&O 2000 [153447]). This purpose is accomplished by performing numerical simulations with stochastic representations of hydrological properties, using the Seepage Model for PA, and evaluating the effects of an alternative drift geometry representing a partially collapsed drift using the Disturbed Drift Seepage Submodel. Seepage of water into waste-emplacement drifts is considered one of the principal factors having the greatest impact of long-term safety of the repository system (CRWMS M&O 2000 [153225], Table 4-1). This AMR supports the analysis and simulation that are used by PA to develop the probability distribution of water seepage into drift, and is therefore a model of primary (Level 1) importance (AP-3.15Q, ''Managing Technical Product Inputs''). The intended purpose of the Seepage Model for PA is to support: (1) PA; (2) Abstraction of Drift-Scale Seepage; and (3) Unsaturated Zone (UZ) Flow and Transport Process Model Report (PMR). Seepage into drifts is evaluated by applying numerical models with stochastic representations of hydrological properties and performing flow simulations with multiple realizations of the permeability field around the drift. The Seepage Model for PA uses the distribution of permeabilities derived from air injection testing in

  19. Vel-IO 3D: A tool for 3D velocity model construction, optimization and time-depth conversion in 3D geological modeling workflow

    Science.gov (United States)

    Maesano, Francesco E.; D'Ambrogi, Chiara

    2017-02-01

    We present Vel-IO 3D, a tool for 3D velocity model creation and time-depth conversion, as part of a workflow for 3D model building. The workflow addresses the management of large subsurface dataset, mainly seismic lines and well logs, and the construction of a 3D velocity model able to describe the variation of the velocity parameters related to strong facies and thickness variability and to high structural complexity. Although it is applicable in many geological contexts (e.g. foreland basins, large intermountain basins), it is particularly suitable in wide flat regions, where subsurface structures have no surface expression. The Vel-IO 3D tool is composed by three scripts, written in Python 2.7.11, that automate i) the 3D instantaneous velocity model building, ii) the velocity model optimization, iii) the time-depth conversion. They determine a 3D geological model that is consistent with the primary geological constraints (e.g. depth of the markers on wells). The proposed workflow and the Vel-IO 3D tool have been tested, during the EU funded Project GeoMol, by the construction of the 3D geological model of a flat region, 5700 km2 in area, located in the central part of the Po Plain. The final 3D model showed the efficiency of the workflow and Vel-IO 3D tool in the management of large amount of data both in time and depth domain. A 4 layer-cake velocity model has been applied to a several thousand (5000-13,000 m) thick succession, with 15 horizons from Triassic up to Pleistocene, complicated by a Mesozoic extensional tectonics and by buried thrusts related to Southern Alps and Northern Apennines.

  20. Enhanced battery model including temperature effects

    NARCIS (Netherlands)

    Rosca, B.; Wilkins, S.

    2013-01-01

    Within electric and hybrid vehicles, batteries are used to provide/buffer the energy required for driving. However, battery performance varies throughout the temperature range specific to automotive applications, and as such, models that describe this behaviour are required. This paper presents a

  1. Image-Rich Radiology Reports: A Value-Based Model to Improve Clinical Workflow.

    Science.gov (United States)

    Patel, Bhavik N; Lopez, Jose M; Jiang, Brian G; Roth, Christopher J; Nelson, Rendon C

    2017-01-01

    To determine the value of image-rich radiology reports (IRRR) by evaluating the interest and preferences of referring physicians, potential impact on clinical workflow, and the willingness of radiologists to create them. Referring physicians and radiologists were interviewed in this prospective, HIPAA-compliant study. Subject willingness to participate in the study was determined by an e-mail. A single investigator conducted all interviews using a standard questionnaire. All subjects reviewed a video mockup demonstration of IRRR and three methods for viewing embedded images, as follows: (1) clickable hyperlinks to access a scrollable stack of images, (2) scrollable and enlargeable small-image thumbnails, and (3) scrollable but not enlargeable medium-sized images. Questionnaire responses, free comments, and general impressions were captured and analyzed. Seventy-two physicians (36 clinicians, 36 radiologists) were interviewed. Thirty-one clinicians (86%) expressed interest in using IRRR. Seventy-seven percent of subjects believed IRRR would improve communication. Ten clinicians (28%) preferred method 1, 18 (50%) preferred method 2, and 8 (22%) preferred method 3 for embedding images. Thirty clinicians (83%) stated that IRRR would improve efficiency. Twenty-two radiologists (61%) preferred selecting a tool button with a mouse and right-clicking images to embed them, 13 (36%) preferred pressing a function key, and 11 (31%) preferred dictating series and image numbers. The average time radiologists were willing to expend for embedding images was 66.7 seconds. Referring physicians and radiologist both believe IRRR would add value by improving communication with the potential to improve the workflow efficiency of referring physicians. Copyright © 2016 American College of Radiology. Published by Elsevier Inc. All rights reserved.

  2. Make Your Workflows Smarter

    Science.gov (United States)

    Jones, Corey; Kapatos, Dennis; Skradski, Cory

    2012-01-01

    Do you have workflows with many manual tasks that slow down your business? Or, do you scale back workflows because there are simply too many manual tasks? Basic workflow robots can automate some common tasks, but not everything. This presentation will show how advanced robots called "expression robots" can be set up to perform everything from simple tasks such as: moving, creating folders, renaming, changing or creating an attribute, and revising, to more complex tasks like: creating a pdf, or even launching a session of Creo Parametric and performing a specific modeling task. Expression robots are able to utilize the Java API and Info*Engine to do almost anything you can imagine! Best of all, these tools are supported by PTC and will work with later releases of Windchill. Limited knowledge of Java, Info*Engine, and XML are required. The attendee will learn what task expression robots are capable of performing. The attendee will learn what is involved in setting up an expression robot. The attendee will gain a basic understanding of simple Info*Engine tasks

  3. Workflow User Interfaces Patterns

    Directory of Open Access Journals (Sweden)

    Jean Vanderdonckt

    2012-03-01

    Full Text Available Este trabajo presenta una colección de patrones de diseño de interfaces de usuario para sistemas de información para el flujo de trabajo; la colección incluye cuarenta y tres patrones clasificados en siete categorías identificados a partir de la lógica del ciclo de vida de la tarea sobre la base de la oferta y la asignación de tareas a los responsables de realizarlas (i. e. recursos humanos durante el flujo de trabajo. Cada patrón de la interfaz de usuario de flujo de trabajo (WUIP, por sus siglas en inglés se caracteriza por las propiedades expresadas en el lenguaje PLML para expresar patrones y complementado por otros atributos y modelos que se adjuntan a dicho modelo: la interfaz de usuario abstracta y el modelo de tareas correspondiente. Estos modelos se especifican en un lenguaje de descripción de interfaces de usuario. Todos los WUIPs se almacenan en una biblioteca y se pueden recuperar a través de un editor de flujo de trabajo que vincula a cada patrón de asignación de trabajo a su WUIP correspondiente.A collection of user interface design patterns for workflow information systems is presented that contains forty three resource patterns classified in seven categories. These categories and their corresponding patterns have been logically identified from the task life cycle based on offering and allocation operations. Each Workflow User Interface Pattern (WUIP is characterized by properties expressed in the PLML markup language for expressing patterns and augmented by additional attributes and models attached to the pattern: the abstract user interface and the corresponding task model. These models are specified in a User Interface Description Language. All WUIPs are stored in a library and can be retrieved within a workflow editor that links each workflow pattern to its corresponding WUIP, thus giving rise to a user interface for each workflow pattern.

  4. BEAM: A computational workflow system for managing and modeling material characterization data in HPC environments

    Energy Technology Data Exchange (ETDEWEB)

    Lingerfelt, Eric J [ORNL; Endeve, Eirik [ORNL; Ovchinnikov, Oleg S [ORNL; Borreguero Calvo, Jose M [ORNL; Park, Byung H [ORNL; Archibald, Richard K [ORNL; Symons, Christopher T [ORNL; Kalinin, Sergei V [ORNL; Messer, Bronson [ORNL; Shankar, Mallikarjun [ORNL; Jesse, Stephen [ORNL

    2016-01-01

    Improvements in scientific instrumentation allow imaging at mesoscopic to atomic length scales, many spectroscopic modes, and now with the rise of multimodal acquisition systems and the associated processing capability the era of multidimensional, informationally dense data sets has arrived. Technical issues in these combinatorial scientific fields are exacerbated by computational challenges best summarized as a necessity for drastic improvement in the capability to transfer, store, and analyze large volumes of data. The Bellerophon Environment for Analysis of Materials (BEAM) platform provides material scientists the capability to directly leverage the integrated computational and analytical power of High Performance Computing (HPC) to perform scalable data analysis and simulation via an intuitive, cross-platform client user interface. This framework delivers authenticated, push-button execution of complex user workflows that deploy data analysis algorithms and computational simulations utilizing the converged compute-and-data infrastructure at Oak Ridge National Laboratory s (ORNL) Compute and Data Environment for Science (CADES) and HPC environments like Titan at the Oak Ridge Leadership Computing Facility (OLCF). In this work we address the underlying HPC needs for characterization in the material science community, elaborate how BEAM s design and infrastructure tackle those needs, and present a small sub-set of user cases where scientists utilized BEAM across a broad range of analytical techniques and analysis modes.

  5. DEWEY: the DICOM-enabled workflow engine system.

    Science.gov (United States)

    Erickson, Bradley J; Langer, Steve G; Blezek, Daniel J; Ryan, William J; French, Todd L

    2014-06-01

    Workflow is a widely used term to describe the sequence of steps to accomplish a task. The use of workflow technology in medicine and medical imaging in particular is limited. In this article, we describe the application of a workflow engine to improve workflow in a radiology department. We implemented a DICOM-enabled workflow engine system in our department. We designed it in a way to allow for scalability, reliability, and flexibility. We implemented several workflows, including one that replaced an existing manual workflow and measured the number of examinations prepared in time without and with the workflow system. The system significantly increased the number of examinations prepared in time for clinical review compared to human effort. It also met the design goals defined at its outset. Workflow engines appear to have value as ways to efficiently assure that complex workflows are completed in a timely fashion.

  6. From Peer-Reviewed to Peer-Reproduced in Scholarly Publishing: The Complementary Roles of Data Models and Workflows in Bioinformatics.

    Directory of Open Access Journals (Sweden)

    Alejandra González-Beltrán

    Full Text Available Reproducing the results from a scientific paper can be challenging due to the absence of data and the computational tools required for their analysis. In addition, details relating to the procedures used to obtain the published results can be difficult to discern due to the use of natural language when reporting how experiments have been performed. The Investigation/Study/Assay (ISA, Nanopublications (NP, and Research Objects (RO models are conceptual data modelling frameworks that can structure such information from scientific papers. Computational workflow platforms can also be used to reproduce analyses of data in a principled manner. We assessed the extent by which ISA, NP, and RO models, together with the Galaxy workflow system, can capture the experimental processes and reproduce the findings of a previously published paper reporting on the development of SOAPdenovo2, a de novo genome assembler.Executable workflows were developed using Galaxy, which reproduced results that were consistent with the published findings. A structured representation of the information in the SOAPdenovo2 paper was produced by combining the use of ISA, NP, and RO models. By structuring the information in the published paper using these data and scientific workflow modelling frameworks, it was possible to explicitly declare elements of experimental design, variables, and findings. The models served as guides in the curation of scientific information and this led to the identification of inconsistencies in the original published paper, thereby allowing its authors to publish corrections in the form of an errata.SOAPdenovo2 scripts, data, and results are available through the GigaScience Database: http://dx.doi.org/10.5524/100044; the workflows are available from GigaGalaxy: http://galaxy.cbiit.cuhk.edu.hk; and the representations using the ISA, NP, and RO models are available through the SOAPdenovo2 case study website http://isa-tools.github.io/soapdenovo2

  7. Multiscale cartilage biomechanics: technical challenges in realizing a high-throughput modelling and simulation workflow.

    Science.gov (United States)

    Erdemir, Ahmet; Bennetts, Craig; Davis, Sean; Reddy, Akhil; Sibole, Scott

    2015-04-06

    interpretation of the results. This study aims to summarize various strategies to address the technical challenges of post-processing-based simulations of cartilage and chondrocyte mechanics with the ultimate goal of establishing the foundations of a high-throughput multiscale analysis framework. At the joint-tissue scale, rapid development of regional models of articular contact is possible by automating the process of generating parametric representations of cartilage boundaries and depth-dependent zonal delineation with associated constitutive relationships. At the tissue-cell scale, models descriptive of multicellular and fibrillar architecture of cartilage zones can also be generated in an automated fashion. Through post-processing, scripts can extract biphasic mechanical metrics at a desired point in the cartilage to assign loading and boundary conditions to models at the lower spatial scale of cells. Cell deformation metrics can be extracted from simulation results to provide a simplified description of individual chondrocyte responses. Simulations at the tissue-cell scale can be parallelized owing to the loosely coupled nature of the feed-forward approach. Verification studies illustrated the necessity of a second-order data passing scheme between scales and evaluated the role that the microscale representative volume size plays in appropriately predicting the mechanical response of the chondrocytes. The tools summarized in this study collectively provide a framework for high-throughput exploration of cartilage biomechanics, which includes minimally supervised model generation, and prediction of multiscale biomechanical metrics across a range of spatial scales, from joint regions and cartilage zones, down to that of the chondrocytes.

  8. Designing a road map for geoscience workflows

    Science.gov (United States)

    Duffy, Christopher; Gil, Yolanda; Deelman, Ewa; Marru, Suresh; Pierce, Marlon; Demir, Ibrahim; Wiener, Gerry

    2012-06-01

    Advances in geoscience research and discovery are fundamentally tied to data and computation, but formal strategies for managing the diversity of models and data resources in the Earth sciences have not yet been resolved or fully appreciated. The U.S. National Science Foundation (NSF) EarthCube initiative (http://earthcube.ning.com), which aims to support community-guided cyberinfrastructure to integrate data and information across the geosciences, recently funded four community development activities: Geoscience Workflows; Semantics and Ontologies; Data Discovery, Mining, and Integration; and Governance. The Geoscience Workflows working group, with broad participation from the geosciences, cyberinfrastructure, and other relevant communities, is formulating a workflows road map (http://sites.google.com/site/earthcubeworkflow/). The Geoscience Workflows team coordinates with each of the other community development groups given their direct relevance to workflows. Semantics and ontologies are mechanisms for describing workflows and the data they process.

  9. Pro WF Windows Workflow in NET 40

    CERN Document Server

    Bukovics, Bruce

    2010-01-01

    Windows Workflow Foundation (WF) is a revolutionary part of the .NET 4 Framework that allows you to orchestrate human and system interactions as a series of workflows that can be easily mapped, analyzed, adjusted, and implemented. As business problems become more complex, the need for workflow-based solutions has never been more evident. WF provides a simple and consistent way to model and implement complex problems. As a developer, you focus on developing the business logic for individual workflow tasks. The runtime handles the execution of those tasks after they have been composed into a wor

  10. Multidetector-row CT: economics and workflow

    International Nuclear Information System (INIS)

    Pottala, K.M.; Kalra, M.K.; Saini, S.; Ouellette, K.; Sahani, D.; Thrall, J.H.

    2005-01-01

    With rapid evolution of multidetector-row CT (MDCT) technology and applications, several factors such ad technology upgrade and turf battles for sharing cost and profitability affect MDCT workflow and economics. MDCT workflow optimization can enhance productivity and reduce unit costs as well as increase profitability, in spite of decrease in reimbursement rates. Strategies for workflow management include standardization, automation, and constant assessment of various steps involved in MDCT operations. In this review article, we describe issues related to MDCT economics and workflow. (orig.)

  11. Automatically updating predictive modeling workflows support decision-making in drug design.

    Science.gov (United States)

    Muegge, Ingo; Bentzien, Jörg; Mukherjee, Prasenjit; Hughes, Robert O

    2016-09-01

    Using predictive models for early decision-making in drug discovery has become standard practice. We suggest that model building needs to be automated with minimum input and low technical maintenance requirements. Models perform best when tailored to answering specific compound optimization related questions. If qualitative answers are required, 2-bin classification models are preferred. Integrating predictive modeling results with structural information stimulates better decision making. For in silico models supporting rapid structure-activity relationship cycles the performance deteriorates within weeks. Frequent automated updates of predictive models ensure best predictions. Consensus between multiple modeling approaches increases the prediction confidence. Combining qualified and nonqualified data optimally uses all available information. Dose predictions provide a holistic alternative to multiple individual property predictions for reaching complex decisions.

  12. Olkiluoto surface hydrological modelling: Update 2012 including salt transport modelling

    International Nuclear Information System (INIS)

    Karvonen, T.

    2013-11-01

    Posiva Oy is responsible for implementing a final disposal program for spent nuclear fuel of its owners Teollisuuden Voima Oyj and Fortum Power and Heat Oy. The spent nuclear fuel is planned to be disposed at a depth of about 400-450 meters in the crystalline bedrock at the Olkiluoto site. Leakages located at or close to spent fuel repository may give rise to the upconing of deep highly saline groundwater and this is a concern with regard to the performance of the tunnel backfill material after the closure of the tunnels. Therefore a salt transport sub-model was added to the Olkiluoto surface hydrological model (SHYD). The other improvements include update of the particle tracking algorithm and possibility to estimate the influence of open drillholes in a case where overpressure in inflatable packers decreases causing a hydraulic short-circuit between hydrogeological zones HZ19 and HZ20 along the drillhole. Four new hydrogeological zones HZ056, HZ146, BFZ100 and HZ039 were added to the model. In addition, zones HZ20A and HZ20B intersect with each other in the new structure model, which influences salinity upconing caused by leakages in shafts. The aim of the modelling of long-term influence of ONKALO, shafts and repository tunnels provide computational results that can be used to suggest limits for allowed leakages. The model input data included all the existing leakages into ONKALO (35-38 l/min) and shafts in the present day conditions. The influence of shafts was computed using eight different values for total shaft leakage: 5, 11, 20, 30, 40, 50, 60 and 70 l/min. The selection of the leakage criteria for shafts was influenced by the fact that upconing of saline water increases TDS-values close to the repository areas although HZ20B does not intersect any deposition tunnels. The total limit for all leakages was suggested to be 120 l/min. The limit for HZ20 zones was proposed to be 40 l/min: about 5 l/min the present day leakages to access tunnel, 25 l/min from

  13. Target discovery screens using pooled shRNA libraries and next-generation sequencing: A model workflow and analytical algorithm.

    Directory of Open Access Journals (Sweden)

    Christiane Schaefer

    Full Text Available In the search for novel therapeutic targets, RNA interference screening has become a valuable tool. High-throughput technologies are now broadly accessible but their assay development from baseline remains resource-intensive and challenging. Focusing on this assay development process, we here describe a target discovery screen using pooled shRNA libraries and next-generation sequencing (NGS deconvolution in a cell line model of Ewing sarcoma. In a strategy designed for comparative and synthetic lethal studies, we screened for targets specific to the A673 Ewing sarcoma cell line. Methods, results and pitfalls are described for the entire multi-step screening procedure, from lentiviral shRNA delivery to bioinformatics analysis, illustrating a complete model workflow. We demonstrate that successful studies are feasible from the first assay performance and independent of specialized screening units. Furthermore, we show that a resource-saving screen depth of 100-fold average shRNA representation can suffice to generate reproducible target hits despite heterogeneity in the derived datasets. Because statistical analysis methods are debatable for such datasets, we created ProFED, an analysis package designed to facilitate descriptive data analysis and hit calling using an aim-oriented profile filtering approach. In its versatile design, this open-source online tool provides fast and easy analysis of shRNA and other count-based datasets to complement other analytical algorithms.

  14. GPGPU accelerated Krylov methods for compact modeling of on-chip passive integrated structures within the Chameleon-RF workflow

    Directory of Open Access Journals (Sweden)

    Sebastian Gim

    2012-11-01

    Full Text Available Continued device scaling into the nanometer region and high frequencies of operation well into the multi-GHz region has given rise to new effects that previously had negligible impact but now present greater challenges and unprecedented complexity to designing successful mixed-signal silicon. The Chameleon-RF project was conceived to address these challenges. Creative use of domain decomposition, multi grid techniques or reduced order modeling techniques (ROM can be selectively applied at all levels of the process to efficiently prune down degrees of freedom (DoFs. However, the simulation of complex systems within a reasonable amount of time remains a computational challenge. This paper presents work done in the incorporation of GPGPU technology to accelerate Krylov based algorithms used for compact modeling of on-chip passive integrated structures within the workflow of the Chameleon-RF project. Based upon insight gained from work done above, a novel GPGPU accelerated algorithm was developed for the Krylov ROM (kROM methods and is described here for the benefit of the wider community.

  15. Decaf: Decoupled Dataflows for In Situ High-Performance Workflows

    Energy Technology Data Exchange (ETDEWEB)

    Dreher, M.; Peterka, T.

    2017-07-31

    Decaf is a dataflow system for the parallel communication of coupled tasks in an HPC workflow. The dataflow can perform arbitrary data transformations ranging from simply forwarding data to complex data redistribution. Decaf does this by allowing the user to allocate resources and execute custom code in the dataflow. All communication through the dataflow is efficient parallel message passing over MPI. The runtime for calling tasks is entirely message-driven; Decaf executes a task when all messages for the task have been received. Such a messagedriven runtime allows cyclic task dependencies in the workflow graph, for example, to enact computational steering based on the result of downstream tasks. Decaf includes a simple Python API for describing the workflow graph. This allows Decaf to stand alone as a complete workflow system, but Decaf can also be used as the dataflow layer by one or more other workflow systems to form a heterogeneous task-based computing environment. In one experiment, we couple a molecular dynamics code with a visualization tool using the FlowVR and Damaris workflow systems and Decaf for the dataflow. In another experiment, we test the coupling of a cosmology code with Voronoi tessellation and density estimation codes using MPI for the simulation, the DIY programming model for the two analysis codes, and Decaf for the dataflow. Such workflows consisting of heterogeneous software infrastructures exist because components are developed separately with different programming models and runtimes, and this is the first time that such heterogeneous coupling of diverse components was demonstrated in situ on HPC systems.

  16. Brand Licensing Processes and Workflows

    OpenAIRE

    Törmä, Kalle

    2017-01-01

    The purpose of this Bachelor’s thesis project is to provide an end-to-end brand licensing workflow mapping and give the reader understanding of the brand licensing workflows and how they are connected in the overall process. Brand licensing business is not too familiar in Finland and could offer an opportunity for a new income stream for many companies. To manage the brand licensing program, the company needs to understand the processes associated in the business model. The goal is to res...

  17. Understanding latent structures of clinical information logistics: A bottom-up approach for model building and validating the workflow composite score.

    Science.gov (United States)

    Esdar, Moritz; Hübner, Ursula; Liebe, Jan-David; Hüsers, Jens; Thye, Johannes

    2017-01-01

    Clinical information logistics is a construct that aims to describe and explain various phenomena of information provision to drive clinical processes. It can be measured by the workflow composite score, an aggregated indicator of the degree of IT support in clinical processes. This study primarily aimed to investigate the yet unknown empirical patterns constituting this construct. The second goal was to derive a data-driven weighting scheme for the constituents of the workflow composite score and to contrast this scheme with a literature based, top-down procedure. This approach should finally test the validity and robustness of the workflow composite score. Based on secondary data from 183 German hospitals, a tiered factor analytic approach (confirmatory and subsequent exploratory factor analysis) was pursued. A weighting scheme, which was based on factor loadings obtained in the analyses, was put into practice. We were able to identify five statistically significant factors of clinical information logistics that accounted for 63% of the overall variance. These factors were "flow of data and information", "mobility", "clinical decision support and patient safety", "electronic patient record" and "integration and distribution". The system of weights derived from the factor loadings resulted in values for the workflow composite score that differed only slightly from the score values that had been previously published based on a top-down approach. Our findings give insight into the internal composition of clinical information logistics both in terms of factors and weights. They also allowed us to propose a coherent model of clinical information logistics from a technical perspective that joins empirical findings with theoretical knowledge. Despite the new scheme of weights applied to the calculation of the workflow composite score, the score behaved robustly, which is yet another hint of its validity and therefore its usefulness. Copyright © 2016 Elsevier Ireland

  18. Workflow in Almaraz NPP

    International Nuclear Information System (INIS)

    Gonzalez Crego, E.; Martin Lopez-Suevos, C.

    2000-01-01

    Almaraz NPP decided to incorporate Workflow into its information system in response to the need to provide exhaustive follow-up and monitoring of each phase of the different procedures it manages. Oracle's Workflow was chosen for this purpose and it was integrated with previously developed applications. The objectives to be met in the incorporation of Workflow were as follows: Strict monitoring of procedures and processes. Detection of bottlenecks in the flow of information. Notification of those affected by pending tasks. Flexible allocation of tasks to user groups. Improved monitoring of management procedures. Improved communication. Similarly, special care was taken to: Integrate workflow processes with existing control panels. Synchronize workflow with installation procedures. Ensure that the system reflects use of paper forms. At present the Corrective Maintenance Request module is being operated using Workflow and the Work Orders and Notice of Order modules are about to follow suit. (Author)

  19. The standard-based open workflow system in GeoBrain (Invited)

    Science.gov (United States)

    Di, L.; Yu, G.; Zhao, P.; Deng, M.

    2013-12-01

    GeoBrain is an Earth science Web-service system developed and operated by the Center for Spatial Information Science and Systems, George Mason University. In GeoBrain, a standard-based open workflow system has been implemented to accommodate the automated processing of geospatial data through a set of complex geo-processing functions for advanced production generation. The GeoBrain models the complex geoprocessing at two levels, the conceptual and concrete. At the conceptual level, the workflows exist in the form of data and service types defined by ontologies. The workflows at conceptual level are called geo-processing models and cataloged in GeoBrain as virtual product types. A conceptual workflow is instantiated into a concrete, executable workflow when a user requests a product that matches a virtual product type. Both conceptual and concrete workflows are encoded in Business Process Execution Language (BPEL). A BPEL workflow engine, called BPELPower, has been implemented to execute the workflow for the product generation. A provenance capturing service has been implemented to generate the ISO 19115-compliant complete product provenance metadata before and after the workflow execution. The generation of provenance metadata before the workflow execution allows users to examine the usability of the final product before the lengthy and expensive execution takes place. The three modes of workflow executions defined in the ISO 19119, transparent, translucent, and opaque, are available in GeoBrain. A geoprocessing modeling portal has been developed to allow domain experts to develop geoprocessing models at the type level with the support of both data and service/processing ontologies. The geoprocessing models capture the knowledge of the domain experts and are become the operational offering of the products after a proper peer review of models is conducted. An automated workflow composition has been experimented successfully based on ontologies and artificial

  20. Toward Design, Modelling and Analysis of Dynamic Workflow Reconfigurations - A Process Algebra Perspective

    DEFF Research Database (Denmark)

    Mazzara, M.; Abouzaid, F.; Dragoni, Nicola

    2011-01-01

    This paper describes a case study involving the dynamic re- conguration of an oce work ow. We state the requirements on a sys- tem implementing the work ow and its reconguration, and describe the system's design in BPMN. We then use an asynchronous -calculus and Web1 to model the design and to ve...

  1. Capturing microbial sources distributed in a mixed-use watershed within an integrated environmental modeling workflow

    Science.gov (United States)

    Many watershed models simulate overland and instream microbial fate and transport, but few provide loading rates on land surfaces and point sources to the waterbody network. This paper describes the underlying equations for microbial loading rates associated with 1) land-applied ...

  2. The informational system model of Ukrainian national transport workflow improvement based on electronic signature introduction management

    Directory of Open Access Journals (Sweden)

    Grigoriy NECHAEY

    2007-01-01

    Full Text Available Proposed model of informational system supposes improvement of newconceptual method on the work with e-signature in transport nformational systems. Problems and aims that may be solved with the help of this system and the most important economical and technical advantages of the proposed system in comparison with traditional methods of e-signing use are marked out.

  3. 20180318 - Automated workflows for data curation and standardization of chemical structures for QSAR modeling (ACS Spring)

    Science.gov (United States)

    Large collections of chemical structures and associated experimental data are publicly available, and can be used to build robust QSAR models for applications in different fields. One common concern is the quality of both the chemical structure information and associated experime...

  4. Agreement Workflow Tool (AWT)

    Data.gov (United States)

    Social Security Administration — The Agreement Workflow Tool (AWT) is a role-based Intranet application used for processing SSA's Reimbursable Agreements according to SSA's standards. AWT provides...

  5. Soundness of Timed-Arc Workflow Nets

    DEFF Research Database (Denmark)

    Mateo, Jose Antonio; Srba, Jiri; Sørensen, Mathias Grund

    2014-01-01

    Analysis of workflow processes with quantitative aspects like timing is of interest in numerous time-critical applications. We suggest a workflow model based on timed-arc Petri nets and study the foundational problems of soundness and strong (time-bounded) soundness. We explore the decidability...... of these problems and show, among others, that soundness is decidable for monotonic workflow nets while reachability is undecidable. For general timed-arc workflow nets soundness and strong soundness become undecidable, though we can design efficient verification algorithms for the subclass of bounded nets. Finally......, we demonstrate the usability of our theory on the case studies of a Brake System Control Unit used in aircraft certification, the MPEG2 encoding algorithm, and a blood transfusion workflow. The implementation of the algorithms is freely available as a part of the model checker TAPAAL....

  6. Planning bioinformatics workflows using an expert system.

    Science.gov (United States)

    Chen, Xiaoling; Chang, Jeffrey T

    2017-04-15

    Bioinformatic analyses are becoming formidably more complex due to the increasing number of steps required to process the data, as well as the proliferation of methods that can be used in each step. To alleviate this difficulty, pipelines are commonly employed. However, pipelines are typically implemented to automate a specific analysis, and thus are difficult to use for exploratory analyses requiring systematic changes to the software or parameters used. To automate the development of pipelines, we have investigated expert systems. We created the Bioinformatics ExperT SYstem (BETSY) that includes a knowledge base where the capabilities of bioinformatics software is explicitly and formally encoded. BETSY is a backwards-chaining rule-based expert system comprised of a data model that can capture the richness of biological data, and an inference engine that reasons on the knowledge base to produce workflows. Currently, the knowledge base is populated with rules to analyze microarray and next generation sequencing data. We evaluated BETSY and found that it could generate workflows that reproduce and go beyond previously published bioinformatics results. Finally, a meta-investigation of the workflows generated from the knowledge base produced a quantitative measure of the technical burden imposed by each step of bioinformatics analyses, revealing the large number of steps devoted to the pre-processing of data. In sum, an expert system approach can facilitate exploratory bioinformatic analysis by automating the development of workflows, a task that requires significant domain expertise. https://github.com/jefftc/changlab. jeffrey.t.chang@uth.tmc.edu. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  7. Planning bioinformatics workflows using an expert system

    Science.gov (United States)

    Chen, Xiaoling; Chang, Jeffrey T.

    2017-01-01

    Abstract Motivation: Bioinformatic analyses are becoming formidably more complex due to the increasing number of steps required to process the data, as well as the proliferation of methods that can be used in each step. To alleviate this difficulty, pipelines are commonly employed. However, pipelines are typically implemented to automate a specific analysis, and thus are difficult to use for exploratory analyses requiring systematic changes to the software or parameters used. Results: To automate the development of pipelines, we have investigated expert systems. We created the Bioinformatics ExperT SYstem (BETSY) that includes a knowledge base where the capabilities of bioinformatics software is explicitly and formally encoded. BETSY is a backwards-chaining rule-based expert system comprised of a data model that can capture the richness of biological data, and an inference engine that reasons on the knowledge base to produce workflows. Currently, the knowledge base is populated with rules to analyze microarray and next generation sequencing data. We evaluated BETSY and found that it could generate workflows that reproduce and go beyond previously published bioinformatics results. Finally, a meta-investigation of the workflows generated from the knowledge base produced a quantitative measure of the technical burden imposed by each step of bioinformatics analyses, revealing the large number of steps devoted to the pre-processing of data. In sum, an expert system approach can facilitate exploratory bioinformatic analysis by automating the development of workflows, a task that requires significant domain expertise. Availability and Implementation: https://github.com/jefftc/changlab Contact: jeffrey.t.chang@uth.tmc.edu PMID:28052928

  8. Dynamic Reusable Workflows for Ocean Science

    Directory of Open Access Journals (Sweden)

    Richard P. Signell

    2016-10-01

    Full Text Available Digital catalogs of ocean data have been available for decades, but advances in standardized services and software for catalog searches and data access now make it possible to create catalog-driven workflows that automate—end-to-end—data search, analysis, and visualization of data from multiple distributed sources. Further, these workflows may be shared, reused, and adapted with ease. Here we describe a workflow developed within the US Integrated Ocean Observing System (IOOS which automates the skill assessment of water temperature forecasts from multiple ocean forecast models, allowing improved forecast products to be delivered for an open water swim event. A series of Jupyter Notebooks are used to capture and document the end-to-end workflow using a collection of Python tools that facilitate working with standardized catalog and data services. The workflow first searches a catalog of metadata using the Open Geospatial Consortium (OGC Catalog Service for the Web (CSW, then accesses data service endpoints found in the metadata records using the OGC Sensor Observation Service (SOS for in situ sensor data and OPeNDAP services for remotely-sensed and model data. Skill metrics are computed and time series comparisons of forecast model and observed data are displayed interactively, leveraging the capabilities of modern web browsers. The resulting workflow not only solves a challenging specific problem, but highlights the benefits of dynamic, reusable workflows in general. These workflows adapt as new data enter the data system, facilitate reproducible science, provide templates from which new scientific workflows can be developed, and encourage data providers to use standardized services. As applied to the ocean swim event, the workflow exposed problems with two of the ocean forecast products which led to improved regional forecasts once errors were corrected. While the example is specific, the approach is general, and we hope to see increased

  9. A Formal Framework for Workflow Analysis

    Science.gov (United States)

    Cravo, Glória

    2010-09-01

    In this paper we provide a new formal framework to model and analyse workflows. A workflow is the formal definition of a business process that consists in the execution of tasks in order to achieve a certain objective. In our work we describe a workflow as a graph whose vertices represent tasks and the arcs are associated to workflow transitions. Each task has associated an input/output logic operator. This logic operator can be the logical AND (•), the OR (⊗), or the XOR -exclusive-or—(⊕). Moreover, we introduce algebraic concepts in order to completely describe completely the structure of workflows. We also introduce the concept of logical termination. Finally, we provide a necessary and sufficient condition for this property to hold.

  10. Analysis and classification of oncology activities on the way to workflow based single source documentation in clinical information systems.

    Science.gov (United States)

    Wagner, Stefan; Beckmann, Matthias W; Wullich, Bernd; Seggewies, Christof; Ries, Markus; Bürkle, Thomas; Prokosch, Hans-Ulrich

    2015-12-22

    Today, cancer documentation is still a tedious task involving many different information systems even within a single institution and it is rarely supported by appropriate documentation workflows. In a comprehensive 14 step analysis we compiled diagnostic and therapeutic pathways for 13 cancer entities using a mixed approach of document analysis, workflow analysis, expert interviews, workflow modelling and feedback loops. These pathways were stepwise classified and categorized to create a final set of grouped pathways and workflows including electronic documentation forms. A total of 73 workflows for the 13 entities based on 82 paper documentation forms additionally to computer based documentation systems were compiled in a 724 page document comprising 130 figures, 94 tables and 23 tumour classifications as well as 12 follow-up tables. Stepwise classification made it possible to derive grouped diagnostic and therapeutic pathways for the three major classes - solid entities with surgical therapy - solid entities with surgical and additional therapeutic activities and - non-solid entities. For these classes it was possible to deduct common documentation workflows to support workflow-guided single-source documentation. Clinical documentation activities within a Comprehensive Cancer Center can likely be realized in a set of three documentation workflows with conditional branching in a modern workflow supporting clinical information system.

  11. Optimizing Workflow Data Footprint

    Directory of Open Access Journals (Sweden)

    Gurmeet Singh

    2007-01-01

    Full Text Available In this paper we examine the issue of optimizing disk usage and scheduling large-scale scientific workflows onto distributed resources where the workflows are data-intensive, requiring large amounts of data storage, and the resources have limited storage resources. Our approach is two-fold: we minimize the amount of space a workflow requires during execution by removing data files at runtime when they are no longer needed and we demonstrate that workflows may have to be restructured to reduce the overall data footprint of the workflow. We show the results of our data management and workflow restructuring solutions using a Laser Interferometer Gravitational-Wave Observatory (LIGO application and an astronomy application, Montage, running on a large-scale production grid-the Open Science Grid. We show that although reducing the data footprint of Montage by 48% can be achieved with dynamic data cleanup techniques, LIGO Scientific Collaboration workflows require additional restructuring to achieve a 56% reduction in data space usage. We also examine the cost of the workflow restructuring in terms of the application's runtime.

  12. dfnWorks: A HPC Workflow for Discrete Fracture Network Modeling with Subsurface Flow and Transport Applications

    Science.gov (United States)

    Gable, C. W.; Hyman, J.; Karra, S.; Makedonska, N.; Painter, S. L.; Viswanathan, H. S.

    2015-12-01

    dfnWorks generates discrete fracture networks (DFN) of planar polygons, creates a high quality conforming Delaunay triangulation of the intersecting DFN polygons, assigns properties (aperture, permeability) using geostatistics, sets boundary and initial conditions, solves pressure/flow in single or multi-phase fluids (water, air, CO2) using the parallel PFLOTRAN or serial FEHM, and solves for transport using Lagrangian particle tracking. We outline the dfnWorks workflow and present applications from a range of fractured rock systems. dfnWorks (http://www.lanl.gov/expertise/teams/view/dfnworks) is composed of three main components, all of which are freely available. dfnGen generates a distribution of fracture polygons from site characterization data (statistics or deterministic fractures) and utilizes the FRAM (Feature Rejection Algorithm for Meshing) to guarantee the mesh generation package LaGriT (lagrit.lanl.gov) will generate a high quality conforming Delaunay triangular mesh. dfnWorks links the mesh to either PFLOTRAN (pflotran.org) or FEHM (fehm.lanl.gov) for solving flow and transport. The various physics options available in FEHM and PFLOTRAN such as single and multi-phase flow and reactive transport are all available with appropriate initial and boundary conditions and material property models. dfnTrans utilizes explicit Lagrangian particle tracking on the DFN using a velocity field reconstructed from the steady state pressure/flow field solution obtained in PFLOTRAN or FEHM. Applications are demonstrated for nuclear waste repository in fractured granite, CO2 sequestration and extraction of unconventional hydrocarbon resources.

  13. Dynamic hysteresis modeling including skin effect using diffusion equation model

    Energy Technology Data Exchange (ETDEWEB)

    Hamada, Souad, E-mail: souadhamada@yahoo.fr [LSP-IE: Research Laboratory, Electrical Engineering Department, University of Batna, 05000 Batna (Algeria); Louai, Fatima Zohra, E-mail: fz_louai@yahoo.com [LSP-IE: Research Laboratory, Electrical Engineering Department, University of Batna, 05000 Batna (Algeria); Nait-Said, Nasreddine, E-mail: n_naitsaid@yahoo.com [LSP-IE: Research Laboratory, Electrical Engineering Department, University of Batna, 05000 Batna (Algeria); Benabou, Abdelkader, E-mail: Abdelkader.Benabou@univ-lille1.fr [L2EP, Université de Lille1, 59655 Villeneuve d’Ascq (France)

    2016-07-15

    An improved dynamic hysteresis model is proposed for the prediction of hysteresis loop of electrical steel up to mean frequencies, taking into account the skin effect. In previous works, the analytical solution of the diffusion equation for low frequency (DELF) was coupled with the inverse static Jiles-Atherton (JA) model in order to represent the hysteresis behavior for a lamination. In the present paper, this approach is improved to ensure the reproducibility of measured hysteresis loops at mean frequency. The results of simulation are compared with the experimental ones. The selected results for frequencies 50 Hz, 100 Hz, 200 Hz and 400 Hz are presented and discussed.

  14. Stochastic modelling of two-phase flows including phase change

    International Nuclear Information System (INIS)

    Hurisse, O.; Minier, J.P.

    2011-01-01

    Stochastic modelling has already been developed and applied for single-phase flows and incompressible two-phase flows. In this article, we propose an extension of this modelling approach to two-phase flows including phase change (e.g. for steam-water flows). Two aspects are emphasised: a stochastic model accounting for phase transition and a modelling constraint which arises from volume conservation. To illustrate the whole approach, some remarks are eventually proposed for two-fluid models. (authors)

  15. Health information exchange technology on the front lines of healthcare: workflow factors and patterns of use

    Science.gov (United States)

    Johnson, Kevin B; Lorenzi, Nancy M

    2011-01-01

    Objective The goal of this study was to develop an in-depth understanding of how a health information exchange (HIE) fits into clinical workflow at multiple clinical sites. Materials and Methods The ethnographic qualitative study was conducted over a 9-month period in six emergency departments (ED) and eight ambulatory clinics in Memphis, Tennessee, USA. Data were collected using direct observation, informal interviews during observation, and formal semi-structured interviews. The authors observed for over 180 h, during which providers used the exchange 130 times. Results HIE-related workflow was modeled for each ED site and ambulatory clinic group and substantial site-to-site workflow differences were identified. Common patterns in HIE-related workflow were also identified across all sites, leading to the development of two role-based workflow models: nurse based and physician based. The workflow elements framework was applied to the two role-based patterns. An in-depth description was developed of how providers integrated HIE into existing clinical workflow, including prompts for HIE use. Discussion Workflow differed substantially among sites, but two general role-based HIE usage models were identified. Although providers used HIE to improve continuity of patient care, patient–provider trust played a significant role. Types of information retrieved related to roles, with nurses seeking to retrieve recent hospitalization data and more open-ended usage by nurse practitioners and physicians. User and role-specific customization to accommodate differences in workflow and information needs may increase the adoption and use of HIE. Conclusion Understanding end users' perspectives towards HIE technology is crucial to the long-term success of HIE. By applying qualitative methods, an in-depth understanding of HIE usage was developed. PMID:22003156

  16. The equivalency between logic Petri workflow nets and workflow nets.

    Science.gov (United States)

    Wang, Jing; Yu, ShuXia; Du, YuYue

    2015-01-01

    Logic Petri nets (LPNs) can describe and analyze batch processing functions and passing value indeterminacy in cooperative systems. Logic Petri workflow nets (LPWNs) are proposed based on LPNs in this paper. Process mining is regarded as an important bridge between modeling and analysis of data mining and business process. Workflow nets (WF-nets) are the extension to Petri nets (PNs), and have successfully been used to process mining. Some shortcomings cannot be avoided in process mining, such as duplicate tasks, invisible tasks, and the noise of logs. The online shop in electronic commerce in this paper is modeled to prove the equivalence between LPWNs and WF-nets, and advantages of LPWNs are presented.

  17. Modeling Electric Double-Layers Including Chemical Reaction Effects

    DEFF Research Database (Denmark)

    Paz-Garcia, Juan Manuel; Johannesson, Björn; Ottosen, Lisbeth M.

    2014-01-01

    A physicochemical and numerical model for the transient formation of an electric double-layer between an electrolyte and a chemically-active flat surface is presented, based on a finite elements integration of the nonlinear Nernst-Planck-Poisson model including chemical reactions. The model works...

  18. Research on Configurable Workflow Technology in PDM System

    Directory of Open Access Journals (Sweden)

    Cao Kang

    2016-01-01

    Full Text Available This paper analyzed the deficiency of the static process management in the traditional PDM workflow system, and proposed a new configurable workflow system model for the dynamic and multiple characteristics of the equipment product design business process. On the basis of PDM workflow engine, the model introduced the configurable workflow form and logic processing program, the total workflow template definition and customized workflow participant selection module, and put forward the key technology solutions. This model could solve the problem of the lack of flexibility in workflow design and maintenance. It had been successfully applied to the design management process for multiple equipment products, and improved the dynamic process management capability of PDM system.

  19. Deriving DICOM surgical extensions from surgical workflows

    Science.gov (United States)

    Burgert, O.; Neumuth, T.; Gessat, M.; Jacobs, S.; Lemke, H. U.

    2007-03-01

    The generation, storage, transfer, and representation of image data in radiology are standardized by DICOM. To cover the needs of image guided surgery or computer assisted surgery in general one needs to handle patient information besides image data. A large number of objects must be defined in DICOM to address the needs of surgery. We propose an analysis process based on Surgical Workflows that helps to identify these objects together with use cases and requirements motivating for their specification. As the first result we confirmed the need for the specification of representation and transfer of geometric models. The analysis of Surgical Workflows has shown that geometric models are widely used to represent planned procedure steps, surgical tools, anatomical structures, or prosthesis in the context of surgical planning, image guided surgery, augmented reality, and simulation. By now, the models are stored and transferred in several file formats bare of contextual information. The standardization of data types including contextual information and specifications for handling of geometric models allows a broader usage of such models. This paper explains the specification process leading to Geometry Mesh Service Object Pair classes. This process can be a template for the definition of further DICOM classes.

  20. It's All About the Data: Workflow Systems and Weather

    Science.gov (United States)

    Plale, B.

    2009-05-01

    Digital data is fueling new advances in the computational sciences, particularly geospatial research as environmental sensing grows more practical through reduced technology costs, broader network coverage, and better instruments. e-Science research (i.e., cyberinfrastructure research) has responded to data intensive computing with tools, systems, and frameworks that support computationally oriented activities such as modeling, analysis, and data mining. Workflow systems support execution of sequences of tasks on behalf of a scientist. These systems, such as Taverna, Apache ODE, and Kepler, when built as part of a larger cyberinfrastructure framework, give the scientist tools to construct task graphs of execution sequences, often through a visual interface for connecting task boxes together with arcs representing control flow or data flow. Unlike business processing workflows, scientific workflows expose a high degree of detail and control during configuration and execution. Data-driven science imposes unique needs on workflow frameworks. Our research is focused on two issues. The first is the support for workflow-driven analysis over all kinds of data sets, including real time streaming data and locally owned and hosted data. The second is the essential role metadata/provenance collection plays in data driven science, for discovery, determining quality, for science reproducibility, and for long-term preservation. The research has been conducted over the last 6 years in the context of cyberinfrastructure for mesoscale weather research carried out as part of the Linked Environments for Atmospheric Discovery (LEAD) project. LEAD has pioneered new approaches for integrating complex weather data, assimilation, modeling, mining, and cyberinfrastructure systems. Workflow systems have the potential to generate huge volumes of data. Without some form of automated metadata capture, either metadata description becomes largely a manual task that is difficult if not impossible

  1. Responsive web design workflow

    OpenAIRE

    LAAK, TIMO

    2013-01-01

    Responsive Web Design Workflow is a literature review about Responsive Web Design, a web standards based modern web design paradigm. The goals of this research were to define what responsive web design is, determine its importance in building modern websites and describe a workflow for responsive web design projects. Responsive web design is a paradigm to create adaptive websites, which respond to the properties of the media that is used to render them. The three key elements of responsi...

  2. Including investment risk in large-scale power market models

    DEFF Research Database (Denmark)

    Lemming, Jørgen Kjærgaard; Meibom, P.

    2003-01-01

    can be included in large-scale partial equilibrium models of the power market. The analyses are divided into a part about risk measures appropriate for power market investors and a more technical part about the combination of a risk-adjustment model and a partial-equilibrium model. To illustrate...... the analyses quantitatively, a framework based on an iterative interaction between the equilibrium model and a separate risk-adjustment module was constructed. To illustrate the features of the proposed modelling approach we examined how uncertainty in demand and variable costs affects the optimal choice...

  3. Climate Data Analytics Workflow Management

    Science.gov (United States)

    Zhang, J.; Lee, S.; Pan, L.; Mattmann, C. A.; Lee, T. J.

    2016-12-01

    In this project we aim to pave a novel path to create a sustainable building block toward Earth science big data analytics and knowledge sharing. Closely studying how Earth scientists conduct data analytics research in their daily work, we have developed a provenance model to record their activities, and to develop a technology to automatically generate workflows for scientists from the provenance. On top of it, we have built the prototype of a data-centric provenance repository, and establish a PDSW (People, Data, Service, Workflow) knowledge network to support workflow recommendation. To ensure the scalability and performance of the expected recommendation system, we have leveraged the Apache OODT system technology. The community-approved, metrics-based performance evaluation web-service will allow a user to select a metric from the list of several community-approved metrics and to evaluate model performance using the metric as well as the reference dataset. This service will facilitate the use of reference datasets that are generated in support of the model-data intercomparison projects such as Obs4MIPs and Ana4MIPs. The data-centric repository infrastructure will allow us to catch richer provenance to further facilitate knowledge sharing and scientific collaboration in the Earth science community. This project is part of Apache incubator CMDA project.

  4. A standard-enabled workflow for synthetic biology.

    Science.gov (United States)

    Myers, Chris J; Beal, Jacob; Gorochowski, Thomas E; Kuwahara, Hiroyuki; Madsen, Curtis; McLaughlin, James Alastair; Mısırlı, Göksel; Nguyen, Tramy; Oberortner, Ernst; Samineni, Meher; Wipat, Anil; Zhang, Michael; Zundel, Zach

    2017-06-15

    A synthetic biology workflow is composed of data repositories that provide information about genetic parts, sequence-level design tools to compose these parts into circuits, visualization tools to depict these designs, genetic design tools to select parts to create systems, and modeling and simulation tools to evaluate alternative design choices. Data standards enable the ready exchange of information within such a workflow, allowing repositories and tools to be connected from a diversity of sources. The present paper describes one such workflow that utilizes, among others, the Synthetic Biology Open Language (SBOL) to describe genetic designs, the Systems Biology Markup Language to model these designs, and SBOL Visual to visualize these designs. We describe how a standard-enabled workflow can be used to produce types of design information, including multiple repositories and software tools exchanging information using a variety of data standards. Recently, the ACS Synthetic Biology journal has recommended the use of SBOL in their publications. © 2017 The Author(s); published by Portland Press Limited on behalf of the Biochemical Society.

  5. Progressive IRP Models for Power Resources Including EPP

    Directory of Open Access Journals (Sweden)

    Yiping Zhu

    2017-01-01

    Full Text Available In the view of optimizing regional power supply and demand, the paper makes effective planning scheduling of supply and demand side resources including energy efficiency power plant (EPP, to achieve the target of benefit, cost, and environmental constraints. In order to highlight the characteristics of different supply and demand resources in economic, environmental, and carbon constraints, three planning models with progressive constraints are constructed. Results of three models by the same example show that the best solutions to different models are different. The planning model including EPP has obvious advantages considering pollutant and carbon emission constraints, which confirms the advantages of low cost and emissions of EPP. The construction of progressive IRP models for power resources considering EPP has a certain reference value for guiding the planning and layout of EPP within other power resources and achieving cost and environmental objectives.

  6. Progress in digital color workflow understanding in the International Color Consortium (ICC) Workflow WG

    Science.gov (United States)

    McCarthy, Ann

    2006-01-01

    The ICC Workflow WG serves as the bridge between ICC color management technologies and use of those technologies in real world color production applications. ICC color management is applicable to and is used in a wide range of color systems, from highly specialized digital cinema color special effects to high volume publications printing to home photography. The ICC Workflow WG works to align ICC technologies so that the color management needs of these diverse use case systems are addressed in an open, platform independent manner. This report provides a high level summary of the ICC Workflow WG objectives and work to date, focusing on the ways in which workflow can impact image quality and color systems performance. The 'ICC Workflow Primitives' and 'ICC Workflow Patterns and Dimensions' workflow models are covered in some detail. Consider the questions, "How much of dissatisfaction with color management today is the result of 'the wrong color transformation at the wrong time' and 'I can't get to the right conversion at the right point in my work process'?" Put another way, consider how image quality through a workflow can be negatively affected when the coordination and control level of the color management system is not sufficient.

  7. Modeling heart rate variability including the effect of sleep stages

    Science.gov (United States)

    Soliński, Mateusz; Gierałtowski, Jan; Żebrowski, Jan

    2016-02-01

    We propose a model for heart rate variability (HRV) of a healthy individual during sleep with the assumption that the heart rate variability is predominantly a random process. Autonomic nervous system activity has different properties during different sleep stages, and this affects many physiological systems including the cardiovascular system. Different properties of HRV can be observed during each particular sleep stage. We believe that taking into account the sleep architecture is crucial for modeling the human nighttime HRV. The stochastic model of HRV introduced by Kantelhardt et al. was used as the initial starting point. We studied the statistical properties of sleep in healthy adults, analyzing 30 polysomnographic recordings, which provided realistic information about sleep architecture. Next, we generated synthetic hypnograms and included them in the modeling of nighttime RR interval series. The results of standard HRV linear analysis and of nonlinear analysis (Shannon entropy, Poincaré plots, and multiscale multifractal analysis) show that—in comparison with real data—the HRV signals obtained from our model have very similar properties, in particular including the multifractal characteristics at different time scales. The model described in this paper is discussed in the context of normal sleep. However, its construction is such that it should allow to model heart rate variability in sleep disorders. This possibility is briefly discussed.

  8. COSMOS: Python library for massively parallel workflows.

    Science.gov (United States)

    Gafni, Erik; Luquette, Lovelace J; Lancaster, Alex K; Hawkins, Jared B; Jung, Jae-Yoon; Souilmi, Yassine; Wall, Dennis P; Tonellato, Peter J

    2014-10-15

    Efficient workflows to shepherd clinically generated genomic data through the multiple stages of a next-generation sequencing pipeline are of critical importance in translational biomedical science. Here we present COSMOS, a Python library for workflow management that allows formal description of pipelines and partitioning of jobs. In addition, it includes a user interface for tracking the progress of jobs, abstraction of the queuing system and fine-grained control over the workflow. Workflows can be created on traditional computing clusters as well as cloud-based services. Source code is available for academic non-commercial research purposes. Links to code and documentation are provided at http://lpm.hms.harvard.edu and http://wall-lab.stanford.edu. dpwall@stanford.edu or peter_tonellato@hms.harvard.edu. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

  9. A hydrodynamic model for granular material flows including segregation effects

    Directory of Open Access Journals (Sweden)

    Gilberg Dominik

    2017-01-01

    Full Text Available The simulation of granular flows including segregation effects in large industrial processes using particle methods is accurate, but very time-consuming. To overcome the long computation times a macroscopic model is a natural choice. Therefore, we couple a mixture theory based segregation model to a hydrodynamic model of Navier-Stokes-type, describing the flow behavior of the granular material. The granular flow model is a hybrid model derived from kinetic theory and a soil mechanical approach to cover the regime of fast dilute flow, as well as slow dense flow, where the density of the granular material is close to the maximum packing density. Originally, the segregation model has been formulated by Thornton and Gray for idealized avalanches. It is modified and adapted to be in the preferred form for the coupling. In the final coupled model the segregation process depends on the local state of the granular system. On the other hand, the granular system changes as differently mixed regions of the granular material differ i.e. in the packing density. For the modeling process the focus lies on dry granular material flows of two particle types differing only in size but can be easily extended to arbitrary granular mixtures of different particle size and density. To solve the coupled system a finite volume approach is used. To test the model the rotational mixing of small and large particles in a tumbler is simulated.

  10. A hydrodynamic model for granular material flows including segregation effects

    Science.gov (United States)

    Gilberg, Dominik; Klar, Axel; Steiner, Konrad

    2017-06-01

    The simulation of granular flows including segregation effects in large industrial processes using particle methods is accurate, but very time-consuming. To overcome the long computation times a macroscopic model is a natural choice. Therefore, we couple a mixture theory based segregation model to a hydrodynamic model of Navier-Stokes-type, describing the flow behavior of the granular material. The granular flow model is a hybrid model derived from kinetic theory and a soil mechanical approach to cover the regime of fast dilute flow, as well as slow dense flow, where the density of the granular material is close to the maximum packing density. Originally, the segregation model has been formulated by Thornton and Gray for idealized avalanches. It is modified and adapted to be in the preferred form for the coupling. In the final coupled model the segregation process depends on the local state of the granular system. On the other hand, the granular system changes as differently mixed regions of the granular material differ i.e. in the packing density. For the modeling process the focus lies on dry granular material flows of two particle types differing only in size but can be easily extended to arbitrary granular mixtures of different particle size and density. To solve the coupled system a finite volume approach is used. To test the model the rotational mixing of small and large particles in a tumbler is simulated.

  11. Simple suggestions for including vertical physics in oil spill models

    International Nuclear Information System (INIS)

    D'Asaro, Eric; University of Washington, Seatle, WA

    2001-01-01

    Current models of oil spills include no vertical physics. They neglect the effect of vertical water motions on the transport and concentration of floating oil. Some simple ways to introduce vertical physics are suggested here. The major suggestion is to routinely measure the density stratification of the upper ocean during oil spills in order to develop a database on the effect of stratification. (Author)

  12. A workflow for handling heterogeneous 3D models with the TOUGH2 family of codes: Applications to numerical modeling of CO 2 geological storage

    Science.gov (United States)

    Audigane, Pascal; Chiaberge, Christophe; Mathurin, Frédéric; Lions, Julie; Picot-Colbeaux, Géraldine

    2011-04-01

    This paper is addressed to the TOUGH2 user community. It presents a new tool for handling simulations run with the TOUGH2 code with specific application to CO 2 geological storage. This tool is composed of separate FORTRAN subroutines (or modules) that can be run independently, using input and output files in ASCII format for TOUGH2. These modules have been developed specifically for modeling of carbon dioxide geological storage and their use with TOUGH2 and the Equation of State module ECO2N, dedicated to CO 2-water-salt mixture systems, with TOUGHREACT, which is an adaptation of TOUGH2 with ECO2N and geochemical fluid-rock interactions, and with TOUGH2 and the EOS7C module dedicated to CO 2-CH 4 gas mixture is described. The objective is to save time for the pre-processing, execution and visualization of complex geometry for geological system representation. The workflow is rapid and user-friendly and future implementation to other TOUGH2 EOS modules for other contexts (e.g. nuclear waste disposal, geothermal production) is straightforward. Three examples are shown for validation: (i) leakage of CO 2 up through an abandoned well; (ii) 3D reactive transport modeling of CO 2 in a sandy aquifer formation in the Sleipner gas Field, (North Sea, Norway); and (iii) an estimation of enhanced gas recovery technology using CO 2 as the injected and stored gas to produce methane in the K12B Gas Field (North Sea, Denmark).

  13. Ab initio chemical safety assessment: A workflow based on exposure considerations and non-animal methods.

    Science.gov (United States)

    Berggren, Elisabet; White, Andrew; Ouedraogo, Gladys; Paini, Alicia; Richarz, Andrea-Nicole; Bois, Frederic Y; Exner, Thomas; Leite, Sofia; Grunsven, Leo A van; Worth, Andrew; Mahony, Catherine

    2017-11-01

    We describe and illustrate a workflow for chemical safety assessment that completely avoids animal testing. The workflow, which was developed within the SEURAT-1 initiative, is designed to be applicable to cosmetic ingredients as well as to other types of chemicals, e.g. active ingredients in plant protection products, biocides or pharmaceuticals. The aim of this work was to develop a workflow to assess chemical safety without relying on any animal testing, but instead constructing a hypothesis based on existing data, in silico modelling, biokinetic considerations and then by targeted non-animal testing. For illustrative purposes, we consider a hypothetical new ingredient x as a new component in a body lotion formulation. The workflow is divided into tiers in which points of departure are established through in vitro testing and in silico prediction, as the basis for estimating a safe external dose in a repeated use scenario. The workflow includes a series of possible exit (decision) points, with increasing levels of confidence, based on the sequential application of the Threshold of Toxicological (TTC) approach, read-across, followed by an "ab initio" assessment, in which chemical safety is determined entirely by new in vitro testing and in vitro to in vivo extrapolation by means of mathematical modelling. We believe that this workflow could be applied as a tool to inform targeted and toxicologically relevant in vitro testing, where necessary, and to gain confidence in safety decision making without the need for animal testing.

  14. Ferret Workflow Anomaly Detection System

    National Research Council Canada - National Science Library

    Smith, Timothy J; Bryant, Stephany

    2005-01-01

    The Ferret workflow anomaly detection system project 2003-2004 has provided validation and anomaly detection in accredited workflows in secure knowledge management systems through the use of continuous, automated audits...

  15. Exclusive queueing model including the choice of service windows

    Science.gov (United States)

    Tanaka, Masahiro; Yanagisawa, Daichi; Nishinari, Katsuhiro

    2018-01-01

    In a queueing system involving multiple service windows, choice behavior is a significant concern. This paper incorporates the choice of service windows into a queueing model with a floor represented by discrete cells. We contrived a logit-based choice algorithm for agents considering the numbers of agents and the distances to all service windows. Simulations were conducted with various parameters of agent choice preference for these two elements and for different floor configurations, including the floor length and the number of service windows. We investigated the model from the viewpoint of transit times and entrance block rates. The influences of the parameters on these factors were surveyed in detail and we determined that there are optimum floor lengths that minimize the transit times. In addition, we observed that the transit times were determined almost entirely by the entrance block rates. The results of the presented model are relevant to understanding queueing systems including the choice of service windows and can be employed to optimize facility design and floor management.

  16. Secretome Analysis of Lipid-Induced Insulin Resistance in Skeletal Muscle Cells by a Combined Experimental and Bioinformatics Workflow

    DEFF Research Database (Denmark)

    Deshmukh, Atul S; Cox, Juergen; Jensen, Lars Juhl

    2015-01-01

    the secretome of lipid-induced insulin-resistant skeletal muscle cells. Our workflow identified 1073 putative secreted proteins including 32 growth factors, 25 cytokines, and 29 metalloproteinases. In addition to previously reported proteins, we report hundreds of novel ones. Intriguingly, ∼40% of the secreted......-resistant conditions. Our study demonstrates an efficient combined experimental and bioinformatics workflow to identify putative secreted proteins from insulin-resistant skeletal muscle cells, which could easily be adapted to other cellular models....

  17. Tavaxy: integrating Taverna and Galaxy workflows with cloud computing support.

    Science.gov (United States)

    Abouelhoda, Mohamed; Issa, Shadi Alaa; Ghanem, Moustafa

    2012-05-04

    Over the past decade the workflow system paradigm has evolved as an efficient and user-friendly approach for developing complex bioinformatics applications. Two popular workflow systems that have gained acceptance by the bioinformatics community are Taverna and Galaxy. Each system has a large user-base and supports an ever-growing repository of application workflows. However, workflows developed for one system cannot be imported and executed easily on the other. The lack of interoperability is due to differences in the models of computation, workflow languages, and architectures of both systems. This lack of interoperability limits sharing of workflows between the user communities and leads to duplication of development efforts. In this paper, we present Tavaxy, a stand-alone system for creating and executing workflows based on using an extensible set of re-usable workflow patterns. Tavaxy offers a set of new features that simplify and enhance the development of sequence analysis applications: It allows the integration of existing Taverna and Galaxy workflows in a single environment, and supports the use of cloud computing capabilities. The integration of existing Taverna and Galaxy workflows is supported seamlessly at both run-time and design-time levels, based on the concepts of hierarchical workflows and workflow patterns. The use of cloud computing in Tavaxy is flexible, where the users can either instantiate the whole system on the cloud, or delegate the execution of certain sub-workflows to the cloud infrastructure. Tavaxy reduces the workflow development cycle by introducing the use of workflow patterns to simplify workflow creation. It enables the re-use and integration of existing (sub-) workflows from Taverna and Galaxy, and allows the creation of hybrid workflows. Its additional features exploit recent advances in high performance cloud computing to cope with the increasing data size and complexity of analysis.The system can be accessed either through a

  18. Tavaxy: Integrating Taverna and Galaxy workflows with cloud computing support

    Directory of Open Access Journals (Sweden)

    Abouelhoda Mohamed

    2012-05-01

    Full Text Available Abstract Background Over the past decade the workflow system paradigm has evolved as an efficient and user-friendly approach for developing complex bioinformatics applications. Two popular workflow systems that have gained acceptance by the bioinformatics community are Taverna and Galaxy. Each system has a large user-base and supports an ever-growing repository of application workflows. However, workflows developed for one system cannot be imported and executed easily on the other. The lack of interoperability is due to differences in the models of computation, workflow languages, and architectures of both systems. This lack of interoperability limits sharing of workflows between the user communities and leads to duplication of development efforts. Results In this paper, we present Tavaxy, a stand-alone system for creating and executing workflows based on using an extensible set of re-usable workflow patterns. Tavaxy offers a set of new features that simplify and enhance the development of sequence analysis applications: It allows the integration of existing Taverna and Galaxy workflows in a single environment, and supports the use of cloud computing capabilities. The integration of existing Taverna and Galaxy workflows is supported seamlessly at both run-time and design-time levels, based on the concepts of hierarchical workflows and workflow patterns. The use of cloud computing in Tavaxy is flexible, where the users can either instantiate the whole system on the cloud, or delegate the execution of certain sub-workflows to the cloud infrastructure. Conclusions Tavaxy reduces the workflow development cycle by introducing the use of workflow patterns to simplify workflow creation. It enables the re-use and integration of existing (sub- workflows from Taverna and Galaxy, and allows the creation of hybrid workflows. Its additional features exploit recent advances in high performance cloud computing to cope with the increasing data size and

  19. Tavaxy: Integrating Taverna and Galaxy workflows with cloud computing support

    Science.gov (United States)

    2012-01-01

    Background Over the past decade the workflow system paradigm has evolved as an efficient and user-friendly approach for developing complex bioinformatics applications. Two popular workflow systems that have gained acceptance by the bioinformatics community are Taverna and Galaxy. Each system has a large user-base and supports an ever-growing repository of application workflows. However, workflows developed for one system cannot be imported and executed easily on the other. The lack of interoperability is due to differences in the models of computation, workflow languages, and architectures of both systems. This lack of interoperability limits sharing of workflows between the user communities and leads to duplication of development efforts. Results In this paper, we present Tavaxy, a stand-alone system for creating and executing workflows based on using an extensible set of re-usable workflow patterns. Tavaxy offers a set of new features that simplify and enhance the development of sequence analysis applications: It allows the integration of existing Taverna and Galaxy workflows in a single environment, and supports the use of cloud computing capabilities. The integration of existing Taverna and Galaxy workflows is supported seamlessly at both run-time and design-time levels, based on the concepts of hierarchical workflows and workflow patterns. The use of cloud computing in Tavaxy is flexible, where the users can either instantiate the whole system on the cloud, or delegate the execution of certain sub-workflows to the cloud infrastructure. Conclusions Tavaxy reduces the workflow development cycle by introducing the use of workflow patterns to simplify workflow creation. It enables the re-use and integration of existing (sub-) workflows from Taverna and Galaxy, and allows the creation of hybrid workflows. Its additional features exploit recent advances in high performance cloud computing to cope with the increasing data size and complexity of analysis. The system

  20. Pegasus Workflow Management System: Helping Applications From Earth and Space

    Science.gov (United States)

    Mehta, G.; Deelman, E.; Vahi, K.; Silva, F.

    2010-12-01

    Pegasus WMS is a Workflow Management System that can manage large-scale scientific workflows across Grid, local and Cloud resources simultaneously. Pegasus WMS provides a means for representing the workflow of an application in an abstract XML form, agnostic of the resources available to run it and the location of data and executables. It then compiles these workflows into concrete plans by querying catalogs and farming computations across local and distributed computing resources, as well as emerging commercial and community cloud environments in an easy and reliable manner. Pegasus WMS optimizes the execution as well as data movement by leveraging existing Grid and cloud technologies via a flexible pluggable interface and provides advanced features like reusing existing data, automatic cleanup of generated data, and recursive workflows with deferred planning. It also captures all the provenance of the workflow from the planning stage to the execution of the generated data, helping scientists to accurately measure performance metrics of their workflow as well as data reproducibility issues. Pegasus WMS was initially developed as part of the GriPhyN project to support large-scale high-energy physics and astrophysics experiments. Direct funding from the NSF enabled support for a wide variety of applications from diverse domains including earthquake simulation, bacterial RNA studies, helioseismology and ocean modeling. Earthquake Simulation: Pegasus WMS was recently used in a large scale production run in 2009 by the Southern California Earthquake Centre to run 192 million loosely coupled tasks and about 2000 tightly coupled MPI style tasks on National Cyber infrastructure for generating a probabilistic seismic hazard map of the Southern California region. SCEC ran 223 workflows over a period of eight weeks, using on average 4,420 cores, with a peak of 14,540 cores. A total of 192 million files were produced totaling about 165TB out of which 11TB of data was saved

  1. A Re-Engineered Software Interface and Workflow for the Open-Source SimVascular Cardiovascular Modeling Package.

    Science.gov (United States)

    Lan, Hongzhi; Updegrove, Adam; Wilson, Nathan M; Maher, Gabriel D; Shadden, Shawn C; Marsden, Alison L

    2018-02-01

    Patient-specific simulation plays an important role in cardiovascular disease research, diagnosis, surgical planning and medical device design, as well as education in cardiovascular biomechanics. simvascular is an open-source software package encompassing an entire cardiovascular modeling and simulation pipeline from image segmentation, three-dimensional (3D) solid modeling, and mesh generation, to patient-specific simulation and analysis. SimVascular is widely used for cardiovascular basic science and clinical research as well as education, following increased adoption by users and development of a GATEWAY web portal to facilitate educational access. Initial efforts of the project focused on replacing commercial packages with open-source alternatives and adding increased functionality for multiscale modeling, fluid-structure interaction (FSI), and solid modeling operations. In this paper, we introduce a major SimVascular (SV) release that includes a new graphical user interface (GUI) designed to improve user experience. Additional improvements include enhanced data/project management, interactive tools to facilitate user interaction, new boundary condition (BC) functionality, plug-in mechanism to increase modularity, a new 3D segmentation tool, and new computer-aided design (CAD)-based solid modeling capabilities. Here, we focus on major changes to the software platform and outline features added in this new release. We also briefly describe our recent experiences using SimVascular in the classroom for bioengineering education.

  2. Workflows for Full Waveform Inversions

    Science.gov (United States)

    Boehm, Christian; Krischer, Lion; Afanasiev, Michael; van Driel, Martin; May, Dave A.; Rietmann, Max; Fichtner, Andreas

    2017-04-01

    Despite many theoretical advances and the increasing availability of high-performance computing clusters, full seismic waveform inversions still face considerable challenges regarding data and workflow management. While the community has access to solvers which can harness modern heterogeneous computing architectures, the computational bottleneck has fallen to these often manpower-bounded issues that need to be overcome to facilitate further progress. Modern inversions involve huge amounts of data and require a tight integration between numerical PDE solvers, data acquisition and processing systems, nonlinear optimization libraries, and job orchestration frameworks. To this end we created a set of libraries and applications revolving around Salvus (http://salvus.io), a novel software package designed to solve large-scale full waveform inverse problems. This presentation focuses on solving passive source seismic full waveform inversions from local to global scales with Salvus. We discuss (i) design choices for the aforementioned components required for full waveform modeling and inversion, (ii) their implementation in the Salvus framework, and (iii) how it is all tied together by a usable workflow system. We combine state-of-the-art algorithms ranging from high-order finite-element solutions of the wave equation to quasi-Newton optimization algorithms using trust-region methods that can handle inexact derivatives. All is steered by an automated interactive graph-based workflow framework capable of orchestrating all necessary pieces. This naturally facilitates the creation of new Earth models and hopefully sparks new scientific insights. Additionally, and even more importantly, it enhances reproducibility and reliability of the final results.

  3. Two-Layer Transaction Management for Workflow Management Applications

    NARCIS (Netherlands)

    Grefen, P.W.P.J.; Vonk, J.; Boertjes, E.M.; Apers, Peter M.G.

    Workflow management applications require advanced transaction management that is not offered by traditional database systems. For this reason, a number of extended transaction models has been proposed in the past. None of these models seems completely adequate, though, because workflow management

  4. Wildfire: distributed, Grid-enabled workflow construction and execution

    Directory of Open Access Journals (Sweden)

    Issac Praveen

    2005-03-01

    Full Text Available Abstract Background We observe two trends in bioinformatics: (i analyses are increasing in complexity, often requiring several applications to be run as a workflow; and (ii multiple CPU clusters and Grids are available to more scientists. The traditional solution to the problem of running workflows across multiple CPUs required programming, often in a scripting language such as perl. Programming places such solutions beyond the reach of many bioinformatics consumers. Results We present Wildfire, a graphical user interface for constructing and running workflows. Wildfire borrows user interface features from Jemboss and adds a drag-and-drop interface allowing the user to compose EMBOSS (and other programs into workflows. For execution, Wildfire uses GEL, the underlying workflow execution engine, which can exploit available parallelism on multiple CPU machines including Beowulf-class clusters and Grids. Conclusion Wildfire simplifies the tasks of constructing and executing bioinformatics workflows.

  5. Complexity Metrics for Workflow Nets

    DEFF Research Database (Denmark)

    Lassen, Kristian Bisgaard; van der Aalst, Wil M.P.

    2009-01-01

    analysts have difficulties grasping the dynamics implied by a process model. Recent empirical studies show that people make numerous errors when modeling complex business processes, e.g., about 20 percent of the EPCs in the SAP reference model have design flaws resulting in potential deadlocks, livelocks......, etc. It seems obvious that the complexity of the model contributes to design errors and a lack of understanding. It is not easy to measure complexity, however. This paper presents three complexity metrics that have been implemented in the process analysis tool ProM. The metrics are defined...... for a subclass of Petri nets named Workflow nets, but the results can easily be applied to other languages. To demonstrate the applicability of these metrics, we have applied our approach and tool to 262 relatively complex Protos models made in the context of various student projects. This allows us to validate...

  6. The MPO system for automatic workflow documentation

    Energy Technology Data Exchange (ETDEWEB)

    Abla, G.; Coviello, E.N.; Flanagan, S.M. [General Atomics, P.O. Box 85608, San Diego, CA 92186-5608 (United States); Greenwald, M. [Massachusetts Institute of Technology, Cambridge, MA 02139 (United States); Lee, X. [General Atomics, P.O. Box 85608, San Diego, CA 92186-5608 (United States); Romosan, A. [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Schissel, D.P., E-mail: schissel@fusion.gat.com [General Atomics, P.O. Box 85608, San Diego, CA 92186-5608 (United States); Shoshani, A. [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Stillerman, J.; Wright, J. [Massachusetts Institute of Technology, Cambridge, MA 02139 (United States); Wu, K.J. [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States)

    2016-11-15

    Highlights: • Data model, infrastructure, and tools for data tracking, cataloging, and integration. • Automatically document workflow and data provenance in the widest sense. • Fusion Science as test bed but the system’s framework and data model is quite general. - Abstract: Data from large-scale experiments and extreme-scale computing is expensive to produce and may be used for critical applications. However, it is not the mere existence of data that is important, but our ability to make use of it. Experience has shown that when metadata is better organized and more complete, the underlying data becomes more useful. Traditionally, capturing the steps of scientific workflows and metadata was the role of the lab notebook, but the digital era has resulted instead in the fragmentation of data, processing, and annotation. This paper presents the Metadata, Provenance, and Ontology (MPO) System, the software that can automate the documentation of scientific workflows and associated information. Based on recorded metadata, it provides explicit information about the relationships among the elements of workflows in notebook form augmented with directed acyclic graphs. A set of web-based graphical navigation tools and Application Programming Interface (API) have been created for searching and browsing, as well as programmatically accessing the workflows and data. We describe the MPO concepts and its software architecture. We also report the current status of the software as well as the initial deployment experience.

  7. The MPO system for automatic workflow documentation

    International Nuclear Information System (INIS)

    Abla, G.; Coviello, E.N.; Flanagan, S.M.; Greenwald, M.; Lee, X.; Romosan, A.; Schissel, D.P.; Shoshani, A.; Stillerman, J.; Wright, J.; Wu, K.J.

    2016-01-01

    Highlights: • Data model, infrastructure, and tools for data tracking, cataloging, and integration. • Automatically document workflow and data provenance in the widest sense. • Fusion Science as test bed but the system’s framework and data model is quite general. - Abstract: Data from large-scale experiments and extreme-scale computing is expensive to produce and may be used for critical applications. However, it is not the mere existence of data that is important, but our ability to make use of it. Experience has shown that when metadata is better organized and more complete, the underlying data becomes more useful. Traditionally, capturing the steps of scientific workflows and metadata was the role of the lab notebook, but the digital era has resulted instead in the fragmentation of data, processing, and annotation. This paper presents the Metadata, Provenance, and Ontology (MPO) System, the software that can automate the documentation of scientific workflows and associated information. Based on recorded metadata, it provides explicit information about the relationships among the elements of workflows in notebook form augmented with directed acyclic graphs. A set of web-based graphical navigation tools and Application Programming Interface (API) have been created for searching and browsing, as well as programmatically accessing the workflows and data. We describe the MPO concepts and its software architecture. We also report the current status of the software as well as the initial deployment experience.

  8. Beginning WF Windows Workflow in .NET 4.0

    CERN Document Server

    Collins, M

    2010-01-01

    Windows Workflow Foundation is a ground-breaking addition to the core of the .NET Framework that allows you to orchestrate human and system interactions as a series of workflows that can be easily mapped, analyzed, adjusted, and implemented. As business problems become more complex, the need for a workflow-based solution has never been more evident. WF provides a simple and consistent way to model and implement complex problems. As a developer, you focus on developing the business logic for individual workflow tasks. The runtime handles the execution of those tasks after they have been compose

  9. How Workflow Documentation Facilitates Curation Planning

    Science.gov (United States)

    Wickett, K.; Thomer, A. K.; Baker, K. S.; DiLauro, T.; Asangba, A. E.

    2013-12-01

    The description of the specific processes and artifacts that led to the creation of a data product provide a detailed picture of data provenance in the form of a workflow. The Site-Based Data Curation project, hosted by the Center for Informatics Research in Science and Scholarship at the University of Illinois, has been investigating how workflows can be used in developing curation processes and policies that move curation "upstream" in the research process. The team has documented an individual workflow for geobiology data collected during a single field trip to Yellowstone National Park. This specific workflow suggests a generalized three-part process for field data collection that comprises three distinct elements: a Planning Stage, a Fieldwork Stage, and a Processing and Analysis Stage. Beyond supplying an account of data provenance, the workflow has allowed the team to identify 1) points of intervention for curation processes and 2) data products that are likely candidates for sharing or deposit. Although these objects may be viewed by individual researchers as 'intermediate' data products, discussions with geobiology researchers have suggested that with appropriate packaging and description they may serve as valuable observational data for other researchers. Curation interventions may include the introduction of regularized data formats during the planning process, data description procedures, the identification and use of established controlled vocabularies, and data quality and validation procedures. We propose a poster that shows the individual workflow and our generalization into a three-stage process. We plan to discuss with attendees how well the three-stage view applies to other types of field-based research, likely points of intervention, and what kinds of interventions are appropriate and feasible in the example workflow.

  10. The PBase Scientific Workflow Provenance Repository

    Directory of Open Access Journals (Sweden)

    Víctor Cuevas-Vicenttín

    2014-10-01

    Full Text Available Scientific workflows and their supporting systems are becoming increasingly popular for compute-intensive and data-intensive scientific experiments. The advantages scientific workflows offer include rapid and easy workflow design, software and data reuse, scalable execution, sharing and collaboration, and other advantages that altogether facilitate “reproducible science”. In this context, provenance – information about the origin, context, derivation, ownership, or history of some artifact – plays a key role, since scientists are interested in examining and auditing the results of scientific experiments. However, in order to perform such analyses on scientific results as part of extended research collaborations, an adequate environment and tools are required. Concretely, the need arises for a repository that will facilitate the sharing of scientific workflows and their associated execution traces in an interoperable manner, also enabling querying and visualization. Furthermore, such functionality should be supported while taking performance and scalability into account. With this purpose in mind, we introduce PBase: a scientific workflow provenance repository implementing the ProvONE proposed standard, which extends the emerging W3C PROV standard for provenance data with workflow specific concepts. PBase is built on the Neo4j graph database, thus offering capabilities such as declarative and efficient querying. Our experiences demonstrate the power gained by supporting various types of queries for provenance data. In addition, PBase is equipped with a user friendly interface tailored for the visualization of scientific workflow provenance data, making the specification of queries and the interpretation of their results easier and more effective.

  11. Quantitative analysis of probabilistic BPMN workflows

    DEFF Research Database (Denmark)

    Herbert, Luke Thomas; Sharp, Robin

    2012-01-01

    We present a framework for modelling and analysis of realworld business workflows. We present a formalised core subset of the Business Process Modelling and Notation (BPMN) and then proceed to extend this language with probabilistic nondeterministic branching and general-purpose reward annotations...... of events, reward-based properties and best- and worst- case scenarios. We develop a simple example of medical workflow and demonstrate the utility of this analysis in accurate provisioning of drug stocks. Finally, we suggest a path to building upon these techniques to cover the entire BPMN language, allow...... for more complex annotations and ultimately to automatically synthesise workflows by composing predefined sub-processes, in order to achieve a configuration that is optimal for parameters of interest....

  12. Facilitating hydrological data analysis workflows in R: the RHydro package

    Science.gov (United States)

    Buytaert, Wouter; Moulds, Simon; Skoien, Jon; Pebesma, Edzer; Reusser, Dominik

    2015-04-01

    The advent of new technologies such as web-services and big data analytics holds great promise for hydrological data analysis and simulation. Driven by the need for better water management tools, it allows for the construction of much more complex workflows, that integrate more and potentially more heterogeneous data sources with longer tool chains of algorithms and models. With the scientific challenge of designing the most adequate processing workflow comes the technical challenge of implementing the workflow with a minimal risk for errors. A wide variety of new workbench technologies and other data handling systems are being developed. At the same time, the functionality of available data processing languages such as R and Python is increasing at an accelerating pace. Because of the large diversity of scientific questions and simulation needs in hydrology, it is unlikely that one single optimal method for constructing hydrological data analysis workflows will emerge. Nevertheless, languages such as R and Python are quickly gaining popularity because they combine a wide array of functionality with high flexibility and versatility. The object-oriented nature of high-level data processing languages makes them particularly suited for the handling of complex and potentially large datasets. In this paper, we explore how handling and processing of hydrological data in R can be facilitated further by designing and implementing a set of relevant classes and methods in the experimental R package RHydro. We build upon existing efforts such as the sp and raster packages for spatial data and the spacetime package for spatiotemporal data to define classes for hydrological data (HydroST). In order to handle simulation data from hydrological models conveniently, a HM class is defined. Relevant methods are implemented to allow for an optimal integration of the HM class with existing model fitting and simulation functionality in R. Lastly, we discuss some of the design challenges

  13. A Framework for Distributed Preservation Workflows

    Directory of Open Access Journals (Sweden)

    Rainer Schmidt

    2010-07-01

    Full Text Available The Planets Project is developing a service-oriented environment for the definition and evaluation of preservation strategies for human-centric data. It focuses on the question of logically preserving digital materials, as opposed to the physical preservation of content bit-streams. This includes the development of preservation tools for the automated characterisation, migration, and comparison of different types of Digital Objects as well as the emulation of their original runtime environment in order to ensure long-time access and interpretability. The Planets integrated environment provides a number of end-user applications that allow data curators to execute and scientifically evaluate preservation experiments based on composable preservation services. In this paper, we focus on the middleware and programming model and show how it can be utilised in order to create complex preservation workflows.

  14. Workflow patterns the definitive guide

    CERN Document Server

    Russell, Nick; ter Hofstede, Arthur H M

    2016-01-01

    The study of business processes has emerged as a highly effective approach to coordinating an organization's complex service- and knowledge-based activities. The growing field of business process management (BPM) focuses on methods and tools for designing, enacting, and analyzing business processes. This volume offers a definitive guide to the use of patterns, which synthesize the wide range of approaches to modeling business processes. It provides a unique and comprehensive introduction to the well-known workflow patterns collection -- recurrent, generic constructs describing common business process modeling and execution scenarios, presented in the form of problem-solution dialectics. The underlying principles of the patterns approach ensure that they are independent of any specific enabling technology, representational formalism, or modeling approach, and thus broadly applicable across the business process modeling and business process technology domains. The authors, drawing on extensive research done by...

  15. Automation of Flexible Migration Workflows

    Directory of Open Access Journals (Sweden)

    Dirk von Suchodoletz

    2011-03-01

    Full Text Available Many digital preservation scenarios are based on the migration strategy, which itself is heavily tool-dependent. For popular, well-defined and often open file formats – e.g., digital images, such as PNG, GIF, JPEG – a wide range of tools exist. Migration workflows become more difficult with proprietary formats, as used by the several text processing applications becoming available in the last two decades. If a certain file format can not be rendered with actual software, emulation of the original environment remains a valid option. For instance, with the original Lotus AmiPro or Word Perfect, it is not a problem to save an object of this type in ASCII text or Rich Text Format. In specific environments, it is even possible to send the file to a virtual printer, thereby producing a PDF as a migration output. Such manual migration tasks typically involve human interaction, which may be feasible for a small number of objects, but not for larger batches of files.We propose a novel approach using a software-operated VNC abstraction layer in order to replace humans with machine interaction. Emulators or virtualization tools equipped with a VNC interface are very well suited for this approach. But screen, keyboard and mouse interaction is just part of the setup. Furthermore, digital objects need to be transferred into the original environment in order to be extracted after processing. Nevertheless, the complexity of the new generation of migration services is quickly rising; a preservation workflow is now comprised not only of the migration tool itself, but of a complete software and virtual hardware stack with recorded workflows linked to every supported migration scenario. Thus the requirements of OAIS management must include proper software archiving, emulator selection, system image and recording handling. The concept of view-paths could help either to automatically determine the proper pre-configured virtual environment or to set up system

  16. Integrating configuration workflows with project management system

    International Nuclear Information System (INIS)

    Nilsen, Dimitri; Weber, Pavel

    2014-01-01

    The complexity of the heterogeneous computing resources, services and recurring infrastructure changes at the GridKa WLCG Tier-1 computing center require a structured approach to configuration management and optimization of interplay between functional components of the whole system. A set of tools deployed at GridKa, including Puppet, Redmine, Foreman, SVN and Icinga, provides the administrative environment giving the possibility to define and develop configuration workflows, reduce the administrative effort and improve sustainable operation of the whole computing center. In this presentation we discuss the developed configuration scenarios implemented at GridKa, which we use for host installation, service deployment, change management procedures, service retirement etc. The integration of Puppet with a project management tool like Redmine provides us with the opportunity to track problem issues, organize tasks and automate these workflows. The interaction between Puppet and Redmine results in automatic updates of the issues related to the executed workflow performed by different system components. The extensive configuration workflows require collaboration and interaction between different departments like network, security, production etc. at GridKa. Redmine plugins developed at GridKa and integrated in its administrative environment provide an effective way of collaboration within the GridKa team. We present the structural overview of the software components, their connections, communication protocols and show a few working examples of the workflows and their automation.

  17. Automated data reduction workflows for astronomy. The ESO Reflex environment

    Science.gov (United States)

    Freudling, W.; Romaniello, M.; Bramich, D. M.; Ballester, P.; Forchi, V.; García-Dabló, C. E.; Moehler, S.; Neeser, M. J.

    2013-11-01

    Context. Data from complex modern astronomical instruments often consist of a large number of different science and calibration files, and their reduction requires a variety of software tools. The execution chain of the tools represents a complex workflow that needs to be tuned and supervised, often by individual researchers that are not necessarily experts for any specific instrument. Aims: The efficiency of data reduction can be improved by using automatic workflows to organise data and execute a sequence of data reduction steps. To realize such efficiency gains, we designed a system that allows intuitive representation, execution and modification of the data reduction workflow, and has facilities for inspection and interaction with the data. Methods: The European Southern Observatory (ESO) has developed Reflex, an environment to automate data reduction workflows. Reflex is implemented as a package of customized components for the Kepler workflow engine. Kepler provides the graphical user interface to create an executable flowchart-like representation of the data reduction process. Key features of Reflex are a rule-based data organiser, infrastructure to re-use results, thorough book-keeping, data progeny tracking, interactive user interfaces, and a novel concept to exploit information created during data organisation for the workflow execution. Results: Automated workflows can greatly increase the efficiency of astronomical data reduction. In Reflex, workflows can be run non-interactively as a first step. Subsequent optimization can then be carried out while transparently re-using all unchanged intermediate products. We found that such workflows enable the reduction of complex data by non-expert users and minimizes mistakes due to book-keeping errors. Conclusions: Reflex includes novel concepts to increase the efficiency of astronomical data processing. While Reflex is a specific implementation of astronomical scientific workflows within the Kepler workflow

  18. Semantic Workflows and Provenance-Aware Software (Invited)

    Science.gov (United States)

    Gil, Y.

    2013-12-01

    Workflows are increasingly used in science to manage complex computations and data processing at large scale. Intelligent workflow systems provide assistance in setting up parameters and data, validating workflows created by users, and automating the generation of workflows from high-level user guidance. These systems use semantic workflows that extend workflow representations with semantic constraints that express characteristics of the data and analytic models. Reasoning algorithms propagate these semantic constraints throughout the workflow structure, select executable components for underspecified steps, and suggest parameter values. Semantic workflows also enhance provenance records with abstract steps that reflect the overall data analysis method rather than just execution traces. Intelligent workflow systems are provenance-aware, since they both use and generate provenance and metadata as the data is being processed. Provenance-aware software enhances scientific analysis by propagating upstream metadata and provenance to new data products. Through the use of provenance standards, such as the recent W3C PROV recommendation for provenance on the Web, provenance-aware software can significantly enhance scientific data analysis, publication, and reuse. New capabilities are enabled when provenance is brought to the forefront in the design of software systems for science.

  19. The Symbiotic Relationship between Scientific Workflow and Provenance (Invited)

    Science.gov (United States)

    Stephan, E.

    2010-12-01

    The purpose of this presentation is to describe the symbiotic nature of scientific workflows and provenance. We will also discuss the current trends and real world challenges facing these two distinct research areas. Although motivated differently, the needs of the international science communities are the glue that binds this relationship together. Understanding and articulating the science drivers to these communities is paramount as these technologies evolve and mature. Originally conceived for managing business processes, workflows are now becoming invaluable assets in both computational and experimental sciences. These reconfigurable, automated systems provide essential technology to perform complex analyses by coupling together geographically distributed disparate data sources and applications. As a result, workflows are capable of higher throughput in a shorter amount of time than performing the steps manually. Today many different workflow products exist; these could include Kepler and Taverna or similar products like MeDICI, developed at PNNL, that are standardized on the Business Process Execution Language (BPEL). Provenance, originating from the French term Provenir “to come from”, is used to describe the curation process of artwork as art is passed from owner to owner. The concept of provenance was adopted by digital libraries as a means to track the lineage of documents while standards such as the DublinCore began to emerge. In recent years the systems science community has increasingly expressed the need to expand the concept of provenance to formally articulate the history of scientific data. Communities such as the International Provenance and Annotation Workshop (IPAW) have formalized a provenance data model. The Open Provenance Model, and the W3C is hosting a provenance incubator group featuring the Proof Markup Language. Although both workflows and provenance have risen from different communities and operate independently, their mutual

  20. Data intensive ATLAS workflows in the Cloud

    CERN Document Server

    AUTHOR|(INSPIRE)INSPIRE-00396985; The ATLAS collaboration; Keeble, Oliver; Quadt, Arnulf; Kawamura, Gen

    2017-01-01

    This contribution reports on the feasibility of executing data intensive workflows on Cloud infrastructures. In order to assess this, the metric ETC = Events/Time/Cost is formed, which quantifies the different workflow and infrastructure configurations that are tested against each other. In these tests ATLAS reconstruction Jobs are run, examining the effects of overcommitting (more parallel processes running than CPU cores available), scheduling (staggered execution) and scaling (number of cores). The desirability of commissioning storage in the Cloud is evaluated, in conjunction with a simple analytical model of the system, and correlated with questions about the network bandwidth, caches and what kind of storage to utilise. In the end a cost/benefit evaluation of different infrastructure configurations and workflows is undertaken, with the goal to find the maximum of the ETC value.

  1. Data intensive ATLAS workflows in the Cloud

    CERN Document Server

    Rzehorz, Gerhard Ferdinand; The ATLAS collaboration

    2016-01-01

    This contribution reports on the feasibility of executing data intensive workflows on Cloud infrastructures. In order to assess this, the metric ETC = Events/Time/Cost is formed, which quantifies the different workflow and infrastructure configurations that are tested against each other. In these tests ATLAS reconstruction Jobs are run, examining the effects of overcommitting (more parallel processes running than CPU cores available), scheduling (staggered execution) and scaling (number of cores). The desirability of commissioning storage in the cloud is evaluated, in conjunction with a simple analytical model of the system, and correlated with questions about the network bandwidth, caches and what kind of storage to utilise. In the end a cost/benefit evaluation of different infrastructure configurations and workflows is undertaken, with the goal to find the maximum of the ETC value

  2. Distributed Global Transaction Support for Workflow Management Applications

    NARCIS (Netherlands)

    Vonk, J.; Grefen, P.W.P.J.; Boertjes, E.M.; Apers, Peter M.G.

    Workflow management systems require advanced transaction support to cope with their inherently long-running processes. The recent trend to distribute workflow executions requires an even more advanced transaction support system that is able to handle distribution. This report presents a model as

  3. From Paper Based Clinical Practice Guidelines to Declarative Workflow Management

    DEFF Research Database (Denmark)

    Lyng, Karen Marie; Hildebrandt, Thomas; Mukkamala, Raghava Rao

    2009-01-01

    a sub workflow can be described in a declarative workflow management system: the Resultmaker Online Consultant (ROC). The example demonstrates that declarative primitives allow to naturally extend the paper based flowchart to an executable model without introducing a complex cyclic control flow graph....

  4. Distributed Global Transaction Support for Workflow Management Applications

    NARCIS (Netherlands)

    Vonk, J.; Grefen, P.W.P.J.; Boertjes, E.M.; Apers, Peter M.G.

    Workflow management systems require advanced transaction support to cope with their inherently long-running processes. The recent trend to distribute workflow executions requires an even more advanced transaction support system that is able to handle distribution. This paper presents a model as well

  5. Design decisions in workflow management and quality of work.

    NARCIS (Netherlands)

    Waal, B.M.E. de; Batenburg, R.

    2009-01-01

    In this paper, the design and implementation of a workflow management (WFM) system in a large Dutch social insurance organisation is described. The effect of workflow design decisions on the quality of work is explored theoretically and empirically, using the model of Zur Mühlen as a frame of

  6. Impact of CGNS on CFD Workflow

    Science.gov (United States)

    Poinot, M.; Rumsey, C. L.; Mani, M.

    2004-01-01

    CFD tools are an integral part of industrial and research processes, for which the amount of data is increasing at a high rate. These data are used in a multi-disciplinary fluid dynamics environment, including structural, thermal, chemical or even electrical topics. We show that the data specification is an important challenge that must be tackled to achieve an efficient workflow for use in this environment. We compare the process with other software techniques, such as network or database type, where past experiences showed how difficult it was to bridge the gap between completely general specifications and dedicated specific applications. We show two aspects of the use of CFD General Notation System (CGNS) that impact CFD workflow: as a data specification framework and as a data storage means. Then, we give examples of projects involving CFD workflows where the use of the CGNS standard leads to a useful method either for data specification, exchange, or storage.

  7. Including spatial data in nutrient balance modelling on dairy farms

    Science.gov (United States)

    van Leeuwen, Maricke; van Middelaar, Corina; Stoof, Cathelijne; Oenema, Jouke; Stoorvogel, Jetse; de Boer, Imke

    2017-04-01

    The Annual Nutrient Cycle Assessment (ANCA) calculates the nitrogen (N) and phosphorus (P) balance at a dairy farm, while taking into account the subsequent nutrient cycles of the herd, manure, soil and crop components. Since January 2016, Dutch dairy farmers are required to use ANCA in order to increase understanding of nutrient flows and to minimize nutrient losses to the environment. A nutrient balance calculates the difference between nutrient inputs and outputs. Nutrients enter the farm via purchased feed, fertilizers, deposition and fixation by legumes (nitrogen), and leave the farm via milk, livestock, manure, and roughages. A positive balance indicates to which extent N and/or P are lost to the environment via gaseous emissions (N), leaching, run-off and accumulation in soil. A negative balance indicates that N and/or P are depleted from soil. ANCA was designed to calculate average nutrient flows on farm level (for the herd, manure, soil and crop components). ANCA was not designed to perform calculations of nutrient flows at the field level, as it uses averaged nutrient inputs and outputs across all fields, and it does not include field specific soil characteristics. Land management decisions, however, such as the level of N and P application, are typically taken at the field level given the specific crop and soil characteristics. Therefore the information that ANCA provides is likely not sufficient to support farmers' decisions on land management to minimize nutrient losses to the environment. This is particularly a problem when land management and soils vary between fields. For an accurate estimate of nutrient flows in a given farming system that can be used to optimize land management, the spatial scale of nutrient inputs and outputs (and thus the effect of land management and soil variation) could be essential. Our aim was to determine the effect of the spatial scale of nutrient inputs and outputs on modelled nutrient flows and nutrient use efficiencies

  8. Analysis of Enterprise Workflow Solutions

    Science.gov (United States)

    Chen, Cui-E.; Wang, Shulin; Chen, Ying; Meng, Yang; Ma, Hua

    Since the 90’s, workflow technology has been widely applied in various industries, such as office automation(OA), manufacturing, telecommunications services, banking, securities, insurance and other financial services, research institutes and education services, and so on, to improve business process automation and integration capabilities. In this paper, based on Workflow theory, the author proposed a set of policy-based workflow approach in order to support dynamic workflow patterns. Through the expansion of the functions of Shark, it implemented a Workflow engine component-OAShark which can support retrieval / rollback function. The related classes were programmed. The technology was applied to the OA system of an enterprise project. The realization of the enterprise workflow solutions greatly improved the efficiency of the office automation.

  9. Single-Phase Bundle Flows Including Macroscopic Turbulence Model

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Seung Jun; Yoon, Han Young [KAERI, Daejeon (Korea, Republic of); Yoon, Seok Jong; Cho, Hyoung Kyu [Seoul National University, Seoul (Korea, Republic of)

    2016-05-15

    To deal with various thermal hydraulic phenomena due to rapid change of fluid properties when an accident happens, securing mechanistic approaches as much as possible may reduce the uncertainty arising from improper applications of the experimental models. In this study, the turbulence mixing model, which is well defined in the subchannel analysis code such as VIPRE, COBRA, and MATRA by experiments, is replaced by a macroscopic k-e turbulence model, which represents the aspect of mathematical derivation. The performance of CUPID with macroscopic turbulence model is validated against several bundle experiments: CNEN 4x4 and PNL 7x7 rod bundle tests. In this study, the macroscopic k-e model has been validated for the application to subchannel analysis. It has been implemented in the CUPID code and validated against CNEN 4x4 and PNL 7x7 rod bundle tests. The results showed that the macroscopic k-e turbulence model can estimate the experiments properly.

  10. Understanding the dispensary workflow at the Birmingham Free Clinic: a proposed framework for an informatics intervention.

    Science.gov (United States)

    Fisher, Arielle M; Herbert, Mary I; Douglas, Gerald P

    2016-02-19

    The Birmingham Free Clinic (BFC) in Pittsburgh, Pennsylvania, USA is a free, walk-in clinic that serves medically uninsured populations through the use of volunteer health care providers and an on-site medication dispensary. The introduction of an electronic medical record (EMR) has improved several aspects of clinic workflow. However, pharmacists' tasks involving medication management and dispensing have become more challenging since EMR implementation due to its inability to support workflows between the medical and pharmaceutical services. To inform the design of a systematic intervention, we conducted a needs assessment study to identify workflow challenges and process inefficiencies in the dispensary. We used contextual inquiry to document the dispensary workflow and facilitate identification of critical aspects of intervention design specific to the user. Pharmacists were observed according to contextual inquiry guidelines. Graphical models were produced to aid data and process visualization. We created a list of themes describing workflow challenges and asked the pharmacists to rank them in order of significance to narrow the scope of intervention design. Three pharmacists were observed at the BFC. Observer notes were documented and analyzed to produce 13 themes outlining the primary challenges pharmacists encounter during dispensation at the BFC. The dispensary workflow is labor intensive, redundant, and inefficient when integrated with the clinical service. Observations identified inefficiencies that may benefit from the introduction of informatics interventions including: medication labeling, insufficient process notification, triple documentation, and inventory control. We propose a system for Prescription Management and General Inventory Control (RxMAGIC). RxMAGIC is a framework designed to mitigate workflow challenges and improve the processes of medication management and inventory control. While RxMAGIC is described in the context of the BFC

  11. Spatio-energetic cross-talk in photon counting detectors: Numerical detector model (PcTK) and workflow for CT image quality assessment.

    Science.gov (United States)

    Taguchi, Katsuyuki; Stierstorfer, Karl; Polster, Christoph; Lee, Okkyun; Kappler, Steffen

    2018-03-14

    The inter-pixel cross-talk of energy-sensitive photon counting x-ray detectors (PCDs) has been studied and an analytical model (version 2.1) has been developed for double-counting between neighboring pixels due to charge sharing and K-shell fluorescence x-ray emission followed by its re-absorption [Taguchi K, et al., Medical Physics 2016;43(12):6386-6404]. While the model version 2.1 simulated the spectral degradation well, it had the following problems that has been found to be significant recently: (1) The spectrum is inaccurate with smaller pixel sizes; (2) the charge cloud size must be smaller than the pixel size; (3) the model underestimates the spectrum/counts for 10-40 keV; and (4) the model version 2.1 cannot handle n-tuple-counting with n>2 (i.e., triple-counting or higher). These problems are inherent to the design of the model version 2.1; therefore, we developed a new model and addressed these problems in this study. We propose a new PCD cross-talk model (version 3.2; PcTK for "photon counting toolkit") that is based on a completely different design concept from the previous version. It uses a numerical approach and starts with a 2-D model of charge sharing (as opposed to an analytical approach and a 1-D model with version 2.1) and addresses all of the four problems. The model takes the following factors into account: (a) shift-variant electron density of the charge cloud (Gaussian-distributed), (b) detection efficiency, (c) interactions between photons and PCDs via photoelectric effect, and (d) electronic noise. Correlated noisy PCD data can be generated using either a multivariate normal number generator or a Poisson random number generator. The effect of the two parameters, the effective charge cloud diameter (d 0 ) and pixel size (d pix ), was studied and results were compared with Monte Carlo simulations and the previous model version 2.1. Finally, a script for the workflow for CT image quality assessment has been developed, which started with a

  12. The impact of electronic medical record systems on outpatient workflows: a longitudinal evaluation of its workflow effects.

    Science.gov (United States)

    Vishwanath, Arun; Singh, Sandeep Rajan; Winkelstein, Peter

    2010-11-01

    empirically from the conceptual model. They included 85 items that measured physician perceptions of the EMR's workflow effect on the following eight issues: (1) administration, (2) efficiency in patient processing, (3) basic clinical processes, (4) documentation of patient encounter, (5) economic challenges and reimbursement, (6) technical issues, (7) patient safety and care, and (8) communication and confidentiality. The items were used to track expectations prior to implementation and they served as retrospective measures of satisfaction with the EMR in post-implementation Time 1 and Time 2. The findings suggest that physicians conceptualize EMRs as an incremental extension of older computerized provider order entries (CPOEs) rather than as a new innovation. The EMRs major functional advantages are seen to be very similar to, if not the same as, those of CPOEs. Technology learning curves play a statistically significant though minor role in shaping physician perceptions. The physicians' expectations from the EMR are based on their prior beliefs rather than on a rational evaluation of the EMR's fit, functionality, or performance. Their decision regarding the usefulness of the EMR is made very early, within the first few months of use of the EMR. These early perceptions then remain stable and become the lens through which subsequent experience with the EMR is interpreted. The findings suggest a need for communication based interventions aimed at explaining the value, fit, and usefulness of EMRs to physicians early in the pre- and immediate post-EMR implementation stages. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

  13. Global atmospheric model for mercury including oxidation by bromine atoms

    Directory of Open Access Journals (Sweden)

    C. D. Holmes

    2010-12-01

    Full Text Available Global models of atmospheric mercury generally assume that gas-phase OH and ozone are the main oxidants converting Hg0 to HgII and thus driving mercury deposition to ecosystems. However, thermodynamic considerations argue against the importance of these reactions. We demonstrate here the viability of atomic bromine (Br as an alternative Hg0 oxidant. We conduct a global 3-D simulation with the GEOS-Chem model assuming gas-phase Br to be the sole Hg0 oxidant (Hg + Br model and compare to the previous version of the model with OH and ozone as the sole oxidants (Hg + OH/O3 model. We specify global 3-D Br concentration fields based on our best understanding of tropospheric and stratospheric Br chemistry. In both the Hg + Br and Hg + OH/O3 models, we add an aqueous photochemical reduction of HgII in cloud to impose a tropospheric lifetime for mercury of 6.5 months against deposition, as needed to reconcile observed total gaseous mercury (TGM concentrations with current estimates of anthropogenic emissions. This added reduction would not be necessary in the Hg + Br model if we adjusted the Br oxidation kinetics downward within their range of uncertainty. We find that the Hg + Br and Hg + OH/O3 models are equally capable of reproducing the spatial distribution of TGM and its seasonal cycle at northern mid-latitudes. The Hg + Br model shows a steeper decline of TGM concentrations from the tropics to southern mid-latitudes. Only the Hg + Br model can reproduce the springtime depletion and summer rebound of TGM observed at polar sites; the snowpack component of GEOS-Chem suggests that 40% of HgII deposited to snow in the Arctic is transferred to the ocean and land reservoirs, amounting to a net deposition flux to the Arctic of 60 Mg a−1. Summertime events of depleted Hg0 at Antarctic sites due to subsidence are much better simulated by

  14. Accelerating the scientific exploration process with scientific workflows

    International Nuclear Information System (INIS)

    Altintas, Ilkay; Barney, Oscar; Cheng, Zhengang; Critchlow, Terence; Ludaescher, Bertram; Parker, Steve; Shoshani, Arie; Vouk, Mladen

    2006-01-01

    Although an increasing amount of middleware has emerged in the last few years to achieve remote data access, distributed job execution, and data management, orchestrating these technologies with minimal overhead still remains a difficult task for scientists. Scientific workflow systems improve this situation by creating interfaces to a variety of technologies and automating the execution and monitoring of the workflows. Workflow systems provide domain-independent customizable interfaces and tools that combine different tools and technologies along with efficient methods for using them. As simulations and experiments move into the petascale regime, the orchestration of long running data and compute intensive tasks is becoming a major requirement for the successful steering and completion of scientific investigations. A scientific workflow is the process of combining data and processes into a configurable, structured set of steps that implement semi-automated computational solutions of a scientific problem. Kepler is a cross-project collaboration, co-founded by the SciDAC Scientific Data Management (SDM) Center, whose purpose is to develop a domain-independent scientific workflow system. It provides a workflow environment in which scientists design and execute scientific workflows by specifying the desired sequence of computational actions and the appropriate data flow, including required data transformations, between these steps. Currently deployed workflows range from local analytical pipelines to distributed, high-performance and high-throughput applications, which can be both data- and compute-intensive. The scientific workflow approach offers a number of advantages over traditional scripting-based approaches, including ease of configuration, improved reusability and maintenance of workflows and components (called actors), automated provenance management, 'smart' re-running of different versions of workflow instances, on-the-fly updateable parameters, monitoring

  15. Thematic report: Macroeconomic models including specifically social and environmental aspects

    OpenAIRE

    Kratena, Kurt

    2015-01-01

    WWWforEurope Deliverable No. 8, 30 pages A significant reduction of the global environmental consequences of European consumption and production activities are the main objective of the policy simulations carried out in this paper. For this purpose three different modelling approaches have been chosen. Two macroeconomic models following the philosophy of consistent stock-flow accounting for the main institutional sectors (households, firms, banks, central bank and government) are used for...

  16. The complete digital workflow in fixed prosthodontics: a systematic review.

    Science.gov (United States)

    Joda, Tim; Zarone, Fernando; Ferrari, Marco

    2017-09-19

    The continuous development in dental processing ensures new opportunities in the field of fixed prosthodontics in a complete virtual environment without any physical model situations. The aim was to compare fully digitalized workflows to conventional and/or mixed analog-digital workflows for the treatment with tooth-borne or implant-supported fixed reconstructions. A PICO strategy was executed using an electronic (MEDLINE, EMBASE, Google Scholar) plus manual search up to 2016-09-16 focusing on RCTs investigating complete digital workflows in fixed prosthodontics with regard to economics or esthetics or patient-centered outcomes with or without follow-up or survival/success rate analysis as well as complication assessment of at least 1 year under function. The search strategy was assembled from MeSH-Terms and unspecific free-text words: {(("Dental Prosthesis" [MeSH]) OR ("Crowns" [MeSH]) OR ("Dental Prosthesis, Implant-Supported" [MeSH])) OR ((crown) OR (fixed dental prosthesis) OR (fixed reconstruction) OR (dental bridge) OR (implant crown) OR (implant prosthesis) OR (implant restoration) OR (implant reconstruction))} AND {("Computer-Aided Design" [MeSH]) OR ((digital workflow) OR (digital technology) OR (computerized dentistry) OR (intraoral scan) OR (digital impression) OR (scanbody) OR (virtual design) OR (digital design) OR (cad/cam) OR (rapid prototyping) OR (monolithic) OR (full-contour))} AND {("Dental Technology" [MeSH) OR ((conventional workflow) OR (lost-wax-technique) OR (porcelain-fused-to-metal) OR (PFM) OR (implant impression) OR (hand-layering) OR (veneering) OR (framework))} AND {(("Study, Feasibility" [MeSH]) OR ("Survival" [MeSH]) OR ("Success" [MeSH]) OR ("Economics" [MeSH]) OR ("Costs, Cost Analysis" [MeSH]) OR ("Esthetics, Dental" [MeSH]) OR ("Patient Satisfaction" [MeSH])) OR ((feasibility) OR (efficiency) OR (patient-centered outcome))}. Assessment of risk of bias in selected studies was done at a 'trial level' including random sequence

  17. Comparing the accuracy (trueness and precision) of models of fixed dental prostheses fabricated by digital and conventional workflows.

    Science.gov (United States)

    Sim, Ji-Young; Jang, Yeon; Kim, Woong-Chul; Kim, Hae-Young; Lee, Dong-Hwan; Kim, Ji-Hwan

    2018-03-31

    This study aimed to evaluate and compare the accuracy. A reference model was prepared with three prepared teeth for three types of restorations: single crown, 3-unit bridge, and inlay. Stone models were fabricated from conventional impressions. Digital impressions of the reference model were created using an intraoral scanner (digital models). Physical models were fabricated using a three-dimensional (3D) printer. Reference, stone, and 3D printed models were subsequently scanned using an industrial optical scanner; files were exported in a stereolithography file format. All datasets were superimposed using 3D analysis software to evaluate the accuracy of the complete arch and trueness of the preparations. One-way and two-way analyses of variance (ANOVA) were performed to compare the accuracy among the three model groups and evaluate the trueness among the three types of preparation. For the complete arch, significant intergroup differences in precision were observed for the three groups (pdigital models (p>.05). 3D printed models had the poorest accuracy. A two-way ANOVA revealed significant differences in trueness among the model groups (pDigital models had smaller root mean square values of trueness of the complete arch and preparations than stone models. However, the accuracy of the complete arch and trueness of the preparations of 3D printed models were inferior to those of the other groups. Copyright © 2018 Japan Prosthodontic Society. Published by Elsevier Ltd. All rights reserved.

  18. Identifying Clusters with Mixture Models that Include Radial Velocity Observations

    Science.gov (United States)

    Czarnatowicz, Alexis; Ybarra, Jason E.

    2018-01-01

    The study of stellar clusters plays an integral role in the study of star formation. We present a cluster mixture model that considers radial velocity data in addition to spatial data. Maximum likelihood estimation through the Expectation-Maximization (EM) algorithm is used for parameter estimation. Our mixture model analysis can be used to distinguish adjacent or overlapping clusters, and estimate properties for each cluster.Work supported by awards from the Virginia Foundation for Independent Colleges (VFIC) Undergraduate Science Research Fellowship and The Research Experience @Bridgewater (TREB).

  19. A virtual radiation therapy workflow training simulation

    International Nuclear Information System (INIS)

    Bridge, P.; Crowe, S.B.; Gibson, G.; Ellemor, N.J.; Hargrave, C.; Carmichael, M.

    2016-01-01

    Aim: Simulation forms an increasingly vital component of clinical skills development in a wide range of professional disciplines. Simulation of clinical techniques and equipment is designed to better prepare students for placement by providing an opportunity to learn technical skills in a “safe” academic environment. In radiotherapy training over the last decade or so this has predominantly comprised treatment planning software and small ancillary equipment such as mould room apparatus. Recent virtual reality developments have dramatically changed this approach. Innovative new simulation applications and file processing and interrogation software have helped to fill in the gaps to provide a streamlined virtual workflow solution. This paper outlines the innovations that have enabled this, along with an evaluation of the impact on students and educators. Method: Virtual reality software and workflow applications have been developed to enable the following steps of radiation therapy to be simulated in an academic environment: CT scanning using a 3D virtual CT scanner simulation; batch CT duplication; treatment planning; 3D plan evaluation using a virtual linear accelerator; quantitative plan assessment, patient setup with lasers; and image guided radiotherapy software. Results: Evaluation of the impact of the virtual reality workflow system highlighted substantial time saving for academic staff as well as positive feedback from students relating to preparation for clinical placements. Students valued practice in the “safe” environment and the opportunity to understand the clinical workflow ahead of clinical department experience. Conclusion: Simulation of most of the radiation therapy workflow and tasks is feasible using a raft of virtual reality simulation applications and supporting software. Benefits of this approach include time-saving, embedding of a case-study based approach, increased student confidence, and optimal use of the clinical environment

  20. An extended Intelligent Water Drops algorithm for workflow scheduling in cloud computing environment

    Directory of Open Access Journals (Sweden)

    Shaymaa Elsherbiny

    2018-03-01

    Full Text Available Cloud computing is emerging as a high performance computing environment with a large scale, heterogeneous collection of autonomous systems and flexible computational architecture. Many resource management methods may enhance the efficiency of the whole cloud computing system. The key part of cloud computing resource management is resource scheduling. Optimized scheduling of tasks on the cloud virtual machines is an NP-hard problem and many algorithms have been presented to solve it. The variations among these schedulers are due to the fact that the scheduling strategies of the schedulers are adapted to the changing environment and the types of tasks. The focus of this paper is on workflows scheduling in cloud computing, which is gaining a lot of attention recently because workflows have emerged as a paradigm to represent complex computing problems. We proposed a novel algorithm extending the natural-based Intelligent Water Drops (IWD algorithm that optimizes the scheduling of workflows on the cloud. The proposed algorithm is implemented and embedded within the workflows simulation toolkit and tested in different simulated cloud environments with different cost models. Our algorithm showed noticeable enhancements over the classical workflow scheduling algorithms. We made a comparison between the proposed IWD-based algorithm with other well-known scheduling algorithms, including MIN-MIN, MAX-MIN, Round Robin, FCFS, and MCT, PSO and C-PSO, where the proposed algorithm presented noticeable enhancements in the performance and cost in most situations.

  1. Unsteady panel method for complex configurations including wake modeling

    CSIR Research Space (South Africa)

    Van Zyl, Lourens H

    2008-01-01

    Full Text Available The calculation of unsteady air loads is an essential step in any aeroelastic analysis. The subsonic doublet lattice method (DLM) is used extensively for this purpose due to its simplicity and reliability. The body models available with the popular...

  2. Conventions and workflows for using Situs

    International Nuclear Information System (INIS)

    Wriggers, Willy

    2012-01-01

    Recent developments of the Situs software suite for multi-scale modeling are reviewed. Typical workflows and conventions encountered during processing of biophysical data from electron microscopy, tomography or small-angle X-ray scattering are described. Situs is a modular program package for the multi-scale modeling of atomic resolution structures and low-resolution biophysical data from electron microscopy, tomography or small-angle X-ray scattering. This article provides an overview of recent developments in the Situs package, with an emphasis on workflows and conventions that are important for practical applications. The modular design of the programs facilitates scripting in the bash shell that allows specific programs to be combined in creative ways that go beyond the original intent of the developers. Several scripting-enabled functionalities, such as flexible transformations of data type, the use of symmetry constraints or the creation of two-dimensional projection images, are described. The processing of low-resolution biophysical maps in such workflows follows not only first principles but often relies on implicit conventions. Situs conventions related to map formats, resolution, correlation functions and feature detection are reviewed and summarized. The compatibility of the Situs workflow with CCP4 conventions and programs is discussed

  3. A thermal lens model including the Soret effect

    International Nuclear Information System (INIS)

    Cabrera, Humberto; Sira, Eloy; Rahn, Kareem; Garcia-Sucre, Maximo

    2009-01-01

    In this letter we generalize the thermal lens model to account for the Soret effect in binary liquid mixtures. This formalism permits the precise determination of the Soret coefficient in a steady-state situation. The theory is experimentally verified using the measured values in the ethanol/water mixtures. The time evolution of the Soret signal has been used to derive mass-diffusion times from which mass-diffusion coefficients were calculated. (Author)

  4. Including lateral interactions into microkinetic models of catalytic reactions

    DEFF Research Database (Denmark)

    Hellman, Anders; Honkala, Johanna Karoliina

    2007-01-01

    In many catalytic reactions lateral interactions between adsorbates are believed to have a strong influence on the reaction rates. We apply a microkinetic model to explore the effect of lateral interactions and how to efficiently take them into account in a simple catalytic reaction. Three differ...... different approximations are investigated: site, mean-field, and quasichemical approximations. The obtained results are compared to accurate Monte Carlo numbers. In the end, we apply the approximations to a real catalytic reaction, namely, ammonia synthesis....

  5. A stochastic model of gene expression including splicing events

    OpenAIRE

    Penim, Flávia Alexandra Mendes

    2014-01-01

    Tese de mestrado, Bioinformática e Biologia Computacional, Universidade de Lisboa, Faculdade de Ciências, 2014 Proteins carry out the great majority of the catalytic and structural work within an organism. The RNA templates used in their synthesis determines their identity, and this is dictated by which genes are transcribed. Therefore, gene expression is the fundamental determinant of an organism’s nature. The main objective of this thesis was to develop a stochastic computational model a...

  6. Possibilistic Information Flow Control for Workflow Management Systems

    Directory of Open Access Journals (Sweden)

    Thomas Bauereiss

    2014-04-01

    Full Text Available In workflows and business processes, there are often security requirements on both the data, i.e. confidentiality and integrity, and the process, e.g. separation of duty. Graphical notations exist for specifying both workflows and associated security requirements. We present an approach for formally verifying that a workflow satisfies such security requirements. For this purpose, we define the semantics of a workflow as a state-event system and formalise security properties in a trace-based way, i.e. on an abstract level without depending on details of enforcement mechanisms such as Role-Based Access Control (RBAC. This formal model then allows us to build upon well-known verification techniques for information flow control. We describe how a compositional verification methodology for possibilistic information flow can be adapted to verify that a specification of a distributed workflow management system satisfies security requirements on both data and processes.

  7. Digital workflows in contemporary orthodontics

    Directory of Open Access Journals (Sweden)

    Lars R Christensen

    2017-01-01

    Full Text Available Digital workflows are now increasingly possible in orthodontic practice. Workflows designed to improve the customization of orthodontic appliances are now available through laboratories and orthodontic manufacturing facilities in many parts of the world. These now have the potential to improve certain aspects of patient care.

  8. Text mining for the biocuration workflow.

    Science.gov (United States)

    Hirschman, Lynette; Burns, Gully A P C; Krallinger, Martin; Arighi, Cecilia; Cohen, K Bretonnel; Valencia, Alfonso; Wu, Cathy H; Chatr-Aryamontri, Andrew; Dowell, Karen G; Huala, Eva; Lourenço, Anália; Nash, Robert; Veuthey, Anne-Lise; Wiegers, Thomas; Winter, Andrew G

    2012-01-01

    Molecular biology has become heavily dependent on biological knowledge encoded in expert curated biological databases. As the volume of biological literature increases, biocurators need help in keeping up with the literature; (semi-) automated aids for biocuration would seem to be an ideal application for natural language processing and text mining. However, to date, there have been few documented successes for improving biocuration throughput using text mining. Our initial investigations took place for the workshop on 'Text Mining for the BioCuration Workflow' at the third International Biocuration Conference (Berlin, 2009). We interviewed biocurators to obtain workflows from eight biological databases. This initial study revealed high-level commonalities, including (i) selection of documents for curation; (ii) indexing of documents with biologically relevant entities (e.g. genes); and (iii) detailed curation of specific relations (e.g. interactions); however, the detailed workflows also showed many variabilities. Following the workshop, we conducted a survey of biocurators. The survey identified biocurator priorities, including the handling of full text indexed with biological entities and support for the identification and prioritization of documents for curation. It also indicated that two-thirds of the biocuration teams had experimented with text mining and almost half were using text mining at that time. Analysis of our interviews and survey provide a set of requirements for the integration of text mining into the biocuration workflow. These can guide the identification of common needs across curated databases and encourage joint experimentation involving biocurators, text mining developers and the larger biomedical research community.

  9. Parton recombination model including resonance production. RL-78-040

    International Nuclear Information System (INIS)

    Roberts, R.G.; Hwa, R.C.; Matsuda, S.

    1978-05-01

    Possible effects of resonance production on the meson inclusive distribution in the fragmentation region are investigated in the framework of the parton recombination model. From a detailed study of the data on vector-meson production, a reliable ratio of the vector-to-pseudoscalar rates is determined. Then the influence of the decay of the vector mesons on the pseudoscalar spectrum is examined, and the effect found to be no more than 25% for x > 0.5. The normalization of the non-strange antiquark distributions are still higher than those in a quiescent proton. The agreement between the calculated results and data remain very good. 36 references

  10. Extending PSA models including ageing and asset management - 15291

    International Nuclear Information System (INIS)

    Martorell, S.; Marton, I.; Carlos, S.; Sanchez, A.I.

    2015-01-01

    This paper proposes a new approach to Ageing Probabilistic Safety Assessment (APSA) modelling, which is intended to be used to support risk-informed decisions on the effectiveness of maintenance management programs and technical specification requirements of critical equipment of Nuclear Power Plants (NPP) within the framework of the Risk Informed Decision Making according to R.G. 1.174 principles. This approach focuses on the incorporation of not only equipment ageing but also effectiveness of maintenance and efficiency of surveillance testing explicitly into APSA models and data. This methodology is applied to a motor-operated valve of the auxiliary feed water system (AFWS) of a PWR. This simple example of application focuses on a critical safety-related equipment of a NPP in order to evaluate the risk impact of considering different approaches to APSA and the combined effect of equipment ageing and maintenance and testing alternatives along NPP design life. The risk impact of several alternatives in maintenance strategy is discussed

  11. Constructing Workflows from Script Applications

    Directory of Open Access Journals (Sweden)

    Mikołaj Baranowski

    2012-01-01

    Full Text Available For programming and executing complex applications on grid infrastructures, scientific workflows have been proposed as convenient high-level alternative to solutions based on general-purpose programming languages, APIs and scripts. GridSpace is a collaborative programming and execution environment, which is based on a scripting approach and it extends Ruby language with a high-level API for invoking operations on remote resources. In this paper we describe a tool which enables to convert the GridSpace application source code into a workflow representation which, in turn, may be used for scheduling, provenance, or visualization. We describe how we addressed the issues of analyzing Ruby source code, resolving variable and method dependencies, as well as building workflow representation. The solutions to these problems have been developed and they were evaluated by testing them on complex grid application workflows such as CyberShake, Epigenomics and Montage. Evaluation is enriched by representing typical workflow control flow patterns.

  12. Radiology information system: a workflow-based approach

    International Nuclear Information System (INIS)

    Zhang, Jinyan; Lu, Xudong; Nie, Hongchao; Huang, Zhengxing; Aalst, W.M.P. van der

    2009-01-01

    Introducing workflow management technology in healthcare seems to be prospective in dealing with the problem that the current healthcare Information Systems cannot provide sufficient support for the process management, although several challenges still exist. The purpose of this paper is to study the method of developing workflow-based information system in radiology department as a use case. First, a workflow model of typical radiology process was established. Second, based on the model, the system could be designed and implemented as a group of loosely coupled components. Each component corresponded to one task in the process and could be assembled by the workflow management system. The legacy systems could be taken as special components, which also corresponded to the tasks and were integrated through transferring non-work- flow-aware interfaces to the standard ones. Finally, a workflow dashboard was designed and implemented to provide an integral view of radiology processes. The workflow-based Radiology Information System was deployed in the radiology department of Zhejiang Chinese Medicine Hospital in China. The results showed that it could be adjusted flexibly in response to the needs of changing process, and enhance the process management in the department. It can also provide a more workflow-aware integration method, comparing with other methods such as IHE-based ones. The workflow-based approach is a new method of developing radiology information system with more flexibility, more functionalities of process management and more workflow-aware integration. The work of this paper is an initial endeavor for introducing workflow management technology in healthcare. (orig.)

  13. Quantitative analysis of probabilistic BPMN workflows

    DEFF Research Database (Denmark)

    Herbert, Luke Thomas; Sharp, Robin

    2012-01-01

    We present a framework for modelling and analysis of realworld business workflows. We present a formalised core subset of the Business Process Modelling and Notation (BPMN) and then proceed to extend this language with probabilistic nondeterministic branching and general-purpose reward annotations....... We present an algorithm for the translation of such models into Markov Decision processes expressed in the syntax of the PRISM model checker. This enables analysis of business processes for the following properties: transient and steadystate probabilities, the timing, occurrence and ordering...... of events, reward-based properties and best- and worst- case scenarios. We develop a simple example of medical workflow and demonstrate the utility of this analysis in accurate provisioning of drug stocks. Finally, we suggest a path to building upon these techniques to cover the entire BPMN language, allow...

  14. Distributed Workflow Service Composition Based on CTR Technology

    Science.gov (United States)

    Feng, Zhilin; Ye, Yanming

    Recently, WS-BPEL has gradually become the basis of a standard for web service description and composition. However, WS-BPEL cannot efficiently describe distributed workflow services for lacking of special expressive power and formal semantics. This paper presents a novel method for modeling distributed workflow service composition with Concurrent TRansaction logic (CTR). The syntactic structure of WS-BPEL and CTR are analyzed, and new rules of mapping WS-BPEL into CTR are given. A case study is put forward to show that the proposed method is appropriate for modeling workflow business services under distributed environments.

  15. Toward a Visualization-Supported Workflow for Cyber Alert Management using Threat Models and Human-Centered Design

    Energy Technology Data Exchange (ETDEWEB)

    Franklin, Lyndsey; Pirrung, Megan A.; Blaha, Leslie M.; Dowling, Michelle V.; Feng, Mi

    2017-10-09

    Cyber network analysts follow complex processes in their investigations of potential threats to their network. Much research is dedicated to providing automated tool support in the effort to make their tasks more efficient, accurate, and timely. This tool support comes in a variety of implementations from machine learning algorithms that monitor streams of data to visual analytic environments for exploring rich and noisy data sets. Cyber analysts, however, often speak of a need for tools which help them merge the data they already have and help them establish appropriate baselines against which to compare potential anomalies. Furthermore, existing threat models that cyber analysts regularly use to structure their investigation are not often leveraged in support tools. We report on our work with cyber analysts to understand they analytic process and how one such model, the MITRE ATT&CK Matrix [32], is used to structure their analytic thinking. We present our efforts to map specific data needed by analysts into the threat model to inform our eventual visualization designs. We examine data mapping for gaps where the threat model is under-supported by either data or tools. We discuss these gaps as potential design spaces for future research efforts. We also discuss the design of a prototype tool that combines machine-learning and visualization components to support cyber analysts working with this threat model.

  16. From Requirements via Colored Workflow Nets to an Implementation in Several Workflow Systems

    DEFF Research Database (Denmark)

    Mans, Ronnie S:; van der Aalst, Wil M.P.; Bakker, Piet J.M.

    2007-01-01

    Care organizations, such as hospitals, need to support complex and dynamic workflows. More- over, many disciplines are involved. This makes it important to avoid the typical disconnect between requirements and the actual implementation of the system. This paper proposes an approach where an Execu......Care organizations, such as hospitals, need to support complex and dynamic workflows. More- over, many disciplines are involved. This makes it important to avoid the typical disconnect between requirements and the actual implementation of the system. This paper proposes an approach where...... an Executable Use Case (EUC) and Colored Workflow Net (CWN) are used to close the gap between the given requirements specification and the realization of these requirements with the help of a workflow system. This paper describes a large case study where the diagnostic tra jectory of the gynaecological oncology...... care process of the Academic Medical Center (AMC) hospital is used as reference process. The process consists of hundreds of activities. These have been modeled and analyzed using an EUC and a CWN. Moreover, based on the CWN, the process has been implemented using four different workflow systems...

  17. Developing a Workflow to Identify Inconsistencies in Volunteered Geographic Information: A Phenological Case Study.

    Science.gov (United States)

    Mehdipoor, Hamed; Zurita-Milla, Raul; Rosemartin, Alyssa; Gerst, Katharine L; Weltzin, Jake F

    2015-01-01

    Recent improvements in online information communication and mobile location-aware technologies have led to the production of large volumes of volunteered geographic information. Widespread, large-scale efforts by volunteers to collect data can inform and drive scientific advances in diverse fields, including ecology and climatology. Traditional workflows to check the quality of such volunteered information can be costly and time consuming as they heavily rely on human interventions. However, identifying factors that can influence data quality, such as inconsistency, is crucial when these data are used in modeling and decision-making frameworks. Recently developed workflows use simple statistical approaches that assume that the majority of the information is consistent. However, this assumption is not generalizable, and ignores underlying geographic and environmental contextual variability that may explain apparent inconsistencies. Here we describe an automated workflow to check inconsistency based on the availability of contextual environmental information for sampling locations. The workflow consists of three steps: (1) dimensionality reduction to facilitate further analysis and interpretation of results, (2) model-based clustering to group observations according to their contextual conditions, and (3) identification of inconsistent observations within each cluster. The workflow was applied to volunteered observations of flowering in common and cloned lilac plants (Syringa vulgaris and Syringa x chinensis) in the United States for the period 1980 to 2013. About 97% of the observations for both common and cloned lilacs were flagged as consistent, indicating that volunteers provided reliable information for this case study. Relative to the original dataset, the exclusion of inconsistent observations changed the apparent rate of change in lilac bloom dates by two days per decade, indicating the importance of inconsistency checking as a key step in data quality

  18. Developing a workflow to identify inconsistencies in volunteered geographic information: a phenological case study

    Science.gov (United States)

    Mehdipoor, Hamed; Zurita-Milla, Raul; Rosemartin, Alyssa; Gerst, Katharine L.; Weltzin, Jake F.

    2015-01-01

    Recent improvements in online information communication and mobile location-aware technologies have led to the production of large volumes of volunteered geographic information. Widespread, large-scale efforts by volunteers to collect data can inform and drive scientific advances in diverse fields, including ecology and climatology. Traditional workflows to check the quality of such volunteered information can be costly and time consuming as they heavily rely on human interventions. However, identifying factors that can influence data quality, such as inconsistency, is crucial when these data are used in modeling and decision-making frameworks. Recently developed workflows use simple statistical approaches that assume that the majority of the information is consistent. However, this assumption is not generalizable, and ignores underlying geographic and environmental contextual variability that may explain apparent inconsistencies. Here we describe an automated workflow to check inconsistency based on the availability of contextual environmental information for sampling locations. The workflow consists of three steps: (1) dimensionality reduction to facilitate further analysis and interpretation of results, (2) model-based clustering to group observations according to their contextual conditions, and (3) identification of inconsistent observations within each cluster. The workflow was applied to volunteered observations of flowering in common and cloned lilac plants (Syringa vulgaris and Syringa x chinensis) in the United States for the period 1980 to 2013. About 97% of the observations for both common and cloned lilacs were flagged as consistent, indicating that volunteers provided reliable information for this case study. Relative to the original dataset, the exclusion of inconsistent observations changed the apparent rate of change in lilac bloom dates by two days per decade, indicating the importance of inconsistency checking as a key step in data quality

  19. The future of scientific workflows

    Energy Technology Data Exchange (ETDEWEB)

    Deelman, Ewa [University of Southern California, Information Sciences Institute, Marina del Rey, CA, USA; Peterka, Tom [Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, USA; Altintas, Ilkay [UCSD, San Diego Supercomputing Center, San Diego, CA, USA; Carothers, Christopher D. [Computer Science Department, Rensselaer Polytechnic Institute, New York, NY, USA; van Dam, Kerstin Kleese [Brookhaven National Laboratory, New York, NY, USA; Moreland, Kenneth [Sandia National Laboratories, USA; Parashar, Manish [Computer Science Department, Rutgers University, New Brunswick, NJ, USA; Ramakrishnan, Lavanya [Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Taufer, Michela [Computer Science Department, University of Delaware, Newark, DE, USA; Vetter, Jeffrey [Oak Ridge National Laboratory, Oak Ridge, USA

    2017-04-26

    Today’s computational, experimental, and observational sciences rely on computations that involve many related tasks. The success of a scientific mission often hinges on the computer automation of these workflows. In April 2015, the US Department of Energy (DOE) invited a diverse group of domain and computer scientists from national laboratories supported by the Office of Science, the National Nuclear Security Administration, from industry, and from academia to review the workflow requirements of DOE’s science and national security missions, to assess the current state of the art in science workflows, to understand the impact of emerging extreme-scale computing systems on those workflows, and to develop requirements for automated workflow management in future and existing environments. This article is a summary of the opinions of over 50 leading researchers attending this workshop. We highlight use cases, computing systems, workflow needs and conclude by summarizing the remaining challenges this community sees that inhibit large-scale scientific workflows from becoming a mainstream tool for extreme-scale science.

  20. Essential Grid Workflow Monitoring Elements

    Energy Technology Data Exchange (ETDEWEB)

    Gunter, Daniel K.; Jackson, Keith R.; Konerding, David E.; Lee,Jason R.; Tierney, Brian L.

    2005-07-01

    Troubleshooting Grid workflows is difficult. A typicalworkflow involves a large number of components networks, middleware,hosts, etc. that can fail. Even when monitoring data from all thesecomponents is accessible, it is hard to tell whether failures andanomalies in these components are related toa given workflow. For theGrid to be truly usable, much of this uncertainty must be elim- inated.We propose two new Grid monitoring elements, Grid workflow identifiersand consistent component lifecycle events, that will make Gridtroubleshooting easier, and thus make Grids more usable, by simplifyingthe correlation of Grid monitoring data with a particular Gridworkflow.

  1. Concurrency & Asynchrony in Declarative Workflows

    DEFF Research Database (Denmark)

    Debois, Søren; Hildebrandt, Thomas; Slaats, Tijs

    2015-01-01

    Declarative or constraint-based business process and workflow notations have received increasing interest in the last decade as possible means of addressing the challenge of supporting at the same time flexibility in execution, adaptability and compliance. However, the definition of concurrent...... of concurrency in DCR Graphs admits asynchronous execution of declarative workflows both conceptually and by reporting on a prototype implementation of a distributed declarative workflow engine. Both the theoretical development and the implementation is supported by an extended example; moreover, the theoretical...

  2. From Paper Based Clinical Practice Guidelines to Declarative Workflow Management

    DEFF Research Database (Denmark)

    Lyng, Karen Marie; Hildebrandt, Thomas; Mukkamala, Raghava Rao

    2009-01-01

    We present a field study of oncology workflow, involving doctors, nurses and pharmacists at Danish hospitals and discuss the obstacles, enablers and challenges for the use of computer based clinical practice guidelines. Related to the CIGDec approach of Pesic and van der Aalst we then describe how...... a sub workflow can be described in a declarative workflow management system: the Resultmaker Online Consultant (ROC). The example demonstrates that declarative primitives allow to naturally extend the paper based flowchart to an executable model without introducing a complex cyclic control flow graph....

  3. Summer Student Report - AV Workflow

    CERN Document Server

    Abramson, Jessie

    2014-01-01

    The AV Workflow is web application which allows cern users to publish, update and delete videos from cds. During my summer internship I implemented the backend of the new version of the AV Worklow in python using the django framework.

  4. CSP for Executable Scientific Workflows

    DEFF Research Database (Denmark)

    Friborg, Rune Møllegaard

    is demonstrated through examples. By providing a robust library for organising scientific workflows in a Python application I hope to inspire scientific users to adopt PyCSP. As a proof-of-concept this thesis demonstrates three scientific applications: kNN, stochastic minimum search and McStas to scale well......This thesis presents CSP as a means of orchestrating the execution of tasks in a scientific workflow. Scientific workflow systems are popular in a wide range of scientific areas, where tasks are organised in directed graphs. Execution of such graphs is handled by the scientific workflow systems...... and the readability of Python source code. Python is a popular programming language in the scientific community, with many scientific libraries (modules) and simple integration to external languages. This thesis presents a PyCSP extended with many new features and a more robust implementation to allow scientific...

  5. ERROR HANDLING IN INTEGRATION WORKFLOWS

    Directory of Open Access Journals (Sweden)

    Alexey M. Nazarenko

    2017-01-01

    Full Text Available Simulation experiments performed while solving multidisciplinary engineering and scientific problems require joint usage of multiple software tools. Further, when following a preset plan of experiment or searching for optimum solu- tions, the same sequence of calculations is run multiple times with various simulation parameters, input data, or conditions while overall workflow does not change. Automation of simulations like these requires implementing of a workflow where tool execution and data exchange is usually controlled by a special type of software, an integration environment or plat- form. The result is an integration workflow (a platform-dependent implementation of some computing workflow which, in the context of automation, is a composition of weakly coupled (in terms of communication intensity typical subtasks. These compositions can then be decomposed back into a few workflow patterns (types of subtasks interaction. The pat- terns, in their turn, can be interpreted as higher level subtasks.This paper considers execution control and data exchange rules that should be imposed by the integration envi- ronment in the case of an error encountered by some integrated software tool. An error is defined as any abnormal behavior of a tool that invalidates its result data thus disrupting the data flow within the integration workflow. The main requirementto the error handling mechanism implemented by the integration environment is to prevent abnormal termination of theentire workflow in case of missing intermediate results data. Error handling rules are formulated on the basic pattern level and on the level of a composite task that can combine several basic patterns as next level subtasks. The cases where workflow behavior may be different, depending on user's purposes, when an error takes place, and possible error handling op- tions that can be specified by the user are also noted in the work.

  6. Workflow Lexicons in Healthcare: Validation of the SWIM Lexicon.

    Science.gov (United States)

    Meenan, Chris; Erickson, Bradley; Knight, Nancy; Fossett, Jewel; Olsen, Elizabeth; Mohod, Prerna; Chen, Joseph; Langer, Steve G

    2017-06-01

    For clinical departments seeking to successfully navigate the challenges of modern health reform, obtaining access to operational and clinical data to establish and sustain goals for improving quality is essential. More broadly, health delivery organizations are also seeking to understand performance across multiple facilities and often across multiple electronic medical record (EMR) systems. Interpreting operational data across multiple vendor systems can be challenging, as various manufacturers may describe different departmental workflow steps in different ways and sometimes even within a single vendor's installed customer base. In 2012, The Society for Imaging Informatics in Medicine (SIIM) recognized the need for better quality and performance data standards and formed SIIM's Workflow Initiative for Medicine (SWIM), an initiative designed to consistently describe workflow steps in radiology departments as well as defining operational quality metrics. The SWIM lexicon was published as a working model to describe operational workflow steps and quality measures. We measured the prevalence of the SWIM lexicon workflow steps in both academic and community radiology environments using real-world patient observations and correlated that information with automatically captured workflow steps from our clinical information systems. Our goal was to measure frequency of occurrence of workflow steps identified by the SWIM lexicon in a real-world clinical setting, as well as to correlate how accurately departmental information systems captured patient flow through our health facility.

  7. Agile parallel bioinformatics workflow management using Pwrake.

    Science.gov (United States)

    Mishima, Hiroyuki; Sasaki, Kensaku; Tanaka, Masahiro; Tatebe, Osamu; Yoshiura, Koh-Ichiro

    2011-09-08

    In bioinformatics projects, scientific workflow systems are widely used to manage computational procedures. Full-featured workflow systems have been proposed to fulfil the demand for workflow management. However, such systems tend to be over-weighted for actual bioinformatics practices. We realize that quick deployment of cutting-edge software implementing advanced algorithms and data formats, and continuous adaptation to changes in computational resources and the environment are often prioritized in scientific workflow management. These features have a greater affinity with the agile software development method through iterative development phases after trial and error.Here, we show the application of a scientific workflow system Pwrake to bioinformatics workflows. Pwrake is a parallel workflow extension of Ruby's standard build tool Rake, the flexibility of which has been demonstrated in the astronomy domain. Therefore, we hypothesize that Pwrake also has advantages in actual bioinformatics workflows. We implemented the Pwrake workflows to process next generation sequencing data using the Genomic Analysis Toolkit (GATK) and Dindel. GATK and Dindel workflows are typical examples of sequential and parallel workflows, respectively. We found that in practice, actual scientific workflow development iterates over two phases, the workflow definition phase and the parameter adjustment phase. We introduced separate workflow definitions to help focus on each of the two developmental phases, as well as helper methods to simplify the descriptions. This approach increased iterative development efficiency. Moreover, we implemented combined workflows to demonstrate modularity of the GATK and Dindel workflows. Pwrake enables agile management of scientific workflows in the bioinformatics domain. The internal domain specific language design built on Ruby gives the flexibility of rakefiles for writing scientific workflows. Furthermore, readability and maintainability of rakefiles

  8. Agile parallel bioinformatics workflow management using Pwrake

    Science.gov (United States)

    2011-01-01

    Background In bioinformatics projects, scientific workflow systems are widely used to manage computational procedures. Full-featured workflow systems have been proposed to fulfil the demand for workflow management. However, such systems tend to be over-weighted for actual bioinformatics practices. We realize that quick deployment of cutting-edge software implementing advanced algorithms and data formats, and continuous adaptation to changes in computational resources and the environment are often prioritized in scientific workflow management. These features have a greater affinity with the agile software development method through iterative development phases after trial and error. Here, we show the application of a scientific workflow system Pwrake to bioinformatics workflows. Pwrake is a parallel workflow extension of Ruby's standard build tool Rake, the flexibility of which has been demonstrated in the astronomy domain. Therefore, we hypothesize that Pwrake also has advantages in actual bioinformatics workflows. Findings We implemented the Pwrake workflows to process next generation sequencing data using the Genomic Analysis Toolkit (GATK) and Dindel. GATK and Dindel workflows are typical examples of sequential and parallel workflows, respectively. We found that in practice, actual scientific workflow development iterates over two phases, the workflow definition phase and the parameter adjustment phase. We introduced separate workflow definitions to help focus on each of the two developmental phases, as well as helper methods to simplify the descriptions. This approach increased iterative development efficiency. Moreover, we implemented combined workflows to demonstrate modularity of the GATK and Dindel workflows. Conclusions Pwrake enables agile management of scientific workflows in the bioinformatics domain. The internal domain specific language design built on Ruby gives the flexibility of rakefiles for writing scientific workflows. Furthermore, readability

  9. Examining daily activity routines of older adults using workflow.

    Science.gov (United States)

    Chung, Jane; Ozkaynak, Mustafa; Demiris, George

    2017-07-01

    We evaluated the value of workflow analysis supported by a novel visualization technique to better understand the daily routines of older adults and highlight their patterns of daily activities and normal variability in physical functions. We used a self-reported activity diary to obtain data from six community-dwelling older adults for 14 consecutive days. Workflow for daily routine was analyzed using the EventFlow tool, which aggregates workflow information to highlight patterns and variabilities. A total of 1453 events were included in the data analysis. To demonstrate the patterns and variability of each individual's daily activities, participant activity workflows were visualized and compared. The workflow analysis revealed great variability in activity types, regularity, frequency, duration, and timing of performing certain activities across individuals. Also, when workflow approach was applied to spatial information of activities, the analysis revealed the ability to provide meaningful data on individuals' mobility in different levels of life spaces from home to community. Results suggest that using workflows to characterize the daily activities of older adults will be helpful for clinicians and researchers in understanding their daily routines and preparing education and prevention strategies tailored to each individual's activity level. This tool also has the potential to be integrated into consumer informatics technologies, such as patient portals or personal health records, so that consumers may be encouraged to become actively involved in monitoring and managing their health. Copyright © 2017 Elsevier Inc. All rights reserved.

  10. A Workflow Platform for Simulation on Grids

    OpenAIRE

    Nguyen, Toan; Trifan, Laurentiu; Desideri, Jean-Antoine

    2011-01-01

    International audience; This paper presents the design, implementation and deployment of a simulation platform based on distributed workflows. It supports the smooth integration of existing software, e.g., Matlab, Scilab, Python, OpenFOAM, ParaView and user-defined programs. Additional features include the support for application-level fault-tolerance and exception-handling, i.e., resilience, and the orchestrated execution of distributed codes on remote high-performance clusters.

  11. Successful Completion of FY18/Q1 ASC L2 Milestone 6355: Electrical Analysis Calibration Workflow Capability Demonstration.

    Energy Technology Data Exchange (ETDEWEB)

    Copps, Kevin D. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2017-12-01

    The Sandia Analysis Workbench (SAW) project has developed and deployed a production capability for SIERRA computational mechanics analysis workflows. However, the electrical analysis workflow capability requirements have only been demonstrated in early prototype states, with no real capability deployed for analysts’ use. This milestone aims to improve the electrical analysis workflow capability (via SAW and related tools) and deploy it for ongoing use. We propose to focus on a QASPR electrical analysis calibration workflow use case. We will include a number of new capabilities (versus today’s SAW), such as: 1) support for the XYCE code workflow component, 2) data management coupled to electrical workflow, 3) human-in-theloop workflow capability, and 4) electrical analysis workflow capability deployed on the restricted (and possibly classified) network at Sandia. While far from the complete set of capabilities required for electrical analysis workflow over the long term, this is a substantial first step toward full production support for the electrical analysts.

  12. Development of a High-Throughput Ion-Exchange Resin Characterization Workflow.

    Science.gov (United States)

    Liu, Chun; Dermody, Daniel; Harris, Keith; Boomgaard, Thomas; Sweeney, Jeff; Gisch, Daryl; Goltz, Bob

    2017-06-12

    A novel high-throughout (HTR) ion-exchange (IEX) resin workflow has been developed for characterizing ion exchange equilibrium of commercial and experimental IEX resins against a range of different applications where water environment differs from site to site. Because of its much higher throughput, design of experiment (DOE) methodology can be easily applied for studying the effects of multiple factors on resin performance. Two case studies will be presented to illustrate the efficacy of the combined HTR workflow and DOE method. In case study one, a series of anion exchange resins have been screened for selective removal of NO 3 - and NO 2 - in water environments consisting of multiple other anions, varied pH, and ionic strength. The response surface model (RSM) is developed to statistically correlate the resin performance with the water composition and predict the best resin candidate. In case study two, the same HTR workflow and DOE method have been applied for screening different cation exchange resins in terms of the selective removal of Mg 2+ , Ca 2+ , and Ba 2+ from high total dissolved salt (TDS) water. A master DOE model including all of the cation exchange resins is created to predict divalent cation removal by different IEX resins under specific conditions, from which the best resin candidates can be identified. The successful adoption of HTR workflow and DOE method for studying the ion exchange of IEX resins can significantly reduce the resources and time to address industry and application needs.

  13. Rapid Energy Modeling Workflow Demonstration

    Science.gov (United States)

    2013-10-31

    Motion Picture Theatre, Museum, Office, Penitentiary , Performing Arts Theater, Police Station, Post Office, Religious Building, Retail, School Or...Family 1.00 0.70 N/A 0.06 0.25 Museum 1.00 1.10 9.75 0.2 0.10 Office 1.34 1.01 18.01 0.2 0.10 Parking Garage 0.30 0.30 N/A 1.5 5.00 Penitentiary

  14. Modular Resource Centric Learning for Workflow Performance Prediction

    OpenAIRE

    Singh, Alok; Nguyen, Mai; Purawat, Shweta; Crawl, Daniel; Altintas, Ilkay

    2017-01-01

    Workflows provide an expressive programming model for fine-grained control of large-scale applications in distributed computing environments. Accurate estimates of complex workflow execution metrics on large-scale machines have several key advantages. The performance of scheduling algorithms that rely on estimates of execution metrics degrades when the accuracy of predicted execution metrics decreases. This in-progress paper presents a technique being developed to improve the accuracy of pred...

  15. Enhanced Phosphoproteomic Profiling Workflow For Growth Factor Signaling Analysis

    DEFF Research Database (Denmark)

    Sylvester, Marc; Burbridge, Mike; Leclerc, Gregory

    2010-01-01

    A549 lung carcinoma cells were used as a model and stimulated with hepatocyte growth factor, epidermal growth factor or fibroblast growth factor. We employed a quick protein digestion workflow with spin filters without using urea. Phosphopeptides in general were enriched by sequential elution from...... transfer dissociation adds confidence in modification site assignment. The workflow is relatively simple but the integration of complementary techniques leads to a deeper insight into cellular signaling networks and the potential pharmacological intervention thereof....

  16. Developing integrated workflows for the digitisation of herbarium specimens using a modular and scalable approach.

    Science.gov (United States)

    Haston, Elspeth; Cubey, Robert; Pullan, Martin; Atkins, Hannah; Harris, David J

    2012-01-01

    Digitisation programmes in many institutes frequently involve disparate and irregular funding, diverse selection criteria and scope, with different members of staff managing and operating the processes. These factors have influenced the decision at the Royal Botanic Garden Edinburgh to develop an integrated workflow for the digitisation of herbarium specimens which is modular and scalable to enable a single overall workflow to be used for all digitisation projects. This integrated workflow is comprised of three principal elements: a specimen workflow, a data workflow and an image workflow.The specimen workflow is strongly linked to curatorial processes which will impact on the prioritisation, selection and preparation of the specimens. The importance of including a conservation element within the digitisation workflow is highlighted. The data workflow includes the concept of three main categories of collection data: label data, curatorial data and supplementary data. It is shown that each category of data has its own properties which influence the timing of data capture within the workflow. Development of software has been carried out for the rapid capture of curatorial data, and optical character recognition (OCR) software is being used to increase the efficiency of capturing label data and supplementary data. The large number and size of the images has necessitated the inclusion of automated systems within the image workflow.

  17. WorkflowNet2BPEL4WS: A Tool for Translating Unstructured Workflow Processes to Readable BPEL

    DEFF Research Database (Denmark)

    Lassen, Kristian Bisgaard; van der Aalst, Wil M. P.

    2007-01-01

    This paper presents WorkflowNet2BPEL4WS a tool to automatically map a graphical workflow model expressed in terms of Workflow Nets (WF-nets) onto BPEL. The Business Process Execution Language for Web Services (BPEL) has emerged as the de-facto standard for implementing processes and is supported...... code and not easy to use by end-users. Therefore, we provide a mapping from WF-nets to BPEL. This mapping builds on the rich theory of Petri nets and can also be used to map other languages (e.g., UML, EPC, BPMN, etc.) onto BPEL. To evaluate WorkflowNet2BPEL4WS we used more than 100 processes modeled...

  18. Quantitative workflow based on NN for weighting criteria in landfill suitability mapping

    Science.gov (United States)

    Abujayyab, Sohaib K. M.; Ahamad, Mohd Sanusi S.; Yahya, Ahmad Shukri; Ahmad, Siti Zubaidah; Alkhasawneh, Mutasem Sh.; Aziz, Hamidi Abdul

    2017-10-01

    Our study aims to introduce a new quantitative workflow that integrates neural networks (NNs) and multi criteria decision analysis (MCDA). Existing MCDA workflows reveal a number of drawbacks, because of the reliance on human knowledge in the weighting stage. Thus, new workflow presented to form suitability maps at the regional scale for solid waste planning based on NNs. A feed-forward neural network employed in the workflow. A total of 34 criteria were pre-processed to establish the input dataset for NN modelling. The final learned network used to acquire the weights of the criteria. Accuracies of 95.2% and 93.2% achieved for the training dataset and testing dataset, respectively. The workflow was found to be capable of reducing human interference to generate highly reliable maps. The proposed workflow reveals the applicability of NN in generating landfill suitability maps and the feasibility of integrating them with existing MCDA workflows.

  19. BALANCED SCORECARDS EVALUATION MODEL THAT INCLUDES ELEMENTS OF ENVIRONMENTAL MANAGEMENT SYSTEM USING AHP MODEL

    Directory of Open Access Journals (Sweden)

    Jelena Jovanović

    2010-03-01

    Full Text Available The research is oriented on improvement of environmental management system (EMS using BSC (Balanced Scorecard model that presents strategic model of measurem ents and improvement of organisational performance. The research will present approach of objectives and environmental management me trics involvement (proposed by literature review in conventional BSC in "Ad Barska plovi dba" organisation. Further we will test creation of ECO-BSC model based on business activities of non-profit organisations in order to improve envir onmental management system in parallel with other systems of management. Using this approach we may obtain 4 models of BSC that includ es elements of environmen tal management system for AD "Barska plovidba". Taking into acc ount that implementation and evaluation need long period of time in AD "Barska plovidba", the final choice will be based on 14598 (Information technology - Software product evaluation and ISO 9126 (Software engineering - Product quality using AHP method. Those standards are usually used for evaluation of quality software product and computer programs that serve in organisation as support and factors for development. So, AHP model will be bas ed on evolution criteria based on suggestion of ISO 9126 standards and types of evaluation from two evaluation teams. Members of team & will be experts in BSC and environmental management system that are not em ployed in AD "Barska Plovidba" organisation. The members of team 2 will be managers of AD "Barska Plovidba" organisation (including manage rs from environmental department. Merging results based on previously cr eated two AHP models, one can obtain the most appropriate BSC that includes elements of environmental management system. The chosen model will present at the same time suggestion for approach choice including ecological metrics in conventional BSC model for firm that has at least one ECO strategic orientation.

  20. Optimizing CyberShake Seismic Hazard Workflows for Large HPC Resources

    Science.gov (United States)

    Callaghan, S.; Maechling, P. J.; Juve, G.; Vahi, K.; Deelman, E.; Jordan, T. H.

    2014-12-01

    The CyberShake computational platform is a well-integrated collection of scientific software and middleware that calculates 3D simulation-based probabilistic seismic hazard curves and hazard maps for the Los Angeles region. Currently each CyberShake model comprises about 235 million synthetic seismograms from about 415,000 rupture variations computed at 286 sites. CyberShake integrates large-scale parallel and high-throughput serial seismological research codes into a processing framework in which early stages produce files used as inputs by later stages. Scientific workflow tools are used to manage the jobs, data, and metadata. The Southern California Earthquake Center (SCEC) developed the CyberShake platform using USC High Performance Computing and Communications systems and open-science NSF resources.CyberShake calculations were migrated to the NSF Track 1 system NCSA Blue Waters when it became operational in 2013, via an interdisciplinary team approach including domain scientists, computer scientists, and middleware developers. Due to the excellent performance of Blue Waters and CyberShake software optimizations, we reduced the makespan (a measure of wallclock time-to-solution) of a CyberShake study from 1467 to 342 hours. We will describe the technical enhancements behind this improvement, including judicious introduction of new GPU software, improved scientific software components, increased workflow-based automation, and Blue Waters-specific workflow optimizations.Our CyberShake performance improvements highlight the benefits of scientific workflow tools. The CyberShake workflow software stack includes the Pegasus Workflow Management System (Pegasus-WMS, which includes Condor DAGMan), HTCondor, and Globus GRAM, with Pegasus-mpi-cluster managing the high-throughput tasks on the HPC resources. The workflow tools handle data management, automatically transferring about 13 TB back to SCEC storage.We will present performance metrics from the most recent Cyber

  1. A Workflow to Improve the Alignment of Prostate Imaging with Whole-mount Histopathology.

    Science.gov (United States)

    Yamamoto, Hidekazu; Nir, Dror; Vyas, Lona; Chang, Richard T; Popert, Rick; Cahill, Declan; Challacombe, Ben; Dasgupta, Prokar; Chandra, Ashish

    2014-08-01

    Evaluation of prostate imaging tests against whole-mount histology specimens requires accurate alignment between radiologic and histologic data sets. Misalignment results in false-positive and -negative zones as assessed by imaging. We describe a workflow for three-dimensional alignment of prostate imaging data against whole-mount prostatectomy reference specimens and assess its performance against a standard workflow. Ethical approval was granted. Patients underwent motorized transrectal ultrasound (Prostate Histoscanning) to generate a three-dimensional image of the prostate before radical prostatectomy. The test workflow incorporated steps for axial alignment between imaging and histology, size adjustments following formalin fixation, and use of custom-made parallel cutters and digital caliper instruments. The control workflow comprised freehand cutting and assumed homogeneous block thicknesses at the same relative angles between pathology and imaging sections. Thirty radical prostatectomy specimens were histologically and radiologically processed, either by an alignment-optimized workflow (n = 20) or a control workflow (n = 10). The optimized workflow generated tissue blocks of heterogeneous thicknesses but with no significant drifting in the cutting plane. The control workflow resulted in significantly nonparallel blocks, accurately matching only one out of four histology blocks to their respective imaging data. The image-to-histology alignment accuracy was 20% greater in the optimized workflow (P workflow. Evaluation of prostate imaging biomarkers using whole-mount histology references should include a test-to-reference spatial alignment workflow. Copyright © 2014 AUR. Published by Elsevier Inc. All rights reserved.

  2. Semi-Automatic Science Workflow Synthesis for High-End Computing on the NASA Earth Exchange

    Data.gov (United States)

    National Aeronautics and Space Administration — Enhance capabilities for collaborative data analysis and modeling in Earth sciences. Develop components for automatic workflow capture, archiving and management....

  3. Schedule-Aware Workflow Management Systems

    Science.gov (United States)

    Mans, Ronny S.; Russell, Nick C.; van der Aalst, Wil M. P.; Moleman, Arnold J.; Bakker, Piet J. M.

    Contemporary workflow management systems offer work-items to users through specific work-lists. Users select the work-items they will perform without having a specific schedule in mind. However, in many environments work needs to be scheduled and performed at particular times. For example, in hospitals many work-items are linked to appointments, e.g., a doctor cannot perform surgery without reserving an operating theater and making sure that the patient is present. One of the problems when applying workflow technology in such domains is the lack of calendar-based scheduling support. In this paper, we present an approach that supports the seamless integration of unscheduled (flow) and scheduled (schedule) tasks. Using CPN Tools we have developed a specification and simulation model for schedule-aware workflow management systems. Based on this a system has been realized that uses YAWL, Microsoft Exchange Server 2007, Outlook, and a dedicated scheduling service. The approach is illustrated using a real-life case study at the AMC hospital in the Netherlands. In addition, we elaborate on the experiences obtained when developing and implementing a system of this scale using formal techniques.

  4. Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology.

    Science.gov (United States)

    Cock, Peter J A; Grüning, Björn A; Paszkiewicz, Konrad; Pritchard, Leighton

    2013-01-01

    The Galaxy Project offers the popular web browser-based platform Galaxy for running bioinformatics tools and constructing simple workflows. Here, we present a broad collection of additional Galaxy tools for large scale analysis of gene and protein sequences. The motivating research theme is the identification of specific genes of interest in a range of non-model organisms, and our central example is the identification and prediction of "effector" proteins produced by plant pathogens in order to manipulate their host plant. This functional annotation of a pathogen's predicted capacity for virulence is a key step in translating sequence data into potential applications in plant pathology. This collection includes novel tools, and widely-used third-party tools such as NCBI BLAST+ wrapped for use within Galaxy. Individual bioinformatics software tools are typically available separately as standalone packages, or in online browser-based form. The Galaxy framework enables the user to combine these and other tools to automate organism scale analyses as workflows, without demanding familiarity with command line tools and scripting. Workflows created using Galaxy can be saved and are reusable, so may be distributed within and between research groups, facilitating the construction of a set of standardised, reusable bioinformatic protocols. The Galaxy tools and workflows described in this manuscript are open source and freely available from the Galaxy Tool Shed (http://usegalaxy.org/toolshed or http://toolshed.g2.bx.psu.edu).

  5. Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology

    Directory of Open Access Journals (Sweden)

    Peter J.A. Cock

    2013-09-01

    Full Text Available The Galaxy Project offers the popular web browser-based platform Galaxy for running bioinformatics tools and constructing simple workflows. Here, we present a broad collection of additional Galaxy tools for large scale analysis of gene and protein sequences. The motivating research theme is the identification of specific genes of interest in a range of non-model organisms, and our central example is the identification and prediction of “effector” proteins produced by plant pathogens in order to manipulate their host plant. This functional annotation of a pathogen’s predicted capacity for virulence is a key step in translating sequence data into potential applications in plant pathology.This collection includes novel tools, and widely-used third-party tools such as NCBI BLAST+ wrapped for use within Galaxy. Individual bioinformatics software tools are typically available separately as standalone packages, or in online browser-based form. The Galaxy framework enables the user to combine these and other tools to automate organism scale analyses as workflows, without demanding familiarity with command line tools and scripting. Workflows created using Galaxy can be saved and are reusable, so may be distributed within and between research groups, facilitating the construction of a set of standardised, reusable bioinformatic protocols.The Galaxy tools and workflows described in this manuscript are open source and freely available from the Galaxy Tool Shed (http://usegalaxy.org/toolshed or http://toolshed.g2.bx.psu.edu.

  6. NeuroManager: A workflow analysis based simulation management engine for computational neuroscience

    Directory of Open Access Journals (Sweden)

    David Bruce Stockton

    2015-10-01

    Full Text Available We developed NeuroManager, an object-oriented simulation management software engine for computational neuroscience. NeuroManager automates the workflow of simulation job submissions when using heterogeneous computational resources, simulators, and simulation tasks. The object-oriented approach 1 provides flexibility to adapt to a variety of neuroscience simulators, 2 simplifies the use of heterogeneous computational resources, from desktops to super computer clusters, and 3 improves tracking of simulator/simulation evolution. We implemented NeuroManager in Matlab, a widely used engineering and scientific language, for its signal and image processing tools, prevalence in electrophysiology analysis, and increasing use in college Biology education. To design and develop NeuroManager we analyzed the workflow of simulation submission for a variety of simulators, operating systems, and computational resources, including the handling of input parameters, data, models, results, and analyses. This resulted in twenty-two stages of simulation submission workflow. The software incorporates progress notification, automatic organization, labeling, and time-stamping of data and results, and integrated access to Matlab's analysis and visualization tools. NeuroManager provides users with the tools to automate daily tasks, and assists principal investigators in tracking and recreating the evolution of research projects performed by multiple people. Overall, NeuroManager provides the infrastructure needed to improve workflow, manage multiple simultaneous simulations, and maintain provenance of the potentially large amounts of data produced during the course of a research project.

  7. Scientific Workflow Management in Proteomics

    Science.gov (United States)

    de Bruin, Jeroen S.; Deelder, André M.; Palmblad, Magnus

    2012-01-01

    Data processing in proteomics can be a challenging endeavor, requiring extensive knowledge of many different software packages, all with different algorithms, data format requirements, and user interfaces. In this article we describe the integration of a number of existing programs and tools in Taverna Workbench, a scientific workflow manager currently being developed in the bioinformatics community. We demonstrate how a workflow manager provides a single, visually clear and intuitive interface to complex data analysis tasks in proteomics, from raw mass spectrometry data to protein identifications and beyond. PMID:22411703

  8. Office 2010 Workflow Developing Collaborative Solutions

    CERN Document Server

    Mann, David; Enterprises, Creative

    2010-01-01

    Workflow is the glue that binds information worker processes, users, and artifacts. Without workflow, information workers are just islands of data and potential. Office 2010 Workflow details how to implement workflow in SharePoint 2010 and the client Microsoft Office 2010 suite to help information workers share data, enforce processes and business rules, and work more efficiently together or solo. This book covers everything you need to know-from what workflow is all about to creating new activities; from the SharePoint Designer to Visual Studio 2010; from out-of-the-box workflows to state mac

  9. Analysing scientific workflows: why workflows not only connect web services

    NARCIS (Netherlands)

    Wassink, I.; van der Vet, P.E.; Wolstencroft, K.; Neerincx, P.B.T.; Roos, M.; Rauwerda, H.; Breit, T.M.; Zhang, LJ.

    2009-01-01

    Life science workflow systems are developed to help life scientists to conveniently connect various programs and web services. In practice however, much time is spent on data conversion, because web services provided by different organisations use different data formats. We have analysed all the

  10. Analysing scientific workflows: Why workflows not only connect web services

    NARCIS (Netherlands)

    Wassink, I.; van der Vet, P.E.; Wolstencroft, K.; Neerincx, P.B.T.; Roos, M.; Rauwerda, H.; Breit, T.M.; Zhang, L.J.

    2009-01-01

    Life science workflow systems are developed to help life scientists to conveniently connect various programs and web services. In practice however, much time is spent on data conversion, because web services provided by different organisations use different data formats. We have analysed all the

  11. Reenginering of the i4 workflow engine

    OpenAIRE

    Likar, Tilen

    2013-01-01

    I4 is an enterprise resource planning system which allows you to manage business processes. Due to increasing demands for managing complex processes and adjusting those processes to global standards, a renewal of a part of the system was required. In this thesis we faced the reengineering of the workflow engine, and corresponding data model. We designed a business process diagram in Bizagi Porcess Modeler. The import to i4 and the export from i4 was developed on XPDL file exported from the mo...

  12. CO2 Storage Feasibility: A Workflow for Site Characterisation

    Directory of Open Access Journals (Sweden)

    Nepveu Manuel

    2015-04-01

    Full Text Available In this paper, we present an overview of the SiteChar workflow model for site characterisation and assessment for CO2 storage. Site characterisation and assessment is required when permits are requested from the legal authorities in the process of starting a CO2 storage process at a given site. The goal is to assess whether a proposed CO2 storage site can indeed be used for permanent storage while meeting the safety requirements demanded by the European Commission (EC Storage Directive (9, Storage Directive 2009/31/EC. Many issues have to be scrutinised, and the workflow presented here is put forward to help efficiently organise this complex task. Three issues are highlighted: communication within the working team and with the authorities; interdependencies in the workflow and feedback loops; and the risk-based character of the workflow. A general overview (helicopter view of the workflow is given; the issues involved in communication and the risk assessment process are described in more detail. The workflow as described has been tested within the SiteChar project on five potential storage sites throughout Europe. This resulted in a list of key aspects of site characterisation which can help prepare and focus new site characterisation studies.

  13. Kronos: a workflow assembler for genome analytics and informatics

    Science.gov (United States)

    Taghiyar, M. Jafar; Rosner, Jamie; Grewal, Diljot; Grande, Bruno M.; Aniba, Radhouane; Grewal, Jasleen; Boutros, Paul C.; Morin, Ryan D.

    2017-01-01

    Abstract Background: The field of next-generation sequencing informatics has matured to a point where algorithmic advances in sequence alignment and individual feature detection methods have stabilized. Practical and robust implementation of complex analytical workflows (where such tools are structured into “best practices” for automated analysis of next-generation sequencing datasets) still requires significant programming investment and expertise. Results: We present Kronos, a software platform for facilitating the development and execution of modular, auditable, and distributable bioinformatics workflows. Kronos obviates the need for explicit coding of workflows by compiling a text configuration file into executable Python applications. Making analysis modules would still require programming. The framework of each workflow includes a run manager to execute the encoded workflows locally (or on a cluster or cloud), parallelize tasks, and log all runtime events. The resulting workflows are highly modular and configurable by construction, facilitating flexible and extensible meta-applications that can be modified easily through configuration file editing. The workflows are fully encoded for ease of distribution and can be instantiated on external systems, a step toward reproducible research and comparative analyses. We introduce a framework for building Kronos components that function as shareable, modular nodes in Kronos workflows. Conclusions: The Kronos platform provides a standard framework for developers to implement custom tools, reuse existing tools, and contribute to the community at large. Kronos is shipped with both Docker and Amazon Web Services Machine Images. It is free, open source, and available through the Python Package Index and at https://github.com/jtaghiyar/kronos. PMID:28655203

  14. Workflows for microarray data processing in the Kepler environment

    Science.gov (United States)

    2012-01-01

    Background Microarray data analysis has been the subject of extensive and ongoing pipeline development due to its complexity, the availability of several options at each analysis step, and the development of new analysis demands, including integration with new data sources. Bioinformatics pipelines are usually custom built for different applications, making them typically difficult to modify, extend and repurpose. Scientific workflow systems are intended to address these issues by providing general-purpose frameworks in which to develop and execute such pipelines. The Kepler workflow environment is a well-established system under continual development that is employed in several areas of scientific research. Kepler provides a flexible graphical interface, featuring clear display of parameter values, for design and modification of workflows. It has capabilities for developing novel computational components in the R, Python, and Java programming languages, all of which are widely used for bioinformatics algorithm development, along with capabilities for invoking external applications and using web services. Results We developed a series of fully functional bioinformatics pipelines addressing common tasks in microarray processing in the Kepler workflow environment. These pipelines consist of a set of tools for GFF file processing of NimbleGen chromatin immunoprecipitation on microarray (ChIP-chip) datasets and more comprehensive workflows for Affymetrix gene expression microarray bioinformatics and basic primer design for PCR experiments, which are often used to validate microarray results. Although functional in themselves, these workflows can be easily customized, extended, or repurposed to match the needs of specific projects and are designed to be a toolkit and starting point for specific applications. These workflows illustrate a workflow programming paradigm focusing on local resources (programs and data) and therefore are close to traditional shell scripting or

  15. Workflows for microarray data processing in the Kepler environment

    Directory of Open Access Journals (Sweden)

    Stropp Thomas

    2012-05-01

    Full Text Available Abstract Background Microarray data analysis has been the subject of extensive and ongoing pipeline development due to its complexity, the availability of several options at each analysis step, and the development of new analysis demands, including integration with new data sources. Bioinformatics pipelines are usually custom built for different applications, making them typically difficult to modify, extend and repurpose. Scientific workflow systems are intended to address these issues by providing general-purpose frameworks in which to develop and execute such pipelines. The Kepler workflow environment is a well-established system under continual development that is employed in several areas of scientific research. Kepler provides a flexible graphical interface, featuring clear display of parameter values, for design and modification of workflows. It has capabilities for developing novel computational components in the R, Python, and Java programming languages, all of which are widely used for bioinformatics algorithm development, along with capabilities for invoking external applications and using web services. Results We developed a series of fully functional bioinformatics pipelines addressing common tasks in microarray processing in the Kepler workflow environment. These pipelines consist of a set of tools for GFF file processing of NimbleGen chromatin immunoprecipitation on microarray (ChIP-chip datasets and more comprehensive workflows for Affymetrix gene expression microarray bioinformatics and basic primer design for PCR experiments, which are often used to validate microarray results. Although functional in themselves, these workflows can be easily customized, extended, or repurposed to match the needs of specific projects and are designed to be a toolkit and starting point for specific applications. These workflows illustrate a workflow programming paradigm focusing on local resources (programs and data and therefore are close to

  16. A Kepler Workflow Tool for Reproducible AMBER GPU Molecular Dynamics.

    Science.gov (United States)

    Purawat, Shweta; Ieong, Pek U; Malmstrom, Robert D; Chan, Garrett J; Yeung, Alan K; Walker, Ross C; Altintas, Ilkay; Amaro, Rommie E

    2017-06-20

    With the drive toward high throughput molecular dynamics (MD) simulations involving ever-greater numbers of simulation replicates run for longer, biologically relevant timescales (microseconds), the need for improved computational methods that facilitate fully automated MD workflows gains more importance. Here we report the development of an automated workflow tool to perform AMBER GPU MD simulations. Our workflow tool capitalizes on the capabilities of the Kepler platform to deliver a flexible, intuitive, and user-friendly environment and the AMBER GPU code for a robust and high-performance simulation engine. Additionally, the workflow tool reduces user input time by automating repetitive processes and facilitates access to GPU clusters, whose high-performance processing power makes simulations of large numerical scale possible. The presented workflow tool facilitates the management and deployment of large sets of MD simulations on heterogeneous computing resources. The workflow tool also performs systematic analysis on the simulation outputs and enhances simulation reproducibility, execution scalability, and MD method development including benchmarking and validation. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  17. SMITH: a LIMS for handling next-generation sequencing workflows

    Science.gov (United States)

    2014-01-01

    Background Life-science laboratories make increasing use of Next Generation Sequencing (NGS) for studying bio-macromolecules and their interactions. Array-based methods for measuring gene expression or protein-DNA interactions are being replaced by RNA-Seq and ChIP-Seq. Sequencing is generally performed by specialized facilities that have to keep track of sequencing requests, trace samples, ensure quality and make data available according to predefined privileges. An integrated tool helps to troubleshoot problems, to maintain a high quality standard, to reduce time and costs. Commercial and non-commercial tools called LIMS (Laboratory Information Management Systems) are available for this purpose. However, they often come at prohibitive cost and/or lack the flexibility and scalability needed to adjust seamlessly to the frequently changing protocols employed. In order to manage the flow of sequencing data produced at the Genomic Unit of the Italian Institute of Technology (IIT), we developed SMITH (Sequencing Machine Information Tracking and Handling). Methods SMITH is a web application with a MySQL server at the backend. Wet-lab scientists of the Centre for Genomic Science and database experts from the Politecnico of Milan in the context of a Genomic Data Model Project developed SMITH. The data base schema stores all the information of an NGS experiment, including the descriptions of all protocols and algorithms used in the process. Notably, an attribute-value table allows associating an unconstrained textual description to each sample and all the data produced afterwards. This method permits the creation of metadata that can be used to search the database for specific files as well as for statistical analyses. Results SMITH runs automatically and limits direct human interaction mainly to administrative tasks. SMITH data-delivery procedures were standardized making it easier for biologists and analysts to navigate the data. Automation also helps saving time. The

  18. CMS Distributed Computing Workflow Experience

    CERN Document Server

    Haas, Jeffrey David

    2010-01-01

    The vast majority of the CMS Computing capacity, which is organized in a tiered hierarchy, is located away from CERN. The 7 Tier-1 sites archive the LHC proton-proton collision data that is initially processed at CERN. These sites provide access to all recorded and simulated data for the Tier-2 sites, via wide-area network (WAN) transfers. All central data processing workflows are executed at the Tier-1 level, which contain re-reconstruction and skimming workflows of collision data as well as reprocessing of simulated data to adapt to changing detector conditions. This paper describes the operation of the CMS processing infrastructure at the Tier-1 level. The Tier-1 workflows are described in detail. The operational optimization of resource usage is described. In particular, the variation of different workflows during the data taking period of 2010, their efficiencies and latencies as well as their impact on the delivery of physics results is discussed and lessons are drawn from this experience. The simul...

  19. New Interactions with Workflow Systems

    NARCIS (Netherlands)

    Wassink, I.; van der Vet, P.E.; van der Veer, Gerrit C.; Roos, M.; van Dijk, Elisabeth M.A.G.; Norros, L.; Koskinen, H.; Salo, L.; Savioja, P.

    2009-01-01

    This paper describes the evaluation of our early design ideas of an ad-hoc of workflow system. Using the teach-back technique, we have performed a hermeneutic analysis of the mockup implementation named NIWS to get corrective and creative feedback at the functional, dialogue and representation level

  20. Contracts for Cross-Organizational Workflow Management

    NARCIS (Netherlands)

    Koetsier, M.J.; Grefen, P.W.P.J.; Vonk, J.; Bauknecht, Kurt; Kumar Madria, Sanjay; Pernul, Günther

    Nowadays, many organizations form dynamic partnerships to deal effectively with market requirements. As companies use automated workflow management systems (WFMSs) to control their processes, a way of linking workflow processes in different organizations is required for turning the cooperating

  1. Effects of the Interactions Between LPS and BIM on Workflow in Two Building Design Projects

    OpenAIRE

    Khan, Sheriz; Tzortzopoulos, Patricia

    2014-01-01

    Variability in design workflow causes delays and undermines the performance of building projects. As lean processes, the Last Planner System (LPS) and Building Information Modeling (BIM) can improve workflow in building projects through features that reduce waste. Since its introduction, BIM has had significant positive influence on workflow in building design projects, but these have been rarely considered in combination with LPS. This paper is part of a postgraduate research focusing on the...

  2. Snakemake-a scalable bioinformatics workflow engine

    NARCIS (Netherlands)

    J. Köster (Johannes); S. Rahmann (Sven)

    2012-01-01

    textabstractSnakemake is a workflow engine that provides a readable Python-based workflow definition language and a powerful execution environment that scales from single-core workstations to compute clusters without modifying the workflow. It is the first system to support the use of automatically

  3. CMS data and workflow management system

    CERN Document Server

    Fanfani, A; Bacchi, W; Codispoti, G; De Filippis, N; Pompili, A; My, S; Abbrescia, M; Maggi, G; Donvito, G; Silvestris, L; Calzolari, F; Sarkar, S; Spiga, D; Cinquili, M; Lacaprara, S; Biasotto, M; Farina, F; Merlo, M; Belforte, S; Kavka, C; Sala, L; Harvey, J; Hufnagel, D; Fanzago, F; Corvo, M; Magini, N; Rehn, J; Toteva, Z; Feichtinger, D; Tuura, L; Eulisse, G; Bockelman, B; Lundstedt, C; Egeland, R; Evans, D; Mason, D; Gutsche, O; Sexton-Kennedy, L; Dagenhart, D W; Afaq, A; Guo, Y; Kosyakov, S; Lueking, L; Sekhri, V; Fisk, I; McBride, P; Bauerdick, L; Bakken, J; Rossman, P; Wicklund, E; Wu, Y; Jones, C; Kuznetsov, V; Riley, D; Dolgert, A; van Lingen, F; Narsky, I; Paus, C; Klute, M; Gomez-Ceballos, G; Piedra-Gomez, J; Miller, M; Mohapatra, A; Lazaridis, C; Bradley, D; Elmer, P; Wildish, T; Wuerthwein, F; Letts, J; Bourilkov, D; Kim, B; Smith, P; Hernandez, J M; Caballero, J; Delgado, A; Flix, J; Cabrillo-Bartolome, I; Kasemann, M; Flossdorf, A; Stadie, H; Kreuzer, P; Khomitch, A; Hof, C; Zeidler, C; Kalini, S; Trunov, A; Saout, C; Felzmann, U; Metson, S; Newbold, D; Geddes, N; Brew, C; Jackson, J; Wakefield, S; De Weirdt, S; Adler, V; Maes, J; Van Mulders, P; Villella, I; Hammad, G; Pukhaeva, N; Kurca, T; Semneniouk, I; Guan, W; Lajas, J A; Teodoro, D; Gregores, E; Baquero, M; Shehzad, A; Kadastik, M; Kodolova, O; Chao, Y; Ming Kuo, C; Filippidis, C; Walzel, G; Han, D; Kalinowski, A; Giro de Almeida, N M; Panyam, N

    2008-01-01

    CMS expects to manage many tens of peta bytes of data to be distributed over several computing centers around the world. The CMS distributed computing and analysis model is designed to serve, process and archive the large number of events that will be generated when the CMS detector starts taking data. The underlying concepts and the overall architecture of the CMS data and workflow management system will be presented. In addition the experience in using the system for MC production, initial detector commissioning activities and data analysis will be summarized.

  4. Detecting dissonance in clinical and research workflow for translational psychiatric registries.

    Science.gov (United States)

    Cofiel, Luciana; Bassi, Débora U; Ray, Ryan Kumar; Pietrobon, Ricardo; Brentani, Helena

    2013-01-01

    The interplay between the workflow for clinical tasks and research data collection is often overlooked, ultimately making it ineffective. To the best of our knowledge, no previous studies have developed standards that allow for the comparison of workflow models derived from clinical and research tasks toward the improvement of data collection processes. In this study we used the term dissonance for the occurrences where there was a discord between clinical and research workflows. We developed workflow models for a translational research study in psychiatry and the clinic where its data collection was carried out. After identifying points of dissonance between clinical and research models we derived a corresponding classification system that ultimately enabled us to re-engineer the data collection workflow. We considered (1) the number of patients approached for enrollment and (2) the number of patients enrolled in the study as indicators of efficiency in research workflow. We also recorded the number of dissonances before and after the workflow modification. We identified 22 episodes of dissonance across 6 dissonance categories: actor, communication, information, artifact, time, and space. We were able to eliminate 18 episodes of dissonance and increase the number of patients approached and enrolled in research study trough workflow modification. The classification developed in this study is useful for guiding the identification of dissonances and reveal modifications required to align the workflow of data collection and the clinical setting. The methodology described in this study can be used by researchers to standardize data collection process.

  5. Integrated Sensitivity Analysis Workflow

    Energy Technology Data Exchange (ETDEWEB)

    Friedman-Hill, Ernest J. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Hoffman, Edward L. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Gibson, Marcus J. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Clay, Robert L. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2014-08-01

    Sensitivity analysis is a crucial element of rigorous engineering analysis, but performing such an analysis on a complex model is difficult and time consuming. The mission of the DART Workbench team at Sandia National Laboratories is to lower the barriers to adoption of advanced analysis tools through software integration. The integrated environment guides the engineer in the use of these integrated tools and greatly reduces the cycle time for engineering analysis.

  6. Text mining for the biocuration workflow

    Science.gov (United States)

    Hirschman, Lynette; Burns, Gully A. P. C; Krallinger, Martin; Arighi, Cecilia; Cohen, K. Bretonnel; Valencia, Alfonso; Wu, Cathy H.; Chatr-Aryamontri, Andrew; Dowell, Karen G.; Huala, Eva; Lourenço, Anália; Nash, Robert; Veuthey, Anne-Lise; Wiegers, Thomas; Winter, Andrew G.

    2012-01-01

    Molecular biology has become heavily dependent on biological knowledge encoded in expert curated biological databases. As the volume of biological literature increases, biocurators need help in keeping up with the literature; (semi-) automated aids for biocuration would seem to be an ideal application for natural language processing and text mining. However, to date, there have been few documented successes for improving biocuration throughput using text mining. Our initial investigations took place for the workshop on ‘Text Mining for the BioCuration Workflow’ at the third International Biocuration Conference (Berlin, 2009). We interviewed biocurators to obtain workflows from eight biological databases. This initial study revealed high-level commonalities, including (i) selection of documents for curation; (ii) indexing of documents with biologically relevant entities (e.g. genes); and (iii) detailed curation of specific relations (e.g. interactions); however, the detailed workflows also showed many variabilities. Following the workshop, we conducted a survey of biocurators. The survey identified biocurator priorities, including the handling of full text indexed with biological entities and support for the identification and prioritization of documents for curation. It also indicated that two-thirds of the biocuration teams had experimented with text mining and almost half were using text mining at that time. Analysis of our interviews and survey provide a set of requirements for the integration of text mining into the biocuration workflow. These can guide the identification of common needs across curated databases and encourage joint experimentation involving biocurators, text mining developers and the larger biomedical research community. PMID:22513129

  7. Application of Workflow Technology for Big Data Analysis Service

    Directory of Open Access Journals (Sweden)

    Bin Zhang

    2018-04-01

    Full Text Available This study presents a lightweight representational state transfer-based cloud workflow system to construct a big data intelligent software-as-a-service (SaaS platform. The system supports the dynamic construction and operation of an intelligent data analysis application, and realizes rapid development and flexible deployment of the business analysis process that can improve the interaction and response time of the process. The proposed system integrates offline-batch and online-streaming analysis models that allow users to conduct batch and streaming computing simultaneously. Users can rend cloud capabilities and customize a set of big data analysis applications in the form of workflow processes. This study elucidates the architecture and application modeling, customization, dynamic construction, and scheduling of a cloud workflow system. A chain workflow foundation mechanism is proposed to combine several analysis components into a chain component that can promote efficiency. Four practical application cases are provided to verify the analysis capability of the system. Experimental results show that the proposed system can support multiple users in accessing the system concurrently and effectively uses data analysis algorithms. The proposed SaaS workflow system has been used in network operators and has achieved good results.

  8. Workflows in a secure environment

    Energy Technology Data Exchange (ETDEWEB)

    Klasky, Scott A [ORNL; Podhorszki, Norbert [ORNL

    2008-01-01

    Petascale simulations on the largest supercomputers in the US require advanced data management techniques in order to optimize the application scien- tist time, and to optimize the time spent on the supercomputers. Researchers in such problems are starting to require workflow automation during their simula- tions in order to monitor the simulations, and in order to automate many of the complex analysis which must take place from the data that is generated from these simulations. Scientific workflows are being used to monitor simulations running on these supercomputers by applying a series of complex analysis, and finally producing images and movies from the variables produced in the simulation, or from the derived quantities produced by the analysis. The typical scenario is where the large calculation runs on the supercomputer, and the auxiliary diagnos- tics/monitors are run on resources, which are either on the local area network of the supercomputer, or over the wide area network. The supercomputers at one of the largest centers are highly secure, and the only method to log into the center is interactive authentication by using One Time Passwords (OTP) that are generated by a security device and expire in half a minute. Therefore, grid certificates are not a current option on these machines in the Department of Energy at Oak Ridge Na- tional Laboratory. In this paper we describe how we have extended the Kepler sci- entific workflow management system to be able to run operations on these supercomputers, how workflows themselves can be executed as batch jobs, and fi- nally, how external data-transfer operations can be utilized when they need to per- form authentication for their own as well.

  9. Workflow Management in CLARIN-DK

    DEFF Research Database (Denmark)

    Jongejan, Bart

    2013-01-01

    output, given the input resource at hand. Still, in such cases it may be possible to reach the set goal by chaining a number of tools. The approach presented here frees the user of having to meddle with tools and the construction of workflows. Instead, the user only needs to supply the workflow manager...... with the features that describe her goal, because the workflow manager not only executes chains of tools in a workflow, but also takes care of autonomously devising workflows that serve the user’s intention, given the tools that currently are integrated in the infrastructure as web services. To do this......, the workflow manager needs stringent and complete information about each integrated tool. We discuss how such information is structured in CLARIN-DK. Provided that many tools are made available to and through the CLARIN-DK infrastructure, the automatically created workflows, although simple linear programs...

  10. Development of the workflow kine systems for support on KAIZEN.

    Science.gov (United States)

    Mizuno, Yuki; Ito, Toshihiko; Yoshikawa, Toru; Yomogida, Satoshi; Morio, Koji; Sakai, Kazuhiro

    2012-01-01

    In this paper, we introduce the new workflow line system consisted of the location and image recording, which led to the acquisition of workflow information and the analysis display. From the results of workflow line investigation, we considered the anticipated effects and the problems on KAIZEN. Workflow line information included the location information and action contents information. These technologies suggest the viewpoints to help improvement, for example, exclusion of useless movement, the redesign of layout and the review of work procedure. Manufacturing factory, it was clear that there was much movement from the standard operation place and accumulation residence time. The following was shown as a result of this investigation, to be concrete, the efficient layout was suggested by this system. In the case of the hospital, similarly, it is pointed out that the workflow has the problem of layout and setup operations based on the effective movement pattern of the experts. This system could adapt to routine work, including as well as non-routine work. By the development of this system which can fit and adapt to industrial diversification, more effective "visual management" (visualization of work) is expected in the future.

  11. How to plan workflow changes: a practical quality improvement tool used in an outpatient hospital pharmacy.

    Science.gov (United States)

    Aguilar, Christine; Chau, Connie; Giridharan, Neha; Huh, Youchin; Cooley, Janet; Warholak, Terri L

    2013-06-01

    A quality improvement tool is provided to improve pharmacy workflow with the goal of minimizing errors caused by workflow issues. This study involved workflow evaluation and reorganization, and staff opinions of these proposed changes. The study pharmacy was an outpatient pharmacy in the Tucson area. However, the quality improvement tool may be applied in all pharmacy settings, including but not limited to community, hospital, and independent pharmacies. This tool can help the user to identify potential workflow problem spots, such as high-traffic areas through the creation of current and proposed workflow diagrams. Creating a visual representation can help the user to identify problem spots and to propose changes to optimize workflow. It may also be helpful to assess employees' opinions of these changes. The workflow improvement tool can be used to assess where improvements are needed in a pharmacy's floor plan and workflow. Suggestions for improvements in the study pharmacy included increasing the number of verification points and decreasing high traffic areas in the workflow. The employees of the study pharmacy felt that the proposed changes displayed greater continuity, sufficiency, accessibility, and space within the pharmacy.

  12. Exformatics Declarative Case Management Workflows as DCR Graphs

    DEFF Research Database (Denmark)

    Slaats, Tijs; Mukkamala, Raghava Rao; Hildebrandt, Thomas

    2013-01-01

    Declarative workflow languages have been a growing research subject over the past ten years, but applications of the declarative approach in industry are still uncommon. Over the past two years Exformatics A/S, a Danish provider of Electronic Case Management systems, has been cooperating with res......Declarative workflow languages have been a growing research subject over the past ten years, but applications of the declarative approach in industry are still uncommon. Over the past two years Exformatics A/S, a Danish provider of Electronic Case Management systems, has been cooperating...... with researchers at IT University of Copenhagen (ITU) to create tools for the declarative workflow language Dynamic Condition Response Graphs (DCR Graphs) and incorporate them into their products and in teaching at ITU. In this paper we give a status report over the work. We start with an informal introduction...... to DCR Graphs. We then show how DCR Graphs are being used by Exformatics to model workflows through a case study of an invoice workflow. Finally we give an overview of the tools that have been developed by Exformatics to support working with DCR Graphs and evaluate their use in capturing requirements...

  13. Scheduling Multilevel Deadline-Constrained Scientific Workflows on Clouds Based on Cost Optimization

    Directory of Open Access Journals (Sweden)

    Maciej Malawski

    2015-01-01

    Full Text Available This paper presents a cost optimization model for scheduling scientific workflows on IaaS clouds such as Amazon EC2 or RackSpace. We assume multiple IaaS clouds with heterogeneous virtual machine instances, with limited number of instances per cloud and hourly billing. Input and output data are stored on a cloud object store such as Amazon S3. Applications are scientific workflows modeled as DAGs as in the Pegasus Workflow Management System. We assume that tasks in the workflows are grouped into levels of identical tasks. Our model is specified using mathematical programming languages (AMPL and CMPL and allows us to minimize the cost of workflow execution under deadline constraints. We present results obtained using our model and the benchmark workflows representing real scientific applications in a variety of domains. The data used for evaluation come from the synthetic workflows and from general purpose cloud benchmarks, as well as from the data measured in our own experiments with Montage, an astronomical application, executed on Amazon EC2 cloud. We indicate how this model can be used for scenarios that require resource planning for scientific workflows and their ensembles.

  14. Scientific Workflows and the Sensor Web for Virtual Environmental Observatories

    Science.gov (United States)

    Simonis, I.; Vahed, A.

    2008-12-01

    interfaces. All data sets and sensor communication follow well-defined abstract models and corresponding encodings, mostly developed by the OGC Sensor Web Enablement initiative. Scientific progress is currently accelerated by an emerging new concept called scientific workflows, which organize and manage complex distributed computations. A scientific workflow represents and records the highly complex processes that a domain scientist typically would follow in exploration, discovery and ultimately, transformation of raw data to publishable results. The challenge is now to integrate the benefits of scientific workflows with those provided by the Sensor Web in order to leverage all resources for scientific exploration, problem solving, and knowledge generation. Scientific workflows for the Sensor Web represent the next evolutionary step towards efficient, powerful, and flexible earth observation frameworks and platforms. Those platforms support the entire process from capturing data, sharing and integrating, to requesting additional observations. Multiple sites and organizations will participate on single platforms and scientists from different countries and organizations interact and contribute to large-scale research projects. Simultaneously, the data- and information overload becomes manageable, as multiple layers of abstraction will free scientists to deal with underlying data-, processing or storage peculiarities. The vision are automated investigation and discovery mechanisms that allow scientists to pose queries to the system, which in turn would identify potentially related resources, schedules processing tasks and assembles all parts in workflows that may satisfy the query.

  15. The Lag Model, a Turbulence Model for Wall Bounded Flows Including Separation

    Science.gov (United States)

    Olsen, Michael E.; Coakley, Thomas J.; Kwak, Dochan (Technical Monitor)

    2001-01-01

    A new class of turbulence model is described for wall bounded, high Reynolds number flows. A specific turbulence model is demonstrated, with results for favorable and adverse pressure gradient flowfields. Separation predictions are as good or better than either Spalart Almaras or SST models, do not require specification of wall distance, and have similar or reduced computational effort compared with these models.

  16. BioModels: expanding horizons to include more modelling approaches and formats.

    Science.gov (United States)

    Glont, Mihai; Nguyen, Tung V N; Graesslin, Martin; Hälke, Robert; Ali, Raza; Schramm, Jochen; Wimalaratne, Sarala M; Kothamachu, Varun B; Rodriguez, Nicolas; Swat, Maciej J; Eils, Jurgen; Eils, Roland; Laibe, Camille; Malik-Sheriff, Rahuman S; Chelliah, Vijayalakshmi; Le Novère, Nicolas; Hermjakob, Henning

    2018-01-04

    BioModels serves as a central repository of mathematical models representing biological processes. It offers a platform to make mathematical models easily shareable across the systems modelling community, thereby supporting model reuse. To facilitate hosting a broader range of model formats derived from diverse modelling approaches and tools, a new infrastructure for BioModels has been developed that is available at http://www.ebi.ac.uk/biomodels. This new system allows submitting and sharing of a wide range of models with improved support for formats other than SBML. It also offers a version-control backed environment in which authors and curators can work collaboratively to curate models. This article summarises the features available in the current system and discusses the potential benefit they offer to the users over the previous system. In summary, the new portal broadens the scope of models accepted in BioModels and supports collaborative model curation which is crucial for model reproducibility and sharing. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  17. Integrating the Allen Brain Institute Cell Types Database into Automated Neuroscience Workflow.

    Science.gov (United States)

    Stockton, David B; Santamaria, Fidel

    2017-10-01

    We developed software tools to download, extract features, and organize the Cell Types Database from the Allen Brain Institute (ABI) in order to integrate its whole cell patch clamp characterization data into the automated modeling/data analysis cycle. To expand the potential user base we employed both Python and MATLAB. The basic set of tools downloads selected raw data and extracts cell, sweep, and spike features, using ABI's feature extraction code. To facilitate data manipulation we added a tool to build a local specialized database of raw data plus extracted features. Finally, to maximize automation, we extended our NeuroManager workflow automation suite to include these tools plus a separate investigation database. The extended suite allows the user to integrate ABI experimental and modeling data into an automated workflow deployed on heterogeneous computer infrastructures, from local servers, to high performance computing environments, to the cloud. Since our approach is focused on workflow procedures our tools can be modified to interact with the increasing number of neuroscience databases being developed to cover all scales and properties of the nervous system.

  18. Towards Automated Design, Analysis and Optimization of Declarative Curation Workflows

    Directory of Open Access Journals (Sweden)

    Tianhong Song

    2014-10-01

    Full Text Available Data curation is increasingly important. Our previous work on a Kepler curation package has demonstrated advantages that come from automating data curation pipelines by using workflow systems. However, manually designed curation workflows can be error-prone and inefficient due to a lack of user understanding of the workflow system, misuse of actors, or human error. Correcting problematic workflows is often very time-consuming. A more proactive workflow system can help users avoid such pitfalls. For example, static analysis before execution can be used to detect the potential problems in a workflow and help the user to improve workflow design. In this paper, we propose a declarative workflow approach that supports semi-automated workflow design, analysis and optimization. We show how the workflow design engine helps users to construct data curation workflows, how the workflow analysis engine detects different design problems of workflows and how workflows can be optimized by exploiting parallelism.

  19. Getting Double the Work Done with Half the Effort: Provenance and Metadata with Semantic Workflows

    Science.gov (United States)

    Gil, Y.

    2012-12-01

    The variety, velocity, and volume of big data are dwarfing our ability to analyze it using the computational tools and models at our disposal. Studies report that researchers spend more than 60% of their time just preparing the data for model input or data-model inter-comparison just to start a baseline in a given science project. Computational workflow systems can assist with these tasks by automating the execution of complex computations. When metadata is available, semantic workflow systems can use it to make intelligent decisions based on the type of data and models requirements. This talk will discuss the importance of provenance-aware software that both generates and uses metadata as the data is being processed, and what new capabilities are enabled for researchers. This combined system was used to develop and test a near-real time scientific workflow to facilitate the observation of the spatio-temporal distribution of whole-stream metabolism estimates using available monitoring station flow and water quality data. The data integration steps combined data from public government repositories and local sensors with the implication of different associated properties (data integrity, sampling intervals, units), and (2) the variability of the interim flows requires adaptive model selection within the framework of the metabolism calculations. These challenges are addressed by using a data integration system in which metadata and provenance are generated as the data is prepared and then subsequently used by a semantic workflow system to automatically select and configure models, effectively customizing the analysis to the daily data. Data preparation involves the extraction, cleaning, normalization and integration of the data coming from sensors and third-party data sources. In this process, the metadata and provenance captured includes sensor specifications, data types, data properties, and process documentation, and is passed along with the data on to the workflow

  20. Nexus: A modular workflow management system for quantum simulation codes

    Science.gov (United States)

    Krogel, Jaron T.

    2016-01-01

    The management of simulation workflows represents a significant task for the individual computational researcher. Automation of the required tasks involved in simulation work can decrease the overall time to solution and reduce sources of human error. A new simulation workflow management system, Nexus, is presented to address these issues. Nexus is capable of automated job management on workstations and resources at several major supercomputing centers. Its modular design allows many quantum simulation codes to be supported within the same framework. Current support includes quantum Monte Carlo calculations with QMCPACK, density functional theory calculations with Quantum Espresso or VASP, and quantum chemical calculations with GAMESS. Users can compose workflows through a transparent, text-based interface, resembling the input file of a typical simulation code. A usage example is provided to illustrate the process.

  1. Leveraging workflow control patterns in the domain of clinical practice guidelines.

    Science.gov (United States)

    Kaiser, Katharina; Marcos, Mar

    2016-02-10

    Clinical practice guidelines (CPGs) include recommendations describing appropriate care for the management of patients with a specific clinical condition. A number of representation languages have been developed to support executable CPGs, with associated authoring/editing tools. Even with tool assistance, authoring of CPG models is a labor-intensive task. We aim at facilitating the early stages of CPG modeling task. In this context, we propose to support the authoring of CPG models based on a set of suitable procedural patterns described in an implementation-independent notation that can be then semi-automatically transformed into one of the alternative executable CPG languages. We have started with the workflow control patterns which have been identified in the fields of workflow systems and business process management. We have analyzed the suitability of these patterns by means of a qualitative analysis of CPG texts. Following our analysis we have implemented a selection of workflow patterns in the Asbru and PROforma CPG languages. As implementation-independent notation for the description of patterns we have chosen BPMN 2.0. Finally, we have developed XSLT transformations to convert the BPMN 2.0 version of the patterns into the Asbru and PROforma languages. We showed that although a significant number of workflow control patterns are suitable to describe CPG procedural knowledge, not all of them are applicable in the context of CPGs due to their focus on single-patient care. Moreover, CPGs may require additional patterns not included in the set of workflow control patterns. We also showed that nearly all the CPG-suitable patterns can be conveniently implemented in the Asbru and PROforma languages. Finally, we demonstrated that individual patterns can be semi-automatically transformed from a process specification in BPMN 2.0 to executable implementations in these languages. We propose a pattern and transformation-based approach for the development of CPG models

  2. Flash Builder and Flash Catalyst The New Workflow

    CERN Document Server

    Peeters, Steven

    2010-01-01

    The Flash Platform is changing. Flash Builder and Flash Catalyst have brought a new separation of design and coding to web development that enables a much more efficient and streamlined workflow. For designers and developers used to the close confines of Flash, this is a hugely liberating but at first alien concept. This book teaches you the new workflow for the Flash platform. It gives an overview of the technologies involved and provides you with real-world project examples and best-practice guidelines to get from design to implementation with the tools at hand. * Includes many examples* Foc

  3. Phxnlme: An R package that facilitates pharmacometric workflow of Phoenix NLME analyses.

    Science.gov (United States)

    Lim, Chay Ngee; Liang, Shuang; Feng, Kevin; Chittenden, Jason; Henry, Ana; Mouksassi, Samer; Birnbaum, Angela K

    2017-03-01

    Pharmacometric analyses are integral components of the drug development process, and Phoenix NLME is one of the popular software used to conduct such analyses. To address current limitations with model diagnostic graphics and efficiency of the workflow for this software, we developed an R package, Phxnlme, to facilitate its workflow and provide improved graphical diagnostics. Phxnlme was designed to provide functionality for the major tasks that are usually performed in pharmacometric analyses (i.e. nonlinear mixed effects modeling, basic model diagnostics, visual predictive checks and bootstrap). Various estimation methods for modeling using the R package are made available through the Phoenix NLME engine. The Phxnlme R package utilizes other packages such as ggplot2 and lattice to produce the graphical output, and various features were included to allow customizability of the output. Interactive features for some plots were also added using the manipulate R package. Phxnlme provides enhanced capabilities for nonlinear mixed effects modeling that can be accessed using the phxnlme() command. Output from the model can be graphed to assess the adequacy of model fits and further explore relationships in the data using various functions included in this R package, such as phxplot() and phxvpc.plot(). Bootstraps, stratified up to three variables, can also be performed to obtain confidence intervals around the model estimates. With the use of an R interface, different R projects can be created to allow multi-tasking, which addresses the current limitation of the Phoenix NLME desktop software. In addition, there is a wide selection of diagnostic and exploratory plots in the Phxnlme package, with improvements in the customizability of plots, compared to Phoenix NLME. The Phxnlme package is a flexible tool that allows implementation of the analytical workflow of Phoenix NLME with R, with features for greater overall efficiency and improved customizable graphics. Phxnlme is

  4. Toward Exascale Seismic Imaging: Taming Workflow and I/O Issues

    Science.gov (United States)

    Lefebvre, M. P.; Bozdag, E.; Lei, W.; Rusmanugroho, H.; Smith, J. A.; Tromp, J.; Yuan, Y.

    2013-12-01

    Providing a better understanding of the physics and chemistry of Earth's interior through numerical simulations has always required tremendous computational resources. Post-petascale supercomputers are now available to solve complex scientific problems that were thought unreachable a few decades ago. They also bring a cohort of concerns on how to obtain optimum performance. Several issues are currently being investigated by the HPC community. To name a few, we can list energy consumption, fault resilience, scalability of the current parallel paradigms, large workflow management, I/O performance and feature extraction with large datasets. For this presentation, we focus on the last three issues. In the context of seismic imaging, in particular for simulations based on adjoint methods, workflows are well defined. They consist of a few collective steps (e.g., mesh generation or model updates) and of a large number of independent steps (e.g., forward and adjoint simulations of each seismic event, pre- and postprocessing of seismic traces). The greater goal is to reduce the time to solution, that is, obtaining a more precise representation of the subsurface as fast as possible. This brings us to consider both the workflow in its entirety and the parts composing it. The usual approach is to speedup the purely computational parts by code tuning in order to reach higher FLOPS and better memory usage. This still remains an important concern, but larger scale experiments show that the imaging workflow suffers from a severe I/O bottleneck. This limitation occurs both for purely computational data and seismic time series. The latter are dealt with by the introduction of a new Adaptable Seismic Data Format (ASDF). In both cases, a parallel I/O library, ORNL's ADIOS, is used to drastically lessen the weight of disk access. Moreover, parallel visualization tools, such as VisIt, are able to take advantage of the metadata included in our ADIOS outputs to extract features and

  5. Soundness of Timed-Arc Workflow Nets in Discrete and Continuous-Time Semantics

    DEFF Research Database (Denmark)

    Mateo, Jose Antonio; Srba, Jiri; Sørensen, Mathias Grund

    2015-01-01

    Analysis of workflow processes with quantitative aspectslike timing is of interest in numerous time-critical applications. We suggest a workflow model based on timed-arc Petri nets and studythe foundational problems of soundness and strong (time-bounded) soundness.We first consider the discrete......-time semantics (integer delays)and explore the decidability of the soundness problemsand show, among others, that soundness is decidable for monotonic workflow nets while reachability is undecidable.For general timed-arc workflow nets soundness andstrong soundness become undecidable, though we can design......, and a blood transfusion workflow.The implementation of the algorithms is freely available as a part of the model checker TAPAAL (www.tapaal.net)....

  6. Optimising metadata workflows in a distributed information environment

    OpenAIRE

    Robertson, R. John; Barton, Jane

    2005-01-01

    The different purposes present within a distributed information environment create the potential for repositories to enhance their metadata by capitalising on the diversity of metadata available for any given object. This paper presents three conceptual reference models required to achieve this optimisation of metadata workflow: the ecology of repositories, the object lifecycle model, and the metadata lifecycle model. It suggests a methodology for developing the metadata lifecycle model, and ...

  7. You’ve Got Email: a Workflow Management Extraction System

    NARCIS (Netherlands)

    P. Chaipornkaew (Piyanuch); T. Prexawanprasut (Takorn); M.J. McAleer (Michael)

    2017-01-01

    textabstractEmail is one of the most powerful tools for communication. Many businesses use email as the main channel for communication, so it is possible that substantial data are included in email content. In order to help businesses grow faster, a workflow management system may be required. The

  8. From shared data to sharing workflow: Merging PACS and teleradiology

    International Nuclear Information System (INIS)

    Benjamin, Menashe; Aradi, Yinon; Shreiber, Reuven

    2010-01-01

    Due to a host of technological, interface, operational and workflow limitations, teleradiology and PACS/RIS were historically developed as separate systems serving different purposes. PACS/RIS handled local radiology storage and workflow management while teleradiology addressed remote access to images. Today advanced PACS/RIS support complete site radiology workflow for attending physicians, whether on-site or remote. In parallel, teleradiology has emerged into a service of providing remote, off-hours, coverage for emergency radiology and to a lesser extent subspecialty reading to subscribing sites and radiology groups. When attending radiologists use teleradiology for remote access to a site, they may share all relevant patient data and participate in the site's workflow like their on-site peers. The operation gets cumbersome and time consuming when these radiologists serve multi-sites, each requiring a different remote access, or when the sites do not employ the same PACS/RIS/Reporting Systems and do not share the same ownership. The least efficient operation is of teleradiology companies engaged in reading for multiple facilities. As these services typically employ non-local radiologists, they are allowed to share some of the available patient data necessary to provide an emergency report but, by enlarge, they do not share the workflow of the sites they serve. Radiology stakeholders usually prefer to have their own radiologists perform all radiology tasks including interpretation of off-hour examinations. It is possible with current technology to create a system that combines the benefits of local radiology services to multiple sites with the advantages offered by adding subspecialty and off-hours emergency services through teleradiology. Such a system increases efficiency for the radiology groups by enabling all users, regardless of location, to work 'local' and fully participate in the workflow of every site. We refer to such a system as SuperPACS.

  9. Elastic Scheduling of Scientific Workflows under Deadline Constraints in Cloud Computing Environments

    Directory of Open Access Journals (Sweden)

    Nazia Anwar

    2018-01-01

    Full Text Available Scientific workflow applications are collections of several structured activities and fine-grained computational tasks. Scientific workflow scheduling in cloud computing is a challenging research topic due to its distinctive features. In cloud environments, it has become critical to perform efficient task scheduling resulting in reduced scheduling overhead, minimized cost and maximized resource utilization while still meeting the user-specified overall deadline. This paper proposes a strategy, Dynamic Scheduling of Bag of Tasks based workflows (DSB, for scheduling scientific workflows with the aim to minimize financial cost of leasing Virtual Machines (VMs under a user-defined deadline constraint. The proposed model groups the workflow into Bag of Tasks (BoTs based on data dependency and priority constraints and thereafter optimizes the allocation and scheduling of BoTs on elastic, heterogeneous and dynamically provisioned cloud resources called VMs in order to attain the proposed method’s objectives. The proposed approach considers pay-as-you-go Infrastructure as a Service (IaaS clouds having inherent features such as elasticity, abundance, heterogeneity and VM provisioning delays. A trace-based simulation using benchmark scientific workflows representing real world applications, demonstrates a significant reduction in workflow computation cost while the workflow deadline is met. The results validate that the proposed model produces better success rates to meet deadlines and cost efficiencies in comparison to adapted state-of-the-art algorithms for similar problems.

  10. Automatic Image Processing Workflow for the Keck/NIRC2 Vortex Coronagraph

    Science.gov (United States)

    Xuan, Wenhao; Cook, Therese; Ngo, Henry; Zawol, Zoe; Ruane, Garreth; Mawet, Dimitri

    2018-01-01

    The Keck/NIRC2 camera, equipped with the vortex coronagraph, is an instrument targeted at the high contrast imaging of extrasolar planets. To uncover a faint planet signal from the overwhelming starlight, we utilize the Vortex Image Processing (VIP) library, which carries out principal component analysis to model and remove the stellar point spread function. To bridge the gap between data acquisition and data reduction, we implement a workflow that 1) downloads, sorts, and processes data with VIP, 2) stores the analysis products into a database, and 3) displays the reduced images, contrast curves, and auxiliary information on a web interface. Both angular differential imaging and reference star differential imaging are implemented in the analysis module. A real-time version of the workflow runs during observations, allowing observers to make educated decisions about time distribution on different targets, hence optimizing science yield. The post-night version performs a standardized reduction after the observation, building up a valuable database that not only helps uncover new discoveries, but also enables a statistical study of the instrument itself. We present the workflow, and an examination of the contrast performance of the NIRC2 vortex with respect to factors including target star properties and observing conditions.

  11. Workflow-Oriented Cyberinfrastructure for Sensor Data Analytics

    Science.gov (United States)

    Orcutt, J. A.; Rajasekar, A.; Moore, R. W.; Vernon, F.

    2015-12-01

    Sensor streams comprise an increasingly large part of Earth Science data. Analytics based on sensor data require an easy way to perform operations such as acquisition, conversion to physical units, metadata linking, sensor fusion, analysis and visualization on distributed sensor streams. Furthermore, embedding real-time sensor data into scientific workflows is of growing interest. We have implemented a scalable networked architecture that can be used to dynamically access packets of data in a stream from multiple sensors, and perform synthesis and analysis across a distributed network. Our system is based on the integrated Rule Oriented Data System (irods.org), which accesses sensor data from the Antelope Real Time Data System (brtt.com), and provides virtualized access to collections of data streams. We integrate real-time data streaming from different sources, collected for different purposes, on different time and spatial scales, and sensed by different methods. iRODS, noted for its policy-oriented data management, brings to sensor processing features and facilities such as single sign-on, third party access control lists ( ACLs), location transparency, logical resource naming, and server-side modeling capabilities while reducing the burden on sensor network operators. Rich integrated metadata support also makes it straightforward to discover data streams of interest and maintain data provenance. The workflow support in iRODS readily integrates sensor processing into any analytical pipeline. The system is developed as part of the NSF-funded Datanet Federation Consortium (datafed.org). APIs for selecting, opening, reaping and closing sensor streams are provided, along with other helper functions to associate metadata and convert sensor packets into NetCDF and JSON formats. Near real-time sensor data including seismic sensors, environmental sensors, LIDAR and video streams are available through this interface. A system for archiving sensor data and metadata in Net

  12. Modelling Mediterranean agro-ecosystems by including agricultural trees in the LPJmL model

    Science.gov (United States)

    Fader, M.; von Bloh, W.; Shi, S.; Bondeau, A.; Cramer, W.

    2015-11-01

    In the Mediterranean region, climate and land use change are expected to impact on natural and agricultural ecosystems by warming, reduced rainfall, direct degradation of ecosystems and biodiversity loss. Human population growth and socioeconomic changes, notably on the eastern and southern shores, will require increases in food production and put additional pressure on agro-ecosystems and water resources. Coping with these challenges requires informed decisions that, in turn, require assessments by means of a comprehensive agro-ecosystem and hydrological model. This study presents the inclusion of 10 Mediterranean agricultural plants, mainly perennial crops, in an agro-ecosystem model (Lund-Potsdam-Jena managed Land - LPJmL): nut trees, date palms, citrus trees, orchards, olive trees, grapes, cotton, potatoes, vegetables and fodder grasses. The model was successfully tested in three model outputs: agricultural yields, irrigation requirements and soil carbon density. With the development presented in this study, LPJmL is now able to simulate in good detail and mechanistically the functioning of Mediterranean agriculture with a comprehensive representation of ecophysiological processes for all vegetation types (natural and agricultural) and in a consistent framework that produces estimates of carbon, agricultural and hydrological variables for the entire Mediterranean basin. This development paves the way for further model extensions aiming at the representation of alternative agro-ecosystems (e.g. agroforestry), and opens the door for a large number of applications in the Mediterranean region, for example assessments of the consequences of land use transitions, the influence of management practices and climate change impacts.

  13. Dynamic Voltage Frequency Scaling Simulator for Real Workflows Energy-Aware Management in Green Cloud Computing.

    Science.gov (United States)

    Cotes-Ruiz, Iván Tomás; Prado, Rocío P; García-Galán, Sebastián; Muñoz-Expósito, José Enrique; Ruiz-Reyes, Nicolás

    2017-01-01

    Nowadays, the growing computational capabilities of Cloud systems rely on the reduction of the consumed power of their data centers to make them sustainable and economically profitable. The efficient management of computing resources is at the heart of any energy-aware data center and of special relevance is the adaptation of its performance to workload. Intensive computing applications in diverse areas of science generate complex workload called workflows, whose successful management in terms of energy saving is still at its beginning. WorkflowSim is currently one of the most advanced simulators for research on workflows processing, offering advanced features such as task clustering and failure policies. In this work, an expected power-aware extension of WorkflowSim is presented. This new tool integrates a power model based on a computing-plus-communication design to allow the optimization of new management strategies in energy saving considering computing, reconfiguration and networks costs as well as quality of service, and it incorporates the preeminent strategy for on host energy saving: Dynamic Voltage Frequency Scaling (DVFS). The simulator is designed to be consistent in different real scenarios and to include a wide repertory of DVFS governors. Results showing the validity of the simulator in terms of resources utilization, frequency and voltage scaling, power, energy and time saving are presented. Also, results achieved by the intra-host DVFS strategy with different governors are compared to those of the data center using a recent and successful DVFS-based inter-host scheduling strategy as overlapped mechanism to the DVFS intra-host technique.

  14. Dynamic Voltage Frequency Scaling Simulator for Real Workflows Energy-Aware Management in Green Cloud Computing

    Science.gov (United States)

    Cotes-Ruiz, Iván Tomás; Prado, Rocío P.; García-Galán, Sebastián; Muñoz-Expósito, José Enrique; Ruiz-Reyes, Nicolás

    2017-01-01

    Nowadays, the growing computational capabilities of Cloud systems rely on the reduction of the consumed power of their data centers to make them sustainable and economically profitable. The efficient management of computing resources is at the heart of any energy-aware data center and of special relevance is the adaptation of its performance to workload. Intensive computing applications in diverse areas of science generate complex workload called workflows, whose successful management in terms of energy saving is still at its beginning. WorkflowSim is currently one of the most advanced simulators for research on workflows processing, offering advanced features such as task clustering and failure policies. In this work, an expected power-aware extension of WorkflowSim is presented. This new tool integrates a power model based on a computing-plus-communication design to allow the optimization of new management strategies in energy saving considering computing, reconfiguration and networks costs as well as quality of service, and it incorporates the preeminent strategy for on host energy saving: Dynamic Voltage Frequency Scaling (DVFS). The simulator is designed to be consistent in different real scenarios and to include a wide repertory of DVFS governors. Results showing the validity of the simulator in terms of resources utilization, frequency and voltage scaling, power, energy and time saving are presented. Also, results achieved by the intra-host DVFS strategy with different governors are compared to those of the data center using a recent and successful DVFS-based inter-host scheduling strategy as overlapped mechanism to the DVFS intra-host technique. PMID:28085932

  15. Dynamic Voltage Frequency Scaling Simulator for Real Workflows Energy-Aware Management in Green Cloud Computing.

    Directory of Open Access Journals (Sweden)

    Iván Tomás Cotes-Ruiz

    Full Text Available Nowadays, the growing computational capabilities of Cloud systems rely on the reduction of the consumed power of their data centers to make them sustainable and economically profitable. The efficient management of computing resources is at the heart of any energy-aware data center and of special relevance is the adaptation of its performance to workload. Intensive computing applications in diverse areas of science generate complex workload called workflows, whose successful management in terms of energy saving is still at its beginning. WorkflowSim is currently one of the most advanced simulators for research on workflows processing, offering advanced features such as task clustering and failure policies. In this work, an expected power-aware extension of WorkflowSim is presented. This new tool integrates a power model based on a computing-plus-communication design to allow the optimization of new management strategies in energy saving considering computing, reconfiguration and networks costs as well as quality of service, and it incorporates the preeminent strategy for on host energy saving: Dynamic Voltage Frequency Scaling (DVFS. The simulator is designed to be consistent in different real scenarios and to include a wide repertory of DVFS governors. Results showing the validity of the simulator in terms of resources utilization, frequency and voltage scaling, power, energy and time saving are presented. Also, results achieved by the intra-host DVFS strategy with different governors are compared to those of the data center using a recent and successful DVFS-based inter-host scheduling strategy as overlapped mechanism to the DVFS intra-host technique.

  16. Mathematical Model of Thyristor Inverter Including a Series-parallel Resonant Circuit

    Directory of Open Access Journals (Sweden)

    Miroslaw Luft

    2008-01-01

    Full Text Available The article presents a mathematical model of thyristor inverter including a series-parallel resonant circuit with theaid of state variable method. Maple procedures are used to compute current and voltage waveforms in the inverter.

  17. Mathematical model of thyristor inverter including a series-parallel resonant circuit

    OpenAIRE

    Luft, M.; Szychta, E.

    2008-01-01

    The article presents a mathematical model of thyristor inverter including a series-parallel resonant circuit with the aid of state variable method. Maple procedures are used to compute current and voltage waveforms in the inverter.

  18. Mathematical Model of Thyristor Inverter Including a Series-parallel Resonant Circuit

    OpenAIRE

    Miroslaw Luft; Elzbieta Szychta

    2008-01-01

    The article presents a mathematical model of thyristor inverter including a series-parallel resonant circuit with theaid of state variable method. Maple procedures are used to compute current and voltage waveforms in the inverter.

  19. Modeling of Pem Fuel Cell Systems Including Controls and Reforming Effects for Hybrid Automotive Applications

    National Research Council Canada - National Science Library

    Boettner, Daisie

    2001-01-01

    .... This study develops models for a stand-alone Proton Exchange Membrane (PEM) fuel cell stack, a direct-hydrogen fuel cell system including auxiliaries, and a methanol reforming fuel cell system for integration into a vehicle performance simulator...

  20. Modeling of the Direct Current Generator Including the Magnetic Saturation and Temperature Effects

    Directory of Open Access Journals (Sweden)

    Alfonso J. Mercado-Samur

    2013-11-01

    Full Text Available In this paper the inclusion of temperature effect on the field resistance on the direct current generator model DC1A, which is valid to stability studies is proposed. First, the linear generator model is presented, after the effect of magnetic saturation and the change in the resistance value due to temperature produced by the field current are included. The comparison of experimental results and model simulations to validate the model is used. A direct current generator model which is a better representation of the generator is obtained. Visual comparison between simulations and experimental results shows the success of the proposed model, because it presents the lowest error of the compared models. The accuracy of the proposed model is observed via Modified Normalized Sum of Squared Errors index equal to 3.8979%.

  1. Atmosphere-soil-vegetation model including CO2 exchange processes: SOLVEG2

    International Nuclear Information System (INIS)

    Nagai, Haruyasu

    2004-11-01

    A new atmosphere-soil-vegetation model named SOLVEG2 (SOLVEG version 2) was developed to study the heat, water, and CO 2 exchanges between the atmosphere and land-surface. The model consists of one-dimensional multilayer sub-models for the atmosphere, soil, and vegetation. It also includes sophisticated processes for solar and long-wave radiation transmission in vegetation canopy and CO 2 exchanges among the atmosphere, soil, and vegetation. Although the model usually simulates only vertical variation of variables in the surface-layer atmosphere, soil, and vegetation canopy by using meteorological data as top boundary conditions, it can be used by coupling with a three-dimensional atmosphere model. In this paper, details of SOLVEG2, which includes the function of coupling with atmosphere model MM5, are described. (author)

  2. Combining prior knowledge with data driven modeling of a batch distillation column including start-up

    NARCIS (Netherlands)

    van Lith, PF; Betlem, BHL; Roffel, B

    2003-01-01

    This paper presents the development of a simple model which describes the product quality and production over time of an experimental batch distillation column, including start-up. The model structure is based on a simple physical framework, which is augmented with fuzzy logic. This provides a way

  3. Enhanced UWB Radio Channel Model for Short-Range Communication Scenarios Including User Dynamics

    DEFF Research Database (Denmark)

    Kovacs, Istvan Zsolt; Nguyen, Tuan Hung; Eggers, Patrick Claus F.

    2005-01-01

    channel model represents an enhancement of the existing IEEE 802.15.3a/4a PAN channel model, where antenna and user-proximity effects are not included. Our investigations showed that significant variations of the received wideband power and time-delay signal clustering are possible due the human body...

  4. Design and implementation of workflow engine for service-oriented architecture

    Science.gov (United States)

    Peng, Shuqing; Duan, Huining; Chen, Deyun

    2009-04-01

    As computer network is developed rapidly and in the situation of the appearance of distribution specialty in enterprise application, traditional workflow engine have some deficiencies, such as complex structure, bad stability, poor portability, little reusability and difficult maintenance. In this paper, in order to improve the stability, scalability and flexibility of workflow management system, a four-layer architecture structure of workflow engine based on SOA is put forward according to the XPDL standard of Workflow Management Coalition, the route control mechanism in control model is accomplished and the scheduling strategy of cyclic routing and acyclic routing is designed, and the workflow engine which adopts the technology such as XML, JSP, EJB and so on is implemented.

  5. Implementing Workflow Reconfiguration in WS-BPEL

    DEFF Research Database (Denmark)

    Mazzara, Manuel; Dragoni, Nicola; Zhou, Mu

    2012-01-01

    This paper investigates the problem of dynamic reconfiguration by means of a workflow-based case study used for discussion. We state the requirements on a system implementing the workflow and its reconfiguration, and we describe the system’s design in BPMN. WS-BPEL, a language that would...

  6. Implementing bioinformatic workflows within the bioextract server

    Science.gov (United States)

    Computational workflows in bioinformatics are becoming increasingly important in the achievement of scientific advances. These workflows typically require the integrated use of multiple, distributed data sources and analytic tools. The BioExtract Server (http://bioextract.org) is a distributed servi...

  7. Including operational data in QMRA model: development and impact of model inputs.

    Science.gov (United States)

    Jaidi, Kenza; Barbeau, Benoit; Carrière, Annie; Desjardins, Raymond; Prévost, Michèle

    2009-03-01

    A Monte Carlo model, based on the Quantitative Microbial Risk Analysis approach (QMRA), has been developed to assess the relative risks of infection associated with the presence of Cryptosporidium and Giardia in drinking water. The impact of various approaches for modelling the initial parameters of the model on the final risk assessments is evaluated. The Monte Carlo simulations that we performed showed that the occurrence of parasites in raw water was best described by a mixed distribution: log-Normal for concentrations > detection limit (DL), and a uniform distribution for concentrations risks significantly. The mean annual risks for conventional treatment are: 1.97E-03 (removal credit adjusted by log parasite = log spores), 1.58E-05 (log parasite = 1.7 x log spores) or 9.33E-03 (regulatory credits based on the turbidity measurement in filtered water). Using full scale validated SCADA data, the simplified calculation of CT performed at the plant was shown to largely underestimate the risk relative to a more detailed CT calculation, which takes into consideration the downtime and system failure events identified at the plant (1.46E-03 vs. 3.93E-02 for the mean risk).

  8. Mathematical modeling of the hypothalamic–pituitary–adrenal gland (HPA) axis, including hippocampal mechanisms

    DEFF Research Database (Denmark)

    Andersen, Morten; Vinther, Frank; Ottesen, Johnny T.

    2013-01-01

    This paper presents a mathematical model of the HPA axis. The HPA axis consists of the hypothalamus, the pituitary and the adrenal glands in which the three hormones CRH, ACTH and cortisol interact through receptor dynamics. Furthermore, it has been suggested that receptors in the hippocampus have...... an influence on the axis.A model is presented with three coupled, non-linear differential equations, with the hormones CRH, ACTH and cortisol as variables. The model includes the known features of the HPA axis, and includes the effects from the hippocampus through its impact on CRH in the hypothalamus...

  9. Modification of TOUGH2 to Include the Dusty Gas Model for Gas Diffusion; TOPICAL

    International Nuclear Information System (INIS)

    WEBB, STEPHEN W.

    2001-01-01

    The GEO-SEQ Project is investigating methods for geological sequestration of CO(sub 2). This project, which is directed by LBNL and includes a number of other industrial, university, and national laboratory partners, is evaluating computer simulation methods including TOUGH2 for this problem. The TOUGH2 code, which is a widely used code for flow and transport in porous and fractured media, includes simplified methods for gas diffusion based on a direct application of Fick's law. As shown by Webb (1998) and others, the Dusty Gas Model (DGM) is better than Fick's Law for modeling gas-phase diffusion in porous media. In order to improve gas-phase diffusion modeling for the GEO-SEQ Project, the EOS7R module in the TOUGH2 code has been modified to include the Dusty Gas Model as documented in this report. In addition, the liquid diffusion model has been changed from a mass-based formulation to a mole-based model. Modifications for separate and coupled diffusion in the gas and liquid phases have also been completed. The results from the DGM are compared to the Fick's law behavior for TCE and PCE diffusion across a capillary fringe. The differences are small due to the relatively high permeability (k= 10(sup -11) m(sup 2)) of the problem and the small mole fraction of the gases. Additional comparisons for lower permeabilities and higher mole fractions may be useful

  10. Numerical Acoustic Models Including Viscous and Thermal losses: Review of Existing and New Methods

    DEFF Research Database (Denmark)

    Andersen, Peter Risby; Cutanda Henriquez, Vicente; Aage, Niels

    2017-01-01

    This work presents an updated overview of numerical methods including acoustic viscous and thermal losses. Numerical modelling of viscothermal losses has gradually become more important due to the general trend of making acoustic devices smaller. Not including viscothermal acoustic losses...... in such numerical computations will therefore lead to inaccurate or even wrong results. Both, Finite Element Method (FEM) and Boundary Element Method (BEM), formulations are available that incorporate these loss mechanisms. Including viscothermal losses in FEM computations can be computationally very demanding, due...... and BEM method including viscothermal dissipation are compared and investigated....

  11. Direct-phase-variable model of a synchronous reluctance motor including all slot and winding harmonics

    International Nuclear Information System (INIS)

    Obe, Emeka S.; Binder, A.

    2011-01-01

    A detailed model in direct-phase variables of a synchronous reluctance motor operating at mains voltage and frequency is presented. The model includes the stator and rotor slot openings, the actual winding layout and the reluctance rotor geometry. Hence, all mmf and permeance harmonics are taken into account. It is seen that non-negligible harmonics introduced by slots are present in the inductances computed by the winding function procedure. These harmonics are usually ignored in d-q models. The machine performance is simulated in the stator reference frame to depict the difference between this new direct-phase model including all harmonics and the conventional rotor reference frame d-q model. Saturation is included by using a polynomial fitting the variation of d-axis inductance with stator current obtained by finite-element software FEMAG DC (registered) . The detailed phase-variable model can yield torque pulsations comparable to those obtained from finite elements while the d-q model cannot.

  12. Images crossing borders: image and workflow sharing on multiple levels.

    Science.gov (United States)

    Ross, Peeter; Pohjonen, Hanna

    2011-04-01

    Digitalisation of medical data makes it possible to share images and workflows between related parties. In addition to linear data flow where healthcare professionals or patients are the information carriers, a new type of matrix of many-to-many connections is emerging. Implementation of shared workflow brings challenges of interoperability and legal clarity. Sharing images or workflows can be implemented on different levels with different challenges: inside the organisation, between organisations, across country borders, or between healthcare institutions and citizens. Interoperability issues vary according to the level of sharing and are either technical or semantic, including language. Legal uncertainty increases when crossing national borders. Teleradiology is regulated by multiple European Union (EU) directives and legal documents, which makes interpretation of the legal system complex. To achieve wider use of eHealth and teleradiology several strategic documents were published recently by the EU. Despite EU activities, responsibility for organising, providing and funding healthcare systems remains with the Member States. Therefore, the implementation of new solutions requires strong co-operation between radiologists, societies of radiology, healthcare administrators, politicians and relevant EU authorities. The aim of this article is to describe different dimensions of image and workflow sharing and to analyse legal acts concerning teleradiology in the EU.

  13. Electronic Health Record-Driven Workflow for Diagnostic Radiologists.

    Science.gov (United States)

    Geeslin, Matthew G; Gaskin, Cree M

    2016-01-01

    In most settings, radiologists maintain a high-throughput practice in which efficiency is crucial. The conversion from film-based to digital study interpretation and data storage launched the era of PACS-driven workflow, leading to significant gains in speed. The advent of electronic health records improved radiologists' access to patient data; however, many still find this aspect of workflow to be relatively cumbersome. Nevertheless, the ability to guide a diagnostic interpretation with clinical information, beyond that provided in the examination indication, can add significantly to the specificity of a radiologist's interpretation. Responsibilities of the radiologist include, but are not limited to, protocoling examinations, interpreting studies, chart review, peer review, writing notes, placing orders, and communicating with referring providers. Most of the aforementioned activities are not PACS-centric and require a login to one or more additional applications. Consolidation of these tasks for completion through a single interface can simplify workflow, save time, and potentially reduce the incidence of errors. Here, the authors describe diagnostic radiology workflow that leverages the electronic health record to significantly add to a radiologist's ability to be part of the health care team, provide relevant interpretations, and improve efficiency and quality. Copyright © 2016 American College of Radiology. Published by Elsevier Inc. All rights reserved.

  14. Experiences with Resource Provisioning for Scientific Workflows Using Corral

    Directory of Open Access Journals (Sweden)

    Gideon Juve

    2010-01-01

    Full Text Available The development of grid and workflow technologies has enabled complex, loosely coupled scientific applications to be executed on distributed resources. Many of these applications consist of large numbers of short-duration tasks whose runtimes are heavily influenced by delays in the execution environment. Such applications often perform poorly on the grid because of the large scheduling overheads commonly found in grids. In this paper we present a provisioning system based on multi-level scheduling that improves workflow runtime by reducing scheduling overheads. The system reserves resources for the exclusive use of the application, and gives applications control over scheduling policies. We describe our experiences with the system when running a suite of real workflow-based applications including in astronomy, earthquake science, and genomics. Provisioning resources with Corral ahead of the workflow execution, reduced the runtime of the astronomy application by up to 78% (45% on average and of a genome mapping application by an order of magnitude when compared to traditional methods. We also show how provisioning can benefit applications both on a small local cluster as well as a large-scale campus resource.

  15. Declarative Event-Based Workflow as Distributed Dynamic Condition Response Graphs

    DEFF Research Database (Denmark)

    Hildebrandt, Thomas; Mukkamala, Raghava Rao

    2010-01-01

    We present Dynamic Condition Response Graphs (DCR Graphs) as a declarative, event-based process model inspired by the workflow language employed by our industrial partner and conservatively generalizing prime event structures. A dynamic condition response graph is a directed graph with nodes repr...... exemplify the use of distributed DCR Graphs on a simple workflow taken from a field study at a Danish hospital, pointing out their flexibility compared to imperative workflow models. Finally we provide a mapping from DCR Graphs to Buchi-automata....

  16. Implementation of Cyberinfrastructure and Data Management Workflow for a Large-Scale Sensor Network

    Science.gov (United States)

    Jones, A. S.; Horsburgh, J. S.

    2014-12-01

    Monitoring with in situ environmental sensors and other forms of field-based observation presents many challenges for data management, particularly for large-scale networks consisting of multiple sites, sensors, and personnel. The availability and utility of these data in addressing scientific questions relies on effective cyberinfrastructure that facilitates transformation of raw sensor data into functional data products. It also depends on the ability of researchers to share and access the data in useable formats. In addition to addressing the challenges presented by the quantity of data, monitoring networks need practices to ensure high data quality, including procedures and tools for post processing. Data quality is further enhanced if practitioners are able to track equipment, deployments, calibrations, and other events related to site maintenance and associate these details with observational data. In this presentation we will describe the overall workflow that we have developed for research groups and sites conducting long term monitoring using in situ sensors. Features of the workflow include: software tools to automate the transfer of data from field sites to databases, a Python-based program for data quality control post-processing, a web-based application for online discovery and visualization of data, and a data model and web interface for managing physical infrastructure. By automating the data management workflow, the time from collection to analysis is reduced and sharing and publication is facilitated. The incorporation of metadata standards and descriptions and the use of open-source tools enhances the sustainability and reusability of the data. We will describe the workflow and tools that we have developed in the context of the iUTAH (innovative Urban Transitions and Aridregion Hydrosustainability) monitoring network. The iUTAH network consists of aquatic and climate sensors deployed in three watersheds to monitor Gradients Along Mountain to Urban

  17. Modeling of Temperature-Dependent Noise in Silicon Nanowire FETs including Self-Heating Effects

    OpenAIRE

    Anandan, P.; Malathi, N.; Mohankumar, N.

    2014-01-01

    Silicon nanowires are leading the CMOS era towards the downsizing limit and its nature will be effectively suppress the short channel effects. Accurate modeling of thermal noise in nanowires is crucial for RF applications of nano-CMOS emerging technologies. In this work, a perfect temperature-dependent model for silicon nanowires including the self-heating effects has been derived and its effects on device parameters have been observed. The power spectral density as a function of thermal resi...

  18. End-to-end workflow for finite element analysis of tumor treating fields in glioblastomas.

    Science.gov (United States)

    Timmons, Joshua J; Lok, Edwin; San, Pyay; Bui, Kevin; Wong, Eric T

    2017-10-12

    Tumor Treating Fields (TTFields) therapy is an approved modality of treatment for glioblastoma. Patient anatomy-based finite element analysis (FEA) has the potential to reveal not only how these fields affect tumor control but also how to improve efficacy. While the automated tools for segmentation speed up the generation of FEA models, multi-step manual corrections are required, including removal of disconnected voxels, incorporation of unsegmented structures and the addition of 36 electrodes plus gel layers matching the TTFields transducers. Existing approaches are also not scalable for the high throughput analysis of large patient volumes. A semi-automated workflow was developed to prepare FEA models for TTFields mapping in the human brain. Magnetic resonance imaging (MRI) pre-processing, segmentation, electrode and gel placement, and post-processing were all automated. The material properties of each tissue were applied to their corresponding mask in silico using COMSOL Multiphysics (COMSOL, Burlington, MA, USA). The fidelity of the segmentations with and without post-processing was compared against the full semi-automated segmentation workflow approach using Dice coefficient analysis. The average relative differences for the electric fields generated by COMSOL were calculated in addition to observed differences in electric field-volume histograms. Furthermore, the mesh file formats in MPHTXT and NASTRAN were also compared using the differences in the electric field-volume histogram. The Dice coefficient was less for auto-segmentation without versus auto-segmentation with post-processing, indicating convergence on a manually corrected model. An existent but marginal relative difference of electric field maps from models with manual correction versus those without was identified, and a clear advantage of using the NASTRAN mesh file format was found. The software and workflow outlined in this article may be used to accelerate the investigation of TTFields in

  19. End-to-end workflow for finite element analysis of tumor treating fields in glioblastomas

    Science.gov (United States)

    Timmons, Joshua J.; Lok, Edwin; San, Pyay; Bui, Kevin; Wong, Eric T.

    2017-11-01

    Tumor Treating Fields (TTFields) therapy is an approved modality of treatment for glioblastoma. Patient anatomy-based finite element analysis (FEA) has the potential to reveal not only how these fields affect tumor control but also how to improve efficacy. While the automated tools for segmentation speed up the generation of FEA models, multi-step manual corrections are required, including removal of disconnected voxels, incorporation of unsegmented structures and the addition of 36 electrodes plus gel layers matching the TTFields transducers. Existing approaches are also not scalable for the high throughput analysis of large patient volumes. A semi-automated workflow was developed to prepare FEA models for TTFields mapping in the human brain. Magnetic resonance imaging (MRI) pre-processing, segmentation, electrode and gel placement, and post-processing were all automated. The material properties of each tissue were applied to their corresponding mask in silico using COMSOL Multiphysics (COMSOL, Burlington, MA, USA). The fidelity of the segmentations with and without post-processing was compared against the full semi-automated segmentation workflow approach using Dice coefficient analysis. The average relative differences for the electric fields generated by COMSOL were calculated in addition to observed differences in electric field-volume histograms. Furthermore, the mesh file formats in MPHTXT and NASTRAN were also compared using the differences in the electric field-volume histogram. The Dice coefficient was less for auto-segmentation without versus auto-segmentation with post-processing, indicating convergence on a manually corrected model. An existent but marginal relative difference of electric field maps from models with manual correction versus those without was identified, and a clear advantage of using the NASTRAN mesh file format was found. The software and workflow outlined in this article may be used to accelerate the investigation of TTFields in

  20. Dipole model analysis of highest precision HERA data, including very low Q2's

    International Nuclear Information System (INIS)

    Luszczak, A.; Kowalski, H.

    2016-12-01

    We analyse, within a dipole model, the final, inclusive HERA DIS cross section data in the low χ region, using fully correlated errors. We show, that these highest precision data are very well described within the dipole model framework starting from Q 2 values of 3.5 GeV 2 to the highest values of Q 2 =250 GeV 2 . To analyze the saturation effects we evaluated the data including also the very low 0.35including this region show a preference of the saturation ansatz.

  1. Watchdog - a workflow management system for the distributed analysis of large-scale experimental data.

    Science.gov (United States)

    Kluge, Michael; Friedel, Caroline C

    2018-03-13

    The development of high-throughput experimental technologies, such as next-generation sequencing, have led to new challenges for handling, analyzing and integrating the resulting large and diverse datasets. Bioinformatical analysis of these data commonly requires a number of mutually dependent steps applied to numerous samples for multiple conditions and replicates. To support these analyses, a number of workflow management systems (WMSs) have been developed to allow automated execution of corresponding analysis workflows. Major advantages of WMSs are the easy reproducibility of results as well as the reusability of workflows or their components. In this article, we present Watchdog, a WMS for the automated analysis of large-scale experimental data. Main features include straightforward processing of replicate data, support for distributed computer systems, customizable error detection and manual intervention into workflow execution. Watchdog is implemented in Java and thus platform-independent and allows easy sharing of workflows and corresponding program modules. It provides a graphical user interface (GUI) for workflow construction using pre-defined modules as well as a helper script for creating new module definitions. Execution of workflows is possible using either the GUI or a command-line interface and a web-interface is provided for monitoring the execution status and intervening in case of errors. To illustrate its potentials on a real-life example, a comprehensive workflow and modules for the analysis of RNA-seq experiments were implemented and are provided with the software in addition to simple test examples. Watchdog is a powerful and flexible WMS for the analysis of large-scale high-throughput experiments. We believe it will greatly benefit both users with and without programming skills who want to develop and apply bioinformatical workflows with reasonable overhead. The software, example workflows and a comprehensive documentation are freely

  2. User-Driven Workflow for Modeling, Monitoring, Product Development, and Flood Map Delivery Using Satellites for Daily Coverage Over Texas May-June 2015

    Science.gov (United States)

    Green, D. S.; Frye, S. W.; Wells, G. L.; Adler, R. F.; Brakenridge, R.; Bolten, J. D.; Murray, J. J.; Slayback, D. A.; Kirschbaum, D.; Wu, H.; Cappelaere, P. G.; Schumann, G.; Howard, T.; Flamig, Z.; Clark, R. A.; Stough, T.; Chini, M.; Matgen, P.

    2015-12-01

    Intense rainfall during late April and early May 2015 in Texas and Oklahoma led to widespread flooding in several river basins in that region. Texas state agencies were activated for the May-June floods and severe weather event that ensued for six weeks from May 8 until June 19 following Tropical Storm Bill. This poster depicts a case study where modeling flood potential informed decision making authorities for user-driven high resolution satellite acquisitions over the most critical areas and how experimental flood mapping techniques provided the capability for daily on-going monitoring of these events through the use of increased automation. Recent improvements in flood models resulting from higher frequency updates, better spatial resolution, and increased accuracy of now cast and forecast precipitation products coupled with advanced technology to improve situational awareness for decision makers. These advances enabled satellites to be tasked, data products to be developed and distributed, and feedback loops between the emergency authorities, satellite operators, and mapping researchers to deliver a daily stream of relevant products that informed deployment of emergency resources and improved management of the large-scale event across the local, state, and national levels. This collaboration was made possible through inter-agency cooperation on an international scale through the Committee on Earth Observation Satellites Flood Pilot activity that is supported in the USA by NASA, NOAA, and USGS and includes numerous civilian space agency assets from the European Space Agency along with national agencies from Italy, France, Germany, Japan, and others. The poster describes the inter-linking technology infrastructure, the development and delivery of mapping products, and the lessons learned for product improvement in the future.

  3. Clinician time used for decision making: a best case workflow study using cardiovascular risk assessments and Ask Mayo Expert algorithmic care process models.

    Science.gov (United States)

    North, Frederick; Fox, Samuel; Chaudhry, Rajeev

    2016-07-20

    Risk calculation is increasingly used in lipid management, congestive heart failure, and atrial fibrillation. The risk scores are then used for decisions about statin use, anticoagulation, and implantable defibrillator use. Calculating risks for patients and making decisions based on these risks is often done at the point of care and is an additional time burden for clinicians that can be decreased by automating the tasks and using clinical decision-making support. Using Morae Recorder software, we timed 30 healthcare providers tasked with calculating the overall risk of cardiovascular events, sudden death in heart failure, and thrombotic event risk in atrial fibrillation. Risk calculators used were the American College of Cardiology Atherosclerotic Cardiovascular Disease risk calculator (AHA-ASCVD risk), Seattle Heart Failure Model (SHFM risk), and CHA2DS2VASc. We also timed the 30 providers using Ask Mayo Expert care process models for lipid management, heart failure management, and atrial fibrillation management based on the calculated risk scores. We used the Mayo Clinic primary care panel to estimate time for calculating an entire panel risk. Mean provider times to complete the CHA2DS2VASc, AHA-ASCVD risk, and SHFM were 36, 45, and 171 s respectively. For decision making about atrial fibrillation, lipids, and heart failure, the mean times (including risk calculations) were 85, 110, and 347 s respectively. Even under best case circumstances, providers take a significant amount of time to complete risk assessments. For a complete panel of patients this can lead to hours of time required to make decisions about prescribing statins, use of anticoagulation, and medications for heart failure. Informatics solutions are needed to capture data in the medical record and serve up automatically calculated risk assessments to physicians and other providers at the point of care.

  4. The No-Core Gamow Shell Model: Including the continuum in the NCSM

    CERN Document Server

    Barrett, B R; Michel, N; Płoszajczak, M

    2015-01-01

    We are witnessing an era of intense experimental efforts that will provide information about the properties of nuclei far from the line of stability, regarding resonant and scattering states as well as (weakly) bound states. This talk describes our formalism for including these necessary ingredients into the No-Core Shell Model by using the Gamow Shell Model approach. Applications of this new approach, known as the No-Core Gamow Shell Model, both to benchmark cases as well as to unstable nuclei will be given.

  5. Ab initio chemical safety assessment: A workflow based on exposure considerations and non-animal methods

    OpenAIRE

    Berggren, Elisabet; White, Andrew; Ouedraogo, Gladys; Paini, Alicia; Richarz, Andrea-Nicole; Bois, Frederic Y.; Exner, Thomas; Leite, Sofia; Grunsven, Leo A. van; Worth, Andrew; Mahony, Catherine

    2017-01-01

    Highlights • A workflow for an exposure driven chemical safety assessment to avoid animal testing. • Hypothesis based on existing data, in silico modelling and biokinetic considerations. • A tool to inform targeted and toxicologically relevant in vitro testing.

  6. A Distributed Collaborative Workflow Based Approach to Data Collection and Analysis

    National Research Council Canada - National Science Library

    Gerecke, William; Enas, Douglas; Gottschlich, Susan

    2004-01-01

    ...) and Modeling and Simulation (M&S) systems and architectures. In our work we have found that in order to be maximally effective, these capabilities must be designed with the military user workflow process in mind...

  7. Conceptualizing a Dynamic Fall Risk Model Including Intrinsic Risks and Exposures.

    Science.gov (United States)

    Klenk, Jochen; Becker, Clemens; Palumbo, Pierpaolo; Schwickert, Lars; Rapp, Kilan; Helbostad, Jorunn L; Todd, Chris; Lord, Stephen R; Kerse, Ngaire

    2017-11-01

    Falls are a major cause of injury and disability in older people, leading to serious health and social consequences including fractures, poor quality of life, loss of independence, and institutionalization. To design and provide adequate prevention measures, accurate understanding and identification of person's individual fall risk is important. However, to date, the performance of fall risk models is weak compared with models estimating, for example, cardiovascular risk. This deficiency may result from 2 factors. First, current models consider risk factors to be stable for each person and not change over time, an assumption that does not reflect real-life experience. Second, current models do not consider the interplay of individual exposure including type of activity (eg, walking, undertaking transfers) and environmental risks (eg, lighting, floor conditions) in which activity is performed. Therefore, we posit a dynamic fall risk model consisting of intrinsic risk factors that vary over time and exposure (activity in context). eHealth sensor technology (eg, smartphones) begins to enable the continuous measurement of both the above factors. We illustrate our model with examples of real-world falls from the FARSEEING database. This dynamic framework for fall risk adds important aspects that may improve understanding of fall mechanisms, fall risk models, and the development of fall prevention interventions. Copyright © 2017 AMDA – The Society for Post-Acute and Long-Term Care Medicine. Published by Elsevier Inc. All rights reserved.

  8. Modeling of cylindrical surrounding gate MOSFETs including the fringing field effects

    International Nuclear Information System (INIS)

    Gupta, Santosh K.; Baishya, Srimanta

    2013-01-01

    A physically based analytical model for surface potential and threshold voltage including the fringing gate capacitances in cylindrical surround gate (CSG) MOSFETs has been developed. Based on this a subthreshold drain current model has also been derived. This model first computes the charge induced in the drain/source region due to the fringing capacitances and considers an effective charge distribution in the cylindrically extended source/drain region for the development of a simple and compact model. The fringing gate capacitances taken into account are outer fringe capacitance, inner fringe capacitance, overlap capacitance, and sidewall capacitance. The model has been verified with the data extracted from 3D TCAD simulations of CSG MOSFETs and was found to be working satisfactorily. (semiconductor devices)

  9. The Watts-Strogatz network model developed by including degree distribution: theory and computer simulation

    International Nuclear Information System (INIS)

    Chen, Y W; Zhang, L F; Huang, J P

    2007-01-01

    By using theoretical analysis and computer simulations, we develop the Watts-Strogatz network model by including degree distribution, in an attempt to improve the comparison between characteristic path lengths and clustering coefficients predicted by the original Watts-Strogatz network model and those of the real networks with the small-world property. Good agreement between the predictions of the theoretical analysis and those of the computer simulations has been shown. It is found that the developed Watts-Strogatz network model can fit the real small-world networks more satisfactorily. Some other interesting results are also reported by adjusting the parameters in a model degree-distribution function. The developed Watts-Strogatz network model is expected to help in the future analysis of various social problems as well as financial markets with the small-world property

  10. Including Effects of Water Stress on Dead Organic Matter Decay to a Forest Carbon Model

    Science.gov (United States)

    Kim, H.; Lee, J.; Han, S. H.; Kim, S.; Son, Y.

    2017-12-01

    Decay of dead organic matter is a key process of carbon (C) cycling in forest ecosystems. The change in decay rate depends on temperature sensitivity and moisture conditions. The Forest Biomass and Dead organic matter Carbon (FBDC) model includes a decay sub-model considering temperature sensitivity, yet does not consider moisture conditions as drivers of the decay rate change. This study aimed to improve the FBDC model by including a water stress function to the decay sub-model. Also, soil C sequestration under climate change with the FBDC model including the water stress function was simulated. The water stress functions were determined with data from decomposition study on Quercus variabilis forests and Pinus densiflora forests of Korea, and adjustment parameters of the functions were determined for both species. The water stress functions were based on the ratio of precipitation to potential evapotranspiration. Including the water stress function increased the explained variances of the decay rate by 19% for the Q. variabilis forests and 7% for the P. densiflora forests, respectively. The increase of the explained variances resulted from large difference in temperature range and precipitation range across the decomposition study plots. During the period of experiment, the mean annual temperature range was less than 3°C, while the annual precipitation ranged from 720mm to 1466mm. Application of the water stress functions to the FBDC model constrained increasing trend of temperature sensitivity under climate change, and thus increased the model-estimated soil C sequestration (Mg C ha-1) by 6.6 for the Q. variabilis forests and by 3.1 for the P. densiflora forests, respectively. The addition of water stress functions increased reliability of the decay rate estimation and could contribute to reducing the bias in estimating soil C sequestration under varying moisture condition. Acknowledgement: This study was supported by Korea Forest Service (2017044B10-1719-BB01)

  11. Including an ocean carbon cycle model into iLOVECLIM (v1.0)

    NARCIS (Netherlands)

    Bouttes, N.; Roche, D.M.V.A.P.; Mariotti, V.; Bopp, L.

    2015-01-01

    The atmospheric carbon dioxide concentration plays a crucial role in the radiative balance and as such has a strong influence on the evolution of climate. Because of the numerous interactions between climate and the carbon cycle, it is necessary to include a model of the carbon cycle within a

  12. Facilitating Stewardship of scientific data through standards based workflows

    Science.gov (United States)

    Bastrakova, I.; Kemp, C.; Potter, A. K.

    2013-12-01

    There are main suites of standards that can be used to define the fundamental scientific methodology of data, methods and results. These are firstly Metadata standards to enable discovery of the data (ISO 19115), secondly the Sensor Web Enablement (SWE) suite of standards that include the O&M and SensorML standards and thirdly Ontology that provide vocabularies to define the scientific concepts and relationships between these concepts. All three types of standards have to be utilised by the practicing scientist to ensure that those who ultimately have to steward the data stewards to ensure that the data can be preserved curated and reused and repurposed. Additional benefits of this approach include transparency of scientific processes from the data acquisition to creation of scientific concepts and models, and provision of context to inform data use. Collecting and recording metadata is the first step in scientific data flow. The primary role of metadata is to provide details of geographic extent, availability and high-level description of data suitable for its initial discovery through common search engines. The SWE suite provides standardised patterns to describe observations and measurements taken for these data, capture detailed information about observation or analytical methods, used instruments and define quality determinations. This information standardises browsing capability over discrete data types. The standardised patterns of the SWE standards simplify aggregation of observation and measurement data enabling scientists to transfer disintegrated data to scientific concepts. The first two steps provide a necessary basis for the reasoning about concepts of ';pure' science, building relationship between concepts of different domains (linked-data), and identifying domain classification and vocabularies. Geoscience Australia is re-examining its marine data flows, including metadata requirements and business processes, to achieve a clearer link between

  13. An imprecise Dirichlet model for Bayesian analysis of failure data including right-censored observations

    International Nuclear Information System (INIS)

    Coolen, F.P.A.

    1997-01-01

    This paper is intended to make researchers in reliability theory aware of a recently introduced Bayesian model with imprecise prior distributions for statistical inference on failure data, that can also be considered as a robust Bayesian model. The model consists of a multinomial distribution with Dirichlet priors, making the approach basically nonparametric. New results for the model are presented, related to right-censored observations, where estimation based on this model is closely related to the product-limit estimator, which is an important statistical method to deal with reliability or survival data including right-censored observations. As for the product-limit estimator, the model considered in this paper aims at not using any information other than that provided by observed data, but our model fits into the robust Bayesian context which has the advantage that all inferences can be based on probabilities or expectations, or bounds for probabilities or expectations. The model uses a finite partition of the time-axis, and as such it is also related to life-tables

  14. MEMLS3&a: Microwave Emission Model of Layered Snowpacks adapted to include backscattering

    Directory of Open Access Journals (Sweden)

    M. Proksch

    2015-08-01

    Full Text Available The Microwave Emission Model of Layered Snowpacks (MEMLS was originally developed for microwave emissions of snowpacks in the frequency range 5–100 GHz. It is based on six-flux theory to describe radiative transfer in snow including absorption, multiple volume scattering, radiation trapping due to internal reflection and a combination of coherent and incoherent superposition of reflections between horizontal layer interfaces. Here we introduce MEMLS3&a, an extension of MEMLS, which includes a backscatter model for active microwave remote sensing of snow. The reflectivity is decomposed into diffuse and specular components. Slight undulations of the snow surface are taken into account. The treatment of like- and cross-polarization is accomplished by an empirical splitting parameter q. MEMLS3&a (as well as MEMLS is set up in a way that snow input parameters can be derived by objective measurement methods which avoid fitting procedures of the scattering efficiency of snow, required by several other models. For the validation of the model we have used a combination of active and passive measurements from the NoSREx (Nordic Snow Radar Experiment campaign in Sodankylä, Finland. We find a reasonable agreement between the measurements and simulations, subject to uncertainties in hitherto unmeasured input parameters of the backscatter model. The model is written in Matlab and the code is publicly available for download through the following website: http://www.iapmw.unibe.ch/research/projects/snowtools/memls.html.

  15. Steady-state analysis of activated sludge processes with a settler model including sludge compression.

    Science.gov (United States)

    Diehl, S; Zambrano, J; Carlsson, B

    2016-01-01

    A reduced model of a completely stirred-tank bioreactor coupled to a settling tank with recycle is analyzed in its steady states. In the reactor, the concentrations of one dominant particulate biomass and one soluble substrate component are modelled. While the biomass decay rate is assumed to be constant, growth kinetics can depend on both substrate and biomass concentrations, and optionally model substrate inhibition. Compressive and hindered settling phenomena are included using the Bürger-Diehl settler model, which consists of a partial differential equation. Steady-state solutions of this partial differential equation are obtained from an ordinary differential equation, making steady-state analysis of the entire plant difficult. A key result showing that the ordinary differential equation can be replaced with an approximate algebraic equation simplifies model analysis. This algebraic equation takes the location of the sludge-blanket during normal operation into account, allowing for the limiting flux capacity caused by compressive settling to easily be included in the steady-state mass balance equations for the entire plant system. This novel approach grants the possibility of more realistic solutions than other previously published reduced models, comprised of yet simpler settler assumptions. The steady-state concentrations, solids residence time, and the wastage flow ratio are functions of the recycle ratio. Solutions are shown for various growth kinetics; with different values of biomass decay rate, influent volumetric flow, and substrate concentration. Copyright © 2015 Elsevier Ltd. All rights reserved.

  16. The Diabetic Retinopathy Screening Workflow

    Science.gov (United States)

    Bolster, Nigel M.; Giardini, Mario E.; Bastawrous, Andrew

    2015-01-01

    Complications of diabetes mellitus, namely diabetic retinopathy and diabetic maculopathy, are the leading cause of blindness in working aged people. Sufferers can avoid blindness if identified early via retinal imaging. Systematic screening of the diabetic population has been shown to greatly reduce the prevalence and incidence of blindness within the population. Many national screening programs have digital fundus photography as their basis. In the past 5 years several techniques and adapters have been developed that allow digital fundus photography to be performed using smartphones. We review recent progress in smartphone-based fundus imaging and discuss its potential for integration into national systematic diabetic retinopathy screening programs. Some systems have produced promising initial results with respect to their agreement with reference standards. However further multisite trialling of such systems’ use within implementable screening workflows is required if an evidence base strong enough to affect policy change is to be established. If this were to occur national diabetic retinopathy screening would, for the first time, become possible in low- and middle-income settings where cost and availability of trained eye care personnel are currently key barriers to implementation. As diabetes prevalence and incidence is increasing sharply in these settings, the impact on global blindness could be profound. PMID:26596630

  17. Security aspects in teleradiology workflow

    Science.gov (United States)

    Soegner, Peter I.; Helweg, Gernot; Holzer, Heimo; zur Nedden, Dieter

    2000-05-01

    The medicolegal necessity of privacy, security and confidentiality was the aim of the attempt to develop a secure teleradiology workflow between the telepartners -- radiologist and the referring physician. To avoid the lack of dataprotection and datasecurity we introduced biometric fingerprint scanners in combination with smart cards to identify the teleradiology partners and communicated over an encrypted TCP/IP satellite link between Innsbruck and Reutte. We used an asymmetric kryptography method to guarantee authentification, integrity of the data-packages and confidentiality of the medical data. It was necessary to use a biometric feature to avoid a case of mistaken identity of persons, who wanted access to the system. Only an invariable electronical identification allowed a legal liability to the final report and only a secure dataconnection allowed the exchange of sensible medical data between different partners of Health Care Networks. In our study we selected the user friendly combination of a smart card and a biometric fingerprint technique, called SkymedTM Double Guard Secure Keyboard (Agfa-Gevaert) to confirm identities and log into the imaging workstations and the electronic patient record. We examined the interoperability of the used software with the existing platforms. Only the WIN-XX operating systems could be protected at the time of our study.

  18. Integrative Workflows for Metagenomic Analysis

    Directory of Open Access Journals (Sweden)

    Efthymios eLadoukakis

    2014-11-01

    Full Text Available The rapid evolution of all sequencing technologies, described by the term Next Generation Sequencing (NGS, have revolutionized metagenomic analysis. They constitute a combination of high-throughput analytical protocols, coupled to delicate measuring techniques, in order to potentially discover, properly assemble and map allelic sequences to the correct genomes, achieving particularly high yields for only a fraction of the cost of traditional processes (i.e. Sanger. From a bioinformatic perspective, this boils down to many gigabytes of data being generated from each single sequencing experiment, rendering the management or even the storage, critical bottlenecks with respect to the overall analytical endeavor. The enormous complexity is even more aggravated by the versatility of the processing steps available, represented by the numerous bioinformatic tools that are essential, for each analytical task, in order to fully unveil the genetic content of a metagenomic dataset. These disparate tasks range from simple, nonetheless non-trivial, quality control of raw data to exceptionally complex protein annotation procedures, requesting a high level of expertise for their proper application or the neat implementation of the whole workflow. Furthermore, a bioinformatic analysis of such scale, requires grand computational resources, imposing as the sole realistic solution, the utilization of cloud computing infrastructures. In this review article we discuss different, integrative, bioinformatic solutions available, which address the aforementioned issues, by performing a critical assessment of the available automated pipelines for data management, quality control and annotation of metagenomic data, embracing various, major sequencing technologies and applications.

  19. A General Framework for Monitoring Image Acquisition Workflow in the Radiology Environment: Timeliness for Acute Stroke CT Imaging.

    Science.gov (United States)

    Szczykutowicz, Timothy P; Brunnquell, Christina L; Avey, Gregory D; Bartels, Carrie; Belden, Daryn S; Bruce, Richard J; Field, Aaron S; Peppler, Walter W; Wasmund, Peter; Wendt, Gary

    2018-04-01

    Many facets of an image acquisition workflow leave a digital footprint, making workflow analysis amenable to an informatics-based solution. This paper describes a detailed framework for analyzing workflow and uses acute stroke response timeliness in CT as a practical demonstration. We review methods for accessing the digital footprints resulting from common technologist/device interactions. This overview lays a foundation for obtaining data for workflow analysis. We demonstrate the method by analyzing CT imaging efficiency in the setting of acute stroke. We successfully used digital footprints of CT technologists to analyze their workflow. We presented an overview of other digital footprints including but not limited to contrast administration, patient positioning, billing, reformat creation, and scheduling. A framework for analyzing image acquisition workflow was presented. This framework is transferable to any modality, as the key steps of image acquisition, image reconstruction, image post processing, and image transfer to PACS are common to any imaging modality in diagnostic radiology.

  20. An open source approach to enable the reproducibility of scientific workflows in the ocean sciences

    Science.gov (United States)

    Di Stefano, M.; Fox, P. A.; West, P.; Hare, J. A.; Maffei, A. R.

    2013-12-01

    Every scientist should be able to rerun data analyses conducted by his or her team and regenerate the figures in a paper. However, all too often the correct version of a script goes missing, or the original raw data is filtered by hand and the filtering process is undocumented, or there is lack of collaboration and communication among scientists working in a team. Here we present 3 different use cases in ocean sciences in which end-to-end workflows are tracked. The main tool that is deployed to address these use cases is based on a web application (IPython Notebook) that provides the ability to work on very diverse and heterogeneous data and information sources, providing an effective way to share the and track changes to source code used to generate data products and associated metadata, as well as to track the overall workflow provenance to allow versioned reproducibility of a data product. Use cases selected for this work are: 1) A partial reproduction of the Ecosystem Status Report (ESR) for the Northeast U.S. Continental Shelf Large Marine Ecosystem. Our goal with this use case is to enable not just the traceability but also the reproducibility of this biannual report, keeping track of all the processes behind the generation and validation of time-series and spatial data and information products. An end-to-end workflow with code versioning is developed so that indicators in the report may be traced back to the source datasets. 2) Realtime generation of web pages to be able to visualize one of the environmental indicators from the Ecosystem Advisory for the Northeast Shelf Large Marine Ecosystem web site. 3) Data and visualization integration for ocean climate forecasting. In this use case, we focus on a workflow to describe how to provide access to online data sources in the NetCDF format and other model data, and make use of multicore processing to generate video animation from time series of gridded data. For each use case we show how complete workflows

  1. TS Fuzzy Model-Based Controller Design for a Class of Nonlinear Systems Including Nonsmooth Functions

    DEFF Research Database (Denmark)

    Vafamand, Navid; Asemani, Mohammad Hassan; Khayatiyan, Alireza

    2018-01-01

    criterion, new robust controller design conditions in terms of linear matrix inequalities are derived. Three practical case studies, electric power steering system, a helicopter model and servo-mechanical system, are presented to demonstrate the importance of such class of nonlinear systems comprising......This paper proposes a novel robust controller design for a class of nonlinear systems including hard nonlinearity functions. The proposed approach is based on Takagi-Sugeno (TS) fuzzy modeling, nonquadratic Lyapunov function, and nonparallel distributed compensation scheme. In this paper, a novel...... TS modeling of the nonlinear dynamics with signum functions is proposed. This model can exactly represent the original nonlinear system with hard nonlinearity while the discontinuous signum functions are not approximated. Based on the bounded-input-bounded-output stability scheme and L₁ performance...

  2. A roller chain drive model including contact with guide-bars

    DEFF Research Database (Denmark)

    Pedersen, Sine Leergaard; Hansen, John Michael; Ambrósio, J. A. C.

    2004-01-01

    as continuous force. The model of the roller-chain drive now proposed departs from an earlier model where two contact/impact methods are proposed to describe the contact between the rollers of the chain and the teeth of the sprockets. These different formulations are based on unilateral constraints....... In the continuous force method the roller-sprocket contact, is represented by forces applied on each seated roller and in the respective sprocket teeth. These forces are functions of the pseudo penetrations between roller and sprocket, impacting velocities and a restitution coefficient. In the continuous force......A model of a roller chain drive is developed and applied to the simulation and analysis of roller chain drives of large marine diesel engines. The model includes the impact with guide-bars that are the motion delimiter components on the chain strands between the sprockets. The main components...

  3. Prospects for genetically modified non-human primate models, including the common marmoset.

    Science.gov (United States)

    Sasaki, Erika

    2015-04-01

    Genetically modified mice have contributed much to studies in the life sciences. In some research fields, however, mouse models are insufficient for analyzing the molecular mechanisms of pathology or as disease models. Often, genetically modified non-human primate (NHP) models are desired, as they are more similar to human physiology, morphology, and anatomy. Recent progress in studies of the reproductive biology in NHPs has enabled the introduction of exogenous genes into NHP genomes or the alteration of endogenous NHP genes. This review summarizes recent progress in the production of genetically modified NHPs, including the common marmoset, and future perspectives for realizing genetically modified NHP models for use in life sciences research. Copyright © 2015 Elsevier Ireland Ltd and the Japan Neuroscience Society. All rights reserved.

  4. Improving weather predictability by including land-surface model parameter uncertainty

    Science.gov (United States)

    Orth, Rene; Dutra, Emanuel; Pappenberger, Florian

    2016-04-01

    The land surface forms an important component of Earth system models and interacts nonlinearly with other parts such as ocean and atmosphere. To capture the complex and heterogenous hydrology of the land surface, land surface models include a large number of parameters impacting the coupling to other components of the Earth system model. Focusing on ECMWF's land-surface model HTESSEL we present in this study a comprehensive parameter sensitivity evaluation using multiple observational datasets in Europe. We select 6 poorly constrained effective parameters (surface runoff effective depth, skin conductivity, minimum stomatal resistance, maximum interception, soil moisture stress function shape, total soil depth) and explore their sensitivity to model outputs such as soil moisture, evapotranspiration and runoff using uncoupled simulations and coupled seasonal forecasts. Additionally we investigate the possibility to construct ensembles from the multiple land surface parameters. In the uncoupled runs we find that minimum stomatal resistance and total soil depth have the most influence on model performance. Forecast skill scores are moreover sensitive to the same parameters as HTESSEL performance in the uncoupled analysis. We demonstrate the robustness of our findings by comparing multiple best performing parameter sets and multiple randomly chosen parameter sets. We find better temperature and precipitation forecast skill with the best-performing parameter perturbations demonstrating representativeness of model performance across uncoupled (and hence less computationally demanding) and coupled settings. Finally, we construct ensemble forecasts from ensemble members derived with different best-performing parameterizations of HTESSEL. This incorporation of parameter uncertainty in the ensemble generation yields an increase in forecast skill, even beyond the skill of the default system. Orth, R., E. Dutra, and F. Pappenberger, 2016: Improving weather predictability by

  5. RABIX: AN OPEN-SOURCE WORKFLOW EXECUTOR SUPPORTING RECOMPUTABILITY AND INTEROPERABILITY OF WORKFLOW DESCRIPTIONS.

    Science.gov (United States)

    Kaushik, Gaurav; Ivkovic, Sinisa; Simonovic, Janko; Tijanic, Nebojsa; Davis-Dusenbery, Brandi; Kural, Deniz

    2017-01-01

    As biomedical data has become increasingly easy to generate in large quantities, the methods used to analyze it have proliferated rapidly. Reproducible and reusable methods are required to learn from large volumes of data reliably. To address this issue, numerous groups have developed workflow specifications or execution engines, which provide a framework with which to perform a sequence of analyses. One such specification is the Common Workflow Language, an emerging standard which provides a robust and flexible framework for describing data analysis tools and workflows. In addition, reproducibility can be furthered by executors or workflow engines which interpret the specification and enable additional features, such as error logging, file organization, optim1izations to computation and job scheduling, and allow for easy computing on large volumes of data. To this end, we have developed the Rabix Executor, an open-source workflow engine for the purposes of improving reproducibility through reusability and interoperability of workflow descriptions.

  6. Global Reference Atmospheric Models, Including Thermospheres, for Mars, Venus and Earth

    Science.gov (United States)

    Justh, Hilary L.; Justus, C. G.; Keller, Vernon W.

    2006-01-01

    This document is the viewgraph slides of the presentation. Marshall Space Flight Center's Natural Environments Branch has developed Global Reference Atmospheric Models (GRAMs) for Mars, Venus, Earth, and other solar system destinations. Mars-GRAM has been widely used for engineering applications including systems design, performance analysis, and operations planning for aerobraking, entry descent and landing, and aerocapture. Preliminary results are presented, comparing Mars-GRAM with measurements from Mars Reconnaissance Orbiter (MRO) during its aerobraking in Mars thermosphere. Venus-GRAM is based on the Committee on Space Research (COSPAR) Venus International Reference Atmosphere (VIRA), and is suitable for similar engineering applications in the thermosphere or other altitude regions of the atmosphere of Venus. Until recently, the thermosphere in Earth-GRAM has been represented by the Marshall Engineering Thermosphere (MET) model. Earth-GRAM has recently been revised. In addition to including an updated version of MET, it now includes an option to use the Naval Research Laboratory Mass Spectrometer Incoherent Scatter Radar Extended Model (NRLMSISE-00) as an alternate thermospheric model. Some characteristics and results from Venus-GRAM and Earth-GRAM thermospheres are also presented.

  7. A numerical model including PID control of a multizone crystal growth furnace

    Science.gov (United States)

    Panzarella, Charles H.; Kassemi, Mohammad

    1992-01-01

    This paper presents a 2D axisymmetric combined conduction and radiation model of a multizone crystal growth furnace. The model is based on a programmable multizone furnace (PMZF) designed and built at NASA Lewis Research Center for growing high quality semiconductor crystals. A novel feature of this model is a control algorithm which automatically adjusts the power in any number of independently controlled heaters to establish the desired crystal temperatures in the furnace model. The control algorithm eliminates the need for numerous trial and error runs previously required to obtain the same results. The finite element code, FIDAP, used to develop the furnace model, was modified to directly incorporate the control algorithm. This algorithm, which presently uses PID control, and the associated heat transfer model are briefly discussed. Together, they have been used to predict the heater power distributions for a variety of furnace configurations and desired temperature profiles. Examples are included to demonstrate the effectiveness of the PID controlled model in establishing isothermal, Bridgman, and other complicated temperature profies in the sample. Finally, an example is given to show how the algorithm can be used to change the desired profile with time according to a prescribed temperature-time evolution.

  8. A New Circuit Model for Spin-Torque Oscillator Including Perpendicular Torque of Magnetic Tunnel Junction

    Directory of Open Access Journals (Sweden)

    Hyein Lim

    2013-01-01

    Full Text Available Spin-torque oscillator (STO is a promising new technology for the future RF oscillators, which is based on the spin-transfer torque (STT effect in magnetic multilayered nanostructure. It is expected to provide a larger tunability, smaller size, lower power consumption, and higher level of integration than the semiconductor-based oscillators. In our previous work, a circuit-level model of the giant magnetoresistance (GMR STO was proposed. In this paper, we present a physics-based circuit-level model of the magnetic tunnel junction (MTJ-based STO. MTJ-STO model includes the effect of perpendicular torque that has been ignored in the GMR-STO model. The variations of three major characteristics, generation frequency, mean oscillation power, and generation linewidth of an MTJ-STO with respect to the amount of perpendicular torque, are investigated, and the results are applied to our model. The operation of the model was verified by HSPICE simulation, and the results show an excellent agreement with the experimental data. The results also prove that a full circuit-level simulation with MJT-STO devices can be made with our proposed model.

  9. Workflow Dynamics and the Imaging Value Chain: Quantifying the Effect of Designating a Nonimage-Interpretive Task Workflow.

    Science.gov (United States)

    Lee, Matthew H; Schemmel, Andrew J; Pooler, B Dustin; Hanley, Taylor; Kennedy, Tabassum A; Field, Aaron S; Wiegmann, Douglas; Yu, John-Paul J

    To assess the impact of separate non-image interpretive task and image-interpretive task workflows in an academic neuroradiology practice. A prospective, randomized, observational investigation of a centralized academic neuroradiology reading room was performed. The primary reading room fellow was observed over a one-month period using a time-and-motion methodology, recording frequency and duration of tasks performed. Tasks were categorized into separate image interpretive and non-image interpretive workflows. Post-intervention observation of the primary fellow was repeated following the implementation of a consult assistant responsible for non-image interpretive tasks. Pre- and post-intervention data were compared. Following separation of image-interpretive and non-image interpretive workflows, time spent on image-interpretive tasks by the primary fellow increased from 53.8% to 73.2% while non-image interpretive tasks decreased from 20.4% to 4.4%. Mean time duration of image interpretation nearly doubled, from 05:44 to 11:01 (p = 0.002). Decreases in specific non-image interpretive tasks, including phone calls/paging (2.86/hr versus 0.80/hr), in-room consultations (1.36/hr versus 0.80/hr), and protocoling (0.99/hr versus 0.10/hr), were observed. The consult assistant experienced 29.4 task switching events per hour. Rates of specific non-image interpretive tasks for the CA were 6.41/hr for phone calls/paging, 3.60/hr for in-room consultations, and 3.83/hr for protocoling. Separating responsibilities into NIT and IIT workflows substantially increased image interpretation time and decreased TSEs for the primary fellow. Consolidation of NITs into a separate workflow may allow for more efficient task completion. Copyright © 2017 Elsevier Inc. All rights reserved.

  10. Evolutionary optimization of production materials workflow processes

    DEFF Research Database (Denmark)

    Herbert, Luke Thomas; Hansen, Zaza Nadja Lee; Jacobsen, Peter

    2014-01-01

    We present an evolutionary optimisation technique for stochastic production processes, which is able to find improved production materials workflow processes with respect to arbitrary combinations of numerical quantities associated with the production process. Working from a core fragment...

  11. A Multilevel Secure Workflow Management System

    National Research Council Canada - National Science Library

    Kang, Myong H; Froscher, Judith N; Sheth, Amit P; Kochut, Krys J; Miller, John A

    1999-01-01

    The Department of Defense (DoD) needs multilevel secure (MLS) workflow management systems to enable globally distributed users and applications to cooperate across classification levels to achieve mission critical goals...

  12. Workflow Based Software Development Environment, Phase II

    Data.gov (United States)

    National Aeronautics and Space Administration — The goal of this proposed research is to investigate and develop a workflow based tool, the Software Developers Assistant, to facilitate the collaboration between...

  13. Workflow Based Software Development Environment Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The goal of this proposed research is to investigate and develop a workflow based tool, the Software Developers Assistant, to facilitate the collaboration between...

  14. Workflow Based Software Development Environment, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — The goal of this proposed research is to investigate and develop a workflow based tool, the Software Developers Assistant, to facilitate the collaboration between...

  15. Structuring clinical workflows for diabetes care: an overview of the OntoHealth approach.

    Science.gov (United States)

    Schweitzer, M; Lasierra, N; Oberbichler, S; Toma, I; Fensel, A; Hoerbst, A

    2014-01-01

    Electronic health records (EHRs) play an important role in the treatment of chronic diseases such as diabetes mellitus. Although the interoperability and selected functionality of EHRs are already addressed by a number of standards and best practices, such as IHE or HL7, the majority of these systems are still monolithic from a user-functionality perspective. The purpose of the OntoHealth project is to foster a functionally flexible, standards-based use of EHRs to support clinical routine task execution by means of workflow patterns and to shift the present EHR usage to a more comprehensive integration concerning complete clinical workflows. The goal of this paper is, first, to introduce the basic architecture of the proposed OntoHealth project and, second, to present selected functional needs and a functional categorization regarding workflow-based interactions with EHRs in the domain of diabetes. A systematic literature review regarding attributes of workflows in the domain of diabetes was conducted. Eligible references were gathered and analyzed using a qualitative content analysis. Subsequently, a functional workflow categorization was derived from diabetes-specific raw data together with existing general workflow patterns. This paper presents the design of the architecture as well as a categorization model which makes it possible to describe the components or building blocks within clinical workflows. The results of our study lead us to identify basic building blocks, named as actions, decisions, and data elements, which allow the composition of clinical workflows within five identified contexts. The categorization model allows for a description of the components or building blocks of clinical workflows from a functional view.

  16. Including Finite Surface Span Effects in Empirical Jet-Surface Interaction Noise Models

    Science.gov (United States)

    Brown, Clifford A.

    2016-01-01

    The effect of finite span on the jet-surface interaction noise source and the jet mixing noise shielding and reflection effects is considered using recently acquired experimental data. First, the experimental setup and resulting data are presented with particular attention to the role of surface span on far-field noise. These effects are then included in existing empirical models that have previously assumed that all surfaces are semi-infinite. This extended abstract briefly describes the experimental setup and data leaving the empirical modeling aspects for the final paper.

  17. Measuring Semantic and Structural Information for Data Oriented Workflow Retrieval with Cost Constraints

    Directory of Open Access Journals (Sweden)

    Yinglong Ma

    2014-01-01

    Full Text Available The reuse of data oriented workflows (DOWs can reduce the cost of workflow system development and control the risk of project failure and therefore is crucial for accelerating the automation of business processes. Reusing workflows can be achieved by measuring the similarity among candidate workflows and selecting the workflow satisfying requirements of users from them. However, due to DOWs being often developed based on an open, distributed, and heterogeneous environment, different users often can impose diverse cost constraints on data oriented workflows. This makes the reuse of DOWs challenging. There is no clear solution for retrieving DOWs with cost constraints. In this paper, we present a novel graph based model of DOWs with cost constraints, called constrained data oriented workflow (CDW, which can express cost constraints that users are often concerned about. An approach is proposed for retrieving CDWs, which seamlessly combines semantic and structural information of CDWs. A distance measure based on matrix theory is adopted to seamlessly combine semantic and structural similarities of CDWs for selecting and reusing them. Finally, the related experiments are made to show the effectiveness and efficiency of our approach.

  18. Modeling of Temperature-Dependent Noise in Silicon Nanowire FETs including Self-Heating Effects

    Directory of Open Access Journals (Sweden)

    P. Anandan

    2014-01-01

    Full Text Available Silicon nanowires are leading the CMOS era towards the downsizing limit and its nature will be effectively suppress the short channel effects. Accurate modeling of thermal noise in nanowires is crucial for RF applications of nano-CMOS emerging technologies. In this work, a perfect temperature-dependent model for silicon nanowires including the self-heating effects has been derived and its effects on device parameters have been observed. The power spectral density as a function of thermal resistance shows significant improvement as the channel length decreases. The effects of thermal noise including self-heating of the device are explored. Moreover, significant reduction in noise with respect to channel thermal resistance, gate length, and biasing is analyzed.

  19. Producing high-accuracy lattice models from protein atomic coordinates including side chains.

    Science.gov (United States)

    Mann, Martin; Saunders, Rhodri; Smith, Cameron; Backofen, Rolf; Deane, Charlotte M

    2012-01-01

    Lattice models are a common abstraction used in the study of protein structure, folding, and refinement. They are advantageous because the discretisation of space can make extensive protein evaluations computationally feasible. Various approaches to the protein chain lattice fitting problem have been suggested but only a single backbone-only tool is available currently. We introduce LatFit, a new tool to produce high-accuracy lattice protein models. It generates both backbone-only and backbone-side-chain models in any user defined lattice. LatFit implements a new distance RMSD-optimisation fitting procedure in addition to the known coordinate RMSD method. We tested LatFit's accuracy and speed using a large nonredundant set of high resolution proteins (SCOP database) on three commonly used lattices: 3D cubic, face-centred cubic, and knight's walk. Fitting speed compared favourably to other methods and both backbone-only and backbone-side-chain models show low deviation from the original data (~1.5 Å RMSD in the FCC lattice). To our knowledge this represents the first comprehensive study of lattice quality for on-lattice protein models including side chains while LatFit is the only available tool for such models.

  20. A High-Rate, Single-Crystal Model including Phase Transformations, Plastic Slip, and Twinning

    Energy Technology Data Exchange (ETDEWEB)

    Addessio, Francis L. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Theoretical Division; Bronkhorst, Curt Allan [Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Theoretical Division; Bolme, Cynthia Anne [Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Explosive Science and Shock Physics Division; Brown, Donald William [Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Materials Science and Technology Division; Cerreta, Ellen Kathleen [Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Materials Science and Technology Division; Lebensohn, Ricardo A. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Materials Science and Technology Division; Lookman, Turab [Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Theoretical Division; Luscher, Darby Jon [Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Theoretical Division; Mayeur, Jason Rhea [Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Theoretical Division; Morrow, Benjamin M. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Materials Science and Technology Division; Rigg, Paulo A. [Washington State Univ., Pullman, WA (United States). Dept. of Physics. Inst. for Shock Physics

    2016-08-09

    An anisotropic, rate-­dependent, single-­crystal approach for modeling materials under the conditions of high strain rates and pressures is provided. The model includes the effects of large deformations, nonlinear elasticity, phase transformations, and plastic slip and twinning. It is envisioned that the model may be used to examine these coupled effects on the local deformation of materials that are subjected to ballistic impact or explosive loading. The model is formulated using a multiplicative decomposition of the deformation gradient. A plate impact experiment on a multi-­crystal sample of titanium was conducted. The particle velocities at the back surface of three crystal orientations relative to the direction of impact were measured. Molecular dynamics simulations were conducted to investigate the details of the high-­rate deformation and pursue issues related to the phase transformation for titanium. Simulations using the single crystal model were conducted and compared to the high-­rate experimental data for the impact loaded single crystals. The model was found to capture the features of the experiments.

  1. Modeling and analysis of the affinity filtration process, including broth feeding, washing, and elution steps.

    Science.gov (United States)

    He, L Z; Dong, X Y; Sun, Y

    1998-01-01

    Affinity filtration is a developing protein purification technique that combines the high selectivity of affinity chromatography and the high processing speed of membrane filtration. In this work a lumped kinetic model was developed to describe the whole affinity filtration process, including broth feeding, contaminant washing, and elution steps. Affinity filtration experiments were conducted to evaluate the model using bovine serum albumin as a model protein and a highly substituted Blue Sepharose as an affinity adsorbent. The model with nonadjustable parameters agreed fairly to the experimental results. Thus, the performance of the affinity filtration in processing a crude broth containing contaminant proteins was analyzed by computer simulations using the lumped model. The simulation results show that there is an optimal protein loading for obtaining the maximum recovery yield of the desired protein with a constant purity at each operating condition. The concentration of a crude broth is beneficial in increasing the recovery yield of the desired protein. Using a constant amount of the affinity adsorbent, the recovery yield can be enhanced by decreasing the solution volume in the stirred tank due to the increase of the adsorbent weight fraction. It was found that the lumped kinetic model was simple and useful in analyzing the whole affinity filtration process.

  2. Multilevel Workflow System in the ATLAS Experiment

    CERN Document Server

    Borodin, M; The ATLAS collaboration; De, K; Golubkov, D; Klimentov, A; Maeno, T; Vaniachine, A

    2014-01-01

    The ATLAS experiment is scaling up Big Data processing for the next LHC run using a multilevel workflow system comprised of many layers. In Big Data processing ATLAS deals with datasets, not individual files. Similarly a task (comprised of many jobs) has become a unit of the ATLAS workflow in distributed computing, with about 0.8M tasks processed per year. In order to manage the diversity of LHC physics (exceeding 35K physics samples per year), the individual data processing tasks are organized into workflows. For example, the Monte Carlo workflow is composed of many steps: generate or configure hard-processes, hadronize signal and minimum-bias (pileup) events, simulate energy deposition in the ATLAS detector, digitize electronics response, simulate triggers, reconstruct data, convert the reconstructed data into ROOT ntuples for physics analysis, etc. Outputs are merged and/or filtered as necessary to optimize the chain. The bi-level workflow manager - ProdSys2 - generates actual workflow tasks and their jobs...

  3. Multilevel Workflow System in the ATLAS Experiment

    CERN Document Server

    Borodin, M; The ATLAS collaboration; Golubkov, D; Klimentov, A; Maeno, T; Vaniachine, A

    2015-01-01

    The ATLAS experiment is scaling up Big Data processing for the next LHC run using a multilevel workflow system comprised of many layers. In Big Data processing ATLAS deals with datasets, not individual files. Similarly a task (comprised of many jobs) has become a unit of the ATLAS workflow in distributed computing, with about 0.8M tasks processed per year. In order to manage the diversity of LHC physics (exceeding 35K physics samples per year), the individual data processing tasks are organized into workflows. For example, the Monte Carlo workflow is composed of many steps: generate or configure hard-processes, hadronize signal and minimum-bias (pileup) events, simulate energy deposition in the ATLAS detector, digitize electronics response, simulate triggers, reconstruct data, convert the reconstructed data into ROOT ntuples for physics analysis, etc. Outputs are merged and/or filtered as necessary to optimize the chain. The bi-level workflow manager - ProdSys2 - generates actual workflow tasks and their jobs...

  4. Automation of Network-Based Scientific Workflows

    Energy Technology Data Exchange (ETDEWEB)

    Altintas, I. [University of California, La Jolla; Barreto, R. [Oak Ridge National Laboratory (ORNL); Blondin, J. M. [North Carolina State University; Cheng, Z. [North Carolina State University; Critchlow, T. [Lawrence Livermore National Laboratory (LLNL); Khan, A. [University of Utah; Klasky, Scott A [ORNL; Ligon, J. [North Carolina State University; Ludaescher, B. [University of California, Davis; Mouallem, P. A. [North Carolina State University; Parker, S. [University of Utah; Podhorszki, Norbert [University of California, Davis; Shoshani, A. [Lawrence Berkeley National Laboratory (LBNL); Silva, C. [University of Utah; Vouk, M. A. [North Carolina State University

    2007-01-01

    Comprehensive, end-to-end, data and workflow management solutions are needed to handle the increasing complexity of processes and data volumes associated with modern distributed scientific problem solving, such as ultra-scale simulations and high-throughput experiments. The key to the solution is an integrated network-based framework that is functional, dependable, fault-tolerant, and supports data and process provenance. Such a framework needs to make development and use of application workflows dramatically easier so that scientists' efforts can shift away from data management and utility software development to scientific research and discovery An integrated view of these activities is provided by the notion of scientific workflows - a series of structured activities and computations that arise in scientific problem-solving. An information technology framework that supports scientific workflows is the Ptolemy II based environment called Kepler. This paper discusses the issues associated with practical automation of scientific processes and workflows and illustrates this with workflows developed using the Kepler framework and tools.

  5. Model for safety reports including descriptive examples; Mall foer saekerhetsrapporter med beskrivande exempel

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-12-01

    Several safety reports will be produced in the process of planning and constructing the system for disposal of high-level radioactive waste in Sweden. The present report gives a model, with detailed examples, of how these reports should be organized and what steps they should include. In the near future safety reports will deal with the encapsulation plant and the repository. Later reports will treat operation of the handling systems and the repository.

  6. Experiences and lessons learned from creating a generalized workflow for data publication of field campaign datasets

    Science.gov (United States)

    Santhana Vannan, S. K.; Ramachandran, R.; Deb, D.; Beaty, T.; Wright, D.

    2017-12-01

    This paper summarizes the workflow challenges of curating and publishing data produced from disparate data sources and provides a generalized workflow solution to efficiently archive data generated by researchers. The Oak Ridge National Laboratory Distributed Active Archive Center (ORNL DAAC) for biogeochemical dynamics and the Global Hydrology Resource Center (GHRC) DAAC have been collaborating on the development of a generalized workflow solution to efficiently manage the data publication process. The generalized workflow presented here are built on lessons learned from implementations of the workflow system. Data publication consists of the following steps: Accepting the data package from the data providers, ensuring the full integrity of the data files. Identifying and addressing data quality issues Assembling standardized, detailed metadata and documentation, including file level details, processing methodology, and characteristics of data files Setting up data access mechanisms Setup of the data in data tools and services for improved data dissemination and user experience Registering the dataset in online search and discovery catalogues Preserving the data location through Digital Object Identifiers (DOI) We will describe the steps taken to automate, and realize efficiencies to the above process. The goals of the workflow system are to reduce the time taken to publish a dataset, to increase the quality of documentation and metadata, and to track individual datasets through the data curation process. Utilities developed to achieve these goal will be described. We will also share metrics driven value of the workflow system and discuss the future steps towards creation of a common software framework.

  7. Collisional-radiative model including recombination processes for W27+ ion★

    Science.gov (United States)

    Murakami, Izumi; Sasaki, Akira; Kato, Daiji; Koike, Fumihiro

    2017-10-01

    We have constructed a collisional-radiative (CR) model for W27+ ions including 226 configurations with n ≤ 9 and ł ≤ 5 for spectroscopic diagnostics. We newly include recombination processes in the model and this is the first result of extreme ultraviolet spectrum calculated for recombining plasma component. Calculated spectra in 40-70 Å range in ionizing and recombining plasma components show similar 3 strong lines and 1 line weak in recombining plasma component at 45-50 Å and many weak lines at 50-65 Å for both components. Recombination processes do not contribute much to the spectrum at around 60 Å for W27+ ion. Dielectronic satellite lines are also minor contribution to the spectrum of recombining plasma component. Dielectronic recombination (DR) rate coefficient from W28+ to W27+ ions is also calculated with the same atomic data in the CR model. We found that larger set of energy levels including many autoionizing states gave larger DR rate coefficients but our rate agree within factor 6 with other works at electron temperature around 1 keV in which W27+ and W28+ ions are usually observed in plasmas. Contribution to the Topical Issue "Atomic and Molecular Data and their Applications", edited by Gordon W.F. Drake, Jung-Sik Yoon, Daiji Kato, and Grzegorz Karwasz.

  8. A 3D model of the oculomotor plant including the pulley system

    Science.gov (United States)

    Viegener, A.; Armentano, R. L.

    2007-11-01

    Early models of the oculomotor plant only considered the eye globes and the muscles that move them. Recently, connective tissue structures have been found enveloping the extraocular muscles (EOMs) and firmly anchored to the orbital wall. These structures act as pulleys; they determine the functional origin of the EOMs and, in consequence, their effective pulling direction. A three dimensional model of the oculomotor plant, including pulleys, has been developed and simulations in Simulink were performed during saccadic eye movements. Listing's law was implemented based on the supposition that there exists an eye orientation related signal. The inclusion of the pulleys in the model makes this assumption plausible and simplifies the problem of the plant noncommutativity.

  9. Double-gate junctionless transistor model including short-channel effects

    International Nuclear Information System (INIS)

    Paz, B C; Pavanello, M A; Ávila-Herrera, F; Cerdeira, A

    2015-01-01

    This work presents a physically based model for double-gate junctionless transistors (JLTs), continuous in all operation regimes. To describe short-channel transistors, short-channel effects (SCEs), such as increase of the channel potential due to drain bias, carrier velocity saturation and mobility degradation due to vertical and longitudinal electric fields, are included in a previous model developed for long-channel double-gate JLTs. To validate the model, an analysis is made by using three-dimensional numerical simulations performed in a Sentaurus Device Simulator from Synopsys. Different doping concentrations, channel widths and channel lengths are considered in this work. Besides that, the series resistance influence is numerically included and validated for a wide range of source and drain extensions. In order to check if the SCEs are appropriately described, besides drain current, transconductance and output conductance characteristics, the following parameters are analyzed to demonstrate the good agreement between model and simulation and the SCEs occurrence in this technology: threshold voltage (V TH ), subthreshold slope (S) and drain induced barrier lowering. (paper)

  10. Modeling the distribution of ammonia across Europe including bi-directional surface–atmosphere exchange

    Directory of Open Access Journals (Sweden)

    R. J. Wichink Kruit

    2012-12-01

    Full Text Available A large shortcoming of current chemistry transport models (CTM for simulating the fate of ammonia in the atmosphere is the lack of a description of the bi-directional surface–atmosphere exchange. In this paper, results of an update of the surface–atmosphere exchange module DEPAC, i.e. DEPosition of Acidifying Compounds, in the chemistry transport model LOTOS-EUROS are discussed. It is shown that with the new description, which includes bi-directional surface–atmosphere exchange, the modeled ammonia concentrations increase almost everywhere, in particular in agricultural source areas. The reason is that by using a compensation point the ammonia lifetime and transport distance is increased. As a consequence, deposition of ammonia and ammonium decreases in agricultural source areas, while it increases in large nature areas and remote regions especially in southern Scandinavia. The inclusion of a compensation point for water reduces the dry deposition over sea and allows reproducing the observed marine background concentrations at coastal locations to a better extent. A comparison with measurements shows that the model results better represent the measured ammonia concentrations. The concentrations in nature areas are slightly overestimated, while the concentrations in agricultural source areas are still underestimated. Although the introduction of the compensation point improves the model performance, the modeling of ammonia remains challenging. Important aspects are emission patterns in space and time as well as a proper approach to deal with the high concentration gradients in relation to model resolution. In short, the inclusion of a bi-directional surface–atmosphere exchange is a significant step forward for modeling ammonia.

  11. a Workflow for UAV's Integration Into a Geodesign Platform

    Science.gov (United States)

    Anca, P.; Calugaru, A.; Alixandroae, I.; Nazarie, R.

    2016-06-01

    This paper presents a workflow for the development of various Geodesign scenarios. The subject is important in the context of identifying patterns and designing solutions for a Smart City with optimized public transportation, efficient buildings, efficient utilities, recreational facilities a.s.o.. The workflow describes the procedures starting with acquiring data in the field, data processing, orthophoto generation, DTM generation, integration into a GIS platform and analyzing for a better support for Geodesign. Esri's City Engine is used mostly for 3D modeling capabilities that enable the user to obtain 3D realistic models. The workflow uses as inputs information extracted from images acquired using UAVs technologies, namely eBee, existing 2D GIS geodatabases, and a set of CGA rules. The method that we used further, is called procedural modeling, and uses rules in order to extrude buildings, the street network, parcel zoning and side details, based on the initial attributes from the geodatabase. The resulted products are various scenarios for redesigning, for analyzing new exploitation sites. Finally, these scenarios can be published as interactive web scenes for internal, groups or pubic consultation. In this way, problems like the impact of new constructions being build, re-arranging green spaces or changing routes for public transportation, etc. are revealed through impact and visibility analysis or shadowing analysis and are brought to the citizen's attention. This leads to better decisions.

  12. Including policy and management in socio-hydrology models: initial conceptualizations

    Science.gov (United States)

    Hermans, Leon; Korbee, Dorien

    2017-04-01

    Socio-hydrology studies the interactions in coupled human-water systems. So far, the use of dynamic models that capture the direct feedback between societal and hydrological systems has been dominant. What has not yet been included with any particular emphasis, is the policy or management layer, which is a central element in for instance integrated water resources management (IWRM) or adaptive delta management (ADM). Studying the direct interactions between human-water systems generates knowledges that eventually helps influence these interactions in ways that may ensure better outcomes - for society and for the health and sustainability of water systems. This influence sometimes occurs through spontaneous emergence, uncoordinated by societal agents - private sector, citizens, consumers, water users. However, the term 'management' in IWRM and ADM also implies an additional coordinated attempt through various public actors. This contribution is a call to include the policy and management dimension more prominently into the research focus of the socio-hydrology field, and offers first conceptual variables that should be considered in attempts to include this policy or management layer in socio-hydrology models. This is done by drawing on existing frameworks to study policy processes throughout both planning and implementation phases. These include frameworks such as the advocacy coalition framework, collective learning and policy arrangements, which all emphasis longer-term dynamics and feedbacks between actor coalitions in strategic planning and implementation processes. A case about longter-term dynamics in the management of the Haringvliet in the Netherlands is used to illustrate the paper.

  13. A framework for service enterprise workflow simulation with multi-agents cooperation

    Science.gov (United States)

    Tan, Wenan; Xu, Wei; Yang, Fujun; Xu, Lida; Jiang, Chuanqun

    2013-11-01

    Process dynamic modelling for service business is the key technique for Service-Oriented information systems and service business management, and the workflow model of business processes is the core part of service systems. Service business workflow simulation is the prevalent approach to be used for analysis of service business process dynamically. Generic method for service business workflow simulation is based on the discrete event queuing theory, which is lack of flexibility and scalability. In this paper, we propose a service workflow-oriented framework for the process simulation of service businesses using multi-agent cooperation to address the above issues. Social rationality of agent is introduced into the proposed framework. Adopting rationality as one social factor for decision-making strategies, a flexible scheduling for activity instances has been implemented. A system prototype has been developed to validate the proposed simulation framework through a business case study.

  14. Modelling of Water Cooled Fuel Including Design Basis and Severe Accidents. Proceedings of a Technical Meeting

    International Nuclear Information System (INIS)

    2015-11-01

    The demands on nuclear fuel have recently been increasing, and include transient regimes, higher discharge burnup and longer fuel cycles. This has resulted in an increase of loads on fuel and core internals. In order to satisfy these demands while ensuring compliance with safety criteria, new national and international programmes have been launched and advanced modelling codes are being developed. The Fukushima Daiichi accident has particularly demonstrated the need for adequate analysis of all aspects of fuel performance to prevent a failure and also to predict fuel behaviour were an accident to occur.This publication presents the Proceedings of the Technical Meeting on Modelling of Water Cooled Fuel Including Design Basis and Severe Accidents, which was hosted by the Nuclear Power Institute of China (NPIC) in Chengdu, China, following the recommendation made in 2013 at the IAEA Technical Working Group on Fuel Performance and Technology. This recommendation was in agreement with IAEA mid-term initiatives, linked to the post-Fukushima IAEA Nuclear Safety Action Plan, as well as the forthcoming Coordinated Research Project (CRP) on Fuel Modelling in Accident Conditions. At the technical meeting in Chengdu, major areas and physical phenomena, as well as types of code and experiment to be studied and used in the CRP, were discussed. The technical meeting provided a forum for international experts to review the state of the art of code development for modelling fuel performance of nuclear fuel for water cooled reactors with regard to steady state and transient conditions, and for design basis and early phases of severe accidents, including experimental support for code validation. A round table discussion focused on the needs and perspectives on fuel modelling in accident conditions. This meeting was the ninth in a series of IAEA meetings, which reflects Member States’ continuing interest in nuclear fuel issues. The previous meetings were held in 1980 (jointly with

  15. Health Promotion Behavior of Chinese International Students in Korea Including Acculturation Factors: A Structural Equation Model.

    Science.gov (United States)

    Kim, Sun Jung; Yoo, Il Young

    2016-03-01

    The purpose of this study was to explain the health promotion behavior of Chinese international students in Korea using a structural equation model including acculturation factors. A survey using self-administered questionnaires was employed. Data were collected from 272 Chinese students who have resided in Korea for longer than 6 months. The data were analyzed using structural equation modeling. The p value of final model is .31. The fitness parameters of the final model such as goodness of fit index, adjusted goodness of fit index, normed fit index, non-normed fit index, and comparative fit index were more than .95. Root mean square of residual and root mean square error of approximation also met the criteria. Self-esteem, perceived health status, acculturative stress and acculturation level had direct effects on health promotion behavior of the participants and the model explained 30.0% of variance. The Chinese students in Korea with higher self-esteem, perceived health status, acculturation level, and lower acculturative stress reported higher health promotion behavior. The findings can be applied to develop health promotion strategies for this population. Copyright © 2016. Published by Elsevier B.V.

  16. A structural model for the in vivo human cornea including collagen-swelling interaction.

    Science.gov (United States)

    Cheng, Xi; Petsche, Steven J; Pinsky, Peter M

    2015-08-06

    A structural model of the in vivo cornea, which accounts for tissue swelling behaviour, for the three-dimensional organization of stromal fibres and for collagen-swelling interaction, is proposed. Modelled as a binary electrolyte gel in thermodynamic equilibrium, the stromal electrostatic free energy is based on the mean-field approximation. To account for active endothelial ionic transport in the in vivo cornea, which modulates osmotic pressure and hydration, stromal mobile ions are shown to satisfy a modified Boltzmann distribution. The elasticity of the stromal collagen network is modelled based on three-dimensional collagen orientation probability distributions for every point in the stroma obtained by synthesizing X-ray diffraction data for azimuthal angle distributions and second harmonic-generated image processing for inclination angle distributions. The model is implemented in a finite-element framework and employed to predict free and confined swelling of stroma in an ionic bath. For the in vivo cornea, the model is used to predict corneal swelling due to increasing intraocular pressure (IOP) and is adapted to model swelling in Fuchs' corneal dystrophy. The biomechanical response of the in vivo cornea to a typical LASIK surgery for myopia is analysed, including tissue fluid pressure and swelling responses. The model provides a new interpretation of the corneal active hydration control (pump-leak) mechanism based on osmotic pressure modulation. The results also illustrate the structural necessity of fibre inclination in stabilizing the corneal refractive surface with respect to changes in tissue hydration and IOP. © 2015 The Author(s).

  17. Data Processing Workflows to Support Reproducible Data-driven Research in Hydrology

    Science.gov (United States)

    Goodall, J. L.; Essawy, B.; Xu, H.; Rajasekar, A.; Moore, R. W.

    2015-12-01

    Geoscience analyses often require the use of existing data sets that are large, heterogeneous, and maintained by different organizations. A particular challenge in creating reproducible analyses using these data sets is automating the workflows required to transform raw datasets into model specific input files and finally into publication ready visualizations. Data grids, such as the Integrated Rule-Oriented Data System (iRODS), are architectures that allow scientists to access and share large data sets that are geographically distributed on the Internet, but appear to the scientist as a single file management system. The DataNet Federation Consortium (DFC) project is built on iRODS and aims to demonstrate data and computational interoperability across scientific communities. This paper leverages iRODS and the DFC to demonstrate how hydrological modeling workflows can be encapsulated as workflows using the iRODS concept of Workflow Structured Objects (WSO). An example use case is presented for automating hydrologic model post-processing routines that demonstrates how WSOs can be created and used within the DFC to automate the creation of data visualizations from large model output collections. By co-locating the workflow used to create the visualization with the data collection, the use case demonstrates how data grid technology aids in reuse, reproducibility, and sharing of workflows within scientific communities.

  18. The critical path method to analyze and modify OR-workflow: integration of an image documentation system.

    Science.gov (United States)

    Endress, A; Aydeniz, B; Wallwiener, D; Kurek, R

    2006-01-01

    Intraoperative image documentation is becoming more and more important for quality management in medicine, in terms of forensic documentation, research and teaching. Up to now, no software-based OR-image-documentation system fits satisfactorily into an OR-workflow. The objective of this study is to transparently show system integration in a clinical workflow for evaluating demands on future system developments. An example of the OR-workflow is presented for the department of obstetrics and gynecology at the University of Tuebingen (Germany). Twelve representative gynecologic laparoscopic surgeries were analyzed by using the critical path method (CPM). CPM network diagrams are shown for an actual laparoscopic workflow and for a workflow including an OR-image-documentation system. With the objective not to increase the total time of actual workflow, the maximum system operation time can be calculated for each period of time. Before surgery the maximum system operation time is x(max) = 7,3 minutes. After surgery it has to be assumed that system operation will increase total workflow time. Using the CPM to analyze requirements for system integration in a medical workflow has not yet been investigated. It is an appropriate method to transparently show integration possibilities and to define workflow-based requirements for the development process of new systems.

  19. Resident Workflow and Psychiatric Emergency Consultation: Identifying Factors for Quality Improvement in a Training Environment.

    Science.gov (United States)

    Blair, Thomas; Wiener, Zev; Seroussi, Ariel; Tang, Lingqi; O'Hora, Jennifer; Cheung, Erick

    2017-06-01

    Quality improvement to optimize workflow has the potential to mitigate resident burnout and enhance patient care. This study applied mixed methods to identify factors that enhance or impede workflow for residents performing emergency psychiatric consultations. The study population consisted of all psychiatry program residents (55 eligible, 42 participating) at the Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles. The authors developed a survey through iterative piloting, surveyed all residents, and then conducted a focus group. The survey included elements hypothesized to enhance or impede workflow, and measures pertaining to self-rated efficiency and stress. Distributional and bivariate analyses were performed. Survey findings were clarified in focus group discussion. This study identified several factors subjectively associated with enhanced or impeded workflow, including difficulty with documentation, the value of personal organization systems, and struggles to communicate with patients' families. Implications for resident education are discussed.

  20. a Standardized Approach to Topographic Data Processing and Workflow Management

    Science.gov (United States)

    Wheaton, J. M.; Bailey, P.; Glenn, N. F.; Hensleigh, J.; Hudak, A. T.; Shrestha, R.; Spaete, L.

    2013-12-01

    An ever-increasing list of options exist for collecting high resolution topographic data, including airborne LIDAR, terrestrial laser scanners, bathymetric SONAR and structure-from-motion. An equally rich, arguably overwhelming, variety of tools exists with which to organize, quality control, filter, analyze and summarize these data. However, scientists are often left to cobble together their analysis as a series of ad hoc steps, often using custom scripts and one-time processes that are poorly documented and rarely shared with the community. Even when literature-cited software tools are used, the input and output parameters differ from tool to tool. These parameters are rarely archived and the steps performed lost, making the analysis virtually impossible to replicate precisely. What is missing is a coherent, robust, framework for combining reliable, well-documented topographic data-processing steps into a workflow that can be repeated and even shared with others. We have taken several popular topographic data processing tools - including point cloud filtering and decimation as well as DEM differencing - and defined a common protocol for passing inputs and outputs between them. This presentation describes a free, public online portal that enables scientists to create custom workflows for processing topographic data using a number of popular topographic processing tools. Users provide the inputs required for each tool and in what sequence they want to combine them. This information is then stored for future reuse (and optionally sharing with others) before the user then downloads a single package that contains all the input and output specifications together with the software tools themselves. The user then launches the included batch file that executes the workflow on their local computer against their topographic data. This ZCloudTools architecture helps standardize, automate and archive topographic data processing. It also represents a forum for discovering and

  1. A satellite relative motion model including J_2 and J_3 via Vinti's intermediary

    Science.gov (United States)

    Biria, Ashley D.; Russell, Ryan P.

    2018-03-01

    Vinti's potential is revisited for analytical propagation of the main satellite problem, this time in the context of relative motion. A particular version of Vinti's spheroidal method is chosen that is valid for arbitrary elliptical orbits, encapsulating J_2, J_3, and generally a partial J_4 in an orbit propagation theory without recourse to perturbation methods. As a child of Vinti's solution, the proposed relative motion model inherits these properties. Furthermore, the problem is solved in oblate spheroidal elements, leading to large regions of validity for the linearization approximation. After offering several enhancements to Vinti's solution, including boosts in accuracy and removal of some singularities, the proposed model is derived and subsequently reformulated so that Vinti's solution is piecewise differentiable. While the model is valid for the critical inclination and nonsingular in the element space, singularities remain in the linear transformation from Earth-centered inertial coordinates to spheroidal elements when the eccentricity is zero or for nearly equatorial orbits. The new state transition matrix is evaluated against numerical solutions including the J_2 through J_5 terms for a wide range of chief orbits and separation distances. The solution is also compared with side-by-side simulations of the original Gim-Alfriend state transition matrix, which considers the J_2 perturbation. Code for computing the resulting state transition matrix and associated reference frame and coordinate transformations is provided online as supplementary material.

  2. Towards a workflow driven design for mHealth devices within temporary eye clinics in low-income settings.

    Science.gov (United States)

    Bolster, Nigel M; Bastawrous, Andrew; Giardini, Mario E

    2015-01-01

    Only a small minority of mobile healthcare technologies that have been successful in pilot studies have subsequently been integrated into healthcare systems. Understanding the reasons behind this discrepancy is crucial if such technologies are to be adopted. We believe that the mismatch is due to a breakdown in the relation between technical soundness of the original mobile health (mHealth) device design, and integration into healthcare provision workflows. Quantitative workflow modelling provides an opportunity to test this hypothesis. In this paper we present our current progress in developing a clinical workflow model for mobile eye assessment in low-income settings. We test the model for determining the appropriateness of design parameters of a mHealth device within this workflow, by assessing their impact on the entire clinical workflow performance.

  3. General hypothesis and shell model for the synthesis of semiconductor nanotubes, including carbon nanotubes

    Science.gov (United States)

    Mohammad, S. Noor

    2010-09-01

    Semiconductor nanotubes, including carbon nanotubes, have vast potential for new technology development. The fundamental physics and growth kinetics of these nanotubes are still obscured. Various models developed to elucidate the growth suffer from limited applicability. An in-depth investigation of the fundamentals of nanotube growth has, therefore, been carried out. For this investigation, various features of nanotube growth, and the role of the foreign element catalytic agent (FECA) in this growth, have been considered. Observed growth anomalies have been analyzed. Based on this analysis, a new shell model and a general hypothesis have been proposed for the growth. The essential element of the shell model is the seed generated from segregation during growth. The seed structure has been defined, and the formation of droplet from this seed has been described. A modified definition of the droplet exhibiting adhesive properties has also been presented. Various characteristics of the droplet, required for alignment and organization of atoms into tubular forms, have been discussed. Employing the shell model, plausible scenarios for the formation of carbon nanotubes, and the variation in the characteristics of these carbon nanotubes have been articulated. The experimental evidences, for example, for the formation of shell around a core, dipole characteristics of the seed, and the existence of nanopores in the seed, have been presented. They appear to justify the validity of the proposed model. The diversities of nanotube characteristics, fundamentals underlying the creation of bamboo-shaped carbon nanotubes, and the impurity generation on the surface of carbon nanotubes have been elucidated. The catalytic action of FECA on growth has been quantified. The applicability of the proposed model to the nanotube growth by a variety of mechanisms has been elaborated. These mechanisms include the vapor-liquid-solid mechanism, the oxide-assisted growth mechanism, the self

  4. A new model for including the effect of fly ash on biochemical methane potential.

    Science.gov (United States)

    Gertner, Pablo; Huiliñir, César; Pinto-Villegas, Paula; Castillo, Alejandra; Montalvo, Silvio; Guerrero, Lorna

    2017-10-01

    The modelling of the effect of trace elements on anaerobic digestion, and specifically the effect of fly ash, has been scarcely studied. Thus, the present work was aimed at the development of a new function that allows accumulated methane models to predict the effect of FA on the volume of methane accumulation. For this, purpose five fly ash concentrations (10, 25, 50, 250 and 500mg/L) using raw and pre-treated sewage sludge were used to calibrate the new function, while three fly ash concentrations were used (40, 150 and 350mg/L) for validation. Three models for accumulated methane volume (the modified Gompertz equation, the logistic function, and the transfer function) were evaluated. The results showed that methane production increased in the presence of FA when the sewage sludge was not pre-treated, while with pretreated sludge there is inhibition of methane production at FA concentrations higher than 50mg/L. In the calibration of the proposed function, it fits well with the experimental data under all the conditions, including the inhibition and stimulating zones, with the values of the parameters of the methane production models falling in the range of those reported in the literature. For validation experiments, the model succeeded in representing the behavior of new experiments in both the stimulating and inhibiting zones, with NRMSE and R 2 ranging from 0.3577 to 0.03714 and 0.2209 to 0.9911, respectively. Thus, the proposed model is robust and valid for the studied conditions. Copyright © 2017 Elsevier Ltd. All rights reserved.

  5. Using semi-automated curation workflows to collect, organize, and curate the data and models necessary to support the EPA CompTox chemical dashboard (ACS Spring meeting)

    Science.gov (United States)

    With the increasing need to leverage data and models to perform cutting edge analyses within the environmental science community, collection and organization of that data into a readily accessible format for consumption is a pressing need. The EPA CompTox chemical dashboard is i...

  6. A curved multi-component aerosol hygroscopicity model framework: Part 2 – Including organic compounds

    Directory of Open Access Journals (Sweden)

    D. O. Topping

    2005-01-01

    Full Text Available This paper describes the inclusion of organic particulate material within the Aerosol Diameter Dependent Equilibrium Model (ADDEM framework described in the companion paper applied to inorganic aerosol components. The performance of ADDEM is analysed in terms of its capability to reproduce the behaviour of various organic and mixed inorganic/organic systems using recently published bulk data. Within the modelling architecture already described two separate thermodynamic models are coupled in an additive approach and combined with a method for solving the Kohler equation in order to develop a tool for predicting the water content associated with an aerosol of known inorganic/organic composition and dry size. For development of the organic module, the widely used group contribution method UNIFAC is employed to explicitly deal with the non-ideality in solution. The UNIFAC predictions for components of atmospheric importance were improved considerably by using revised interaction parameters derived from electro-dynamic balance studies. Using such parameters, the model was found to adequately describe mixed systems including 5–6 dicarboxylic acids, down to low relative humidity conditions. By comparison with electrodynamic balance data, it was also found that the model was capable of capturing the behaviour of aqueous aerosols containing Suwannee River Fulvic acid, a structure previously used to represent the functionality of complex oxidised macromolecules often found in atmospheric aerosols. The additive approach for modelling mixed inorganic/organic systems worked well for a variety of mixtures. As expected, deviations between model predictions and measurements increase with increasing concentration. Available surface tension models, used in evaluating the Kelvin term, were found to reproduce measured data with varying success. Deviations from experimental data increased with increased organic compound complexity. For components only slightly

  7. A curved multi-component aerosol hygroscopicity model framework: Part 2 Including organic compounds

    Science.gov (United States)

    Topping, D. O.; McFiggans, G. B.; Coe, H.

    2005-05-01

    This paper describes the inclusion of organic particulate material within the Aerosol Diameter Dependent Equilibrium Model (ADDEM) framework described in the companion paper applied to inorganic aerosol components. The performance of ADDEM is analysed in terms of its capability to reproduce the behaviour of various organic and mixed inorganic/organic systems using recently published bulk data. Within the modelling architecture already described two separate thermodynamic models are coupled in an additive approach and combined with a method for solving the Kohler equation in order to develop a tool for predicting the water content associated with an aerosol of known inorganic/organic composition and dry size. For development of the organic module, the widely used group contribution method UNIFAC is employed to explicitly deal with the non-ideality in solution. The UNIFAC predictions for components of atmospheric importance were improved considerably by using revised interaction parameters derived from electro-dynamic balance studies. Using such parameters, the model was found to adequately describe mixed systems including 5-6 dicarboxylic acids, down to low relative humidity conditions. By comparison with electrodynamic balance data, it was also found that the model was capable of capturing the behaviour of aqueous aerosols containing Suwannee River Fulvic acid, a structure previously used to represent the functionality of complex oxidised macromolecules often found in atmospheric aerosols. The additive approach for modelling mixed inorganic/organic systems worked well for a variety of mixtures. As expected, deviations between model predictions and measurements increase with increasing concentration. Available surface tension models, used in evaluating the Kelvin term, were found to reproduce measured data with varying success. Deviations from experimental data increased with increased organic compound complexity. For components only slightly soluble in water

  8. A generalized model for optimal transport of images including dissipation and density modulation

    KAUST Repository

    Maas, Jan

    2015-11-01

    © EDP Sciences, SMAI 2015. In this paper the optimal transport and the metamorphosis perspectives are combined. For a pair of given input images geodesic paths in the space of images are defined as minimizers of a resulting path energy. To this end, the underlying Riemannian metric measures the rate of transport cost and the rate of viscous dissipation. Furthermore, the model is capable to deal with strongly varying image contrast and explicitly allows for sources and sinks in the transport equations which are incorporated in the metric related to the metamorphosis approach by Trouvé and Younes. In the non-viscous case with source term existence of geodesic paths is proven in the space of measures. The proposed model is explored on the range from merely optimal transport to strongly dissipative dynamics. For this model a robust and effective variational time discretization of geodesic paths is proposed. This requires to minimize a discrete path energy consisting of a sum of consecutive image matching functionals. These functionals are defined on corresponding pairs of intensity functions and on associated pairwise matching deformations. Existence of time discrete geodesics is demonstrated. Furthermore, a finite element implementation is proposed and applied to instructive test cases and to real images. In the non-viscous case this is compared to the algorithm proposed by Benamou and Brenier including a discretization of the source term. Finally, the model is generalized to define discrete weighted barycentres with applications to textures and objects.

  9. Empirical Validation of a Thermal Model of a Complex Roof Including Phase Change Materials

    Directory of Open Access Journals (Sweden)

    Stéphane Guichard

    2015-12-01

    Full Text Available This paper deals with the empirical validation of a building thermal model of a complex roof including a phase change material (PCM. A mathematical model dedicated to PCMs based on the heat apparent capacity method was implemented in a multi-zone building simulation code, the aim being to increase the understanding of the thermal behavior of the whole building with PCM technologies. In order to empirically validate the model, the methodology is based both on numerical and experimental studies. A parametric sensitivity analysis was performed and a set of parameters of the thermal model has been identified for optimization. The use of the generic optimization program called GenOpt® coupled to the building simulation code enabled to determine the set of adequate parameters. We first present the empirical validation methodology and main results of previous work. We then give an overview of GenOpt® and its coupling with the building simulation code. Finally, once the optimization results are obtained, comparisons of the thermal predictions with measurements are found to be acceptable and are presented.

  10. A multiscale model for glioma spread including cell-tissue interactions and proliferation.

    Science.gov (United States)

    Engwer, Christian; Knappitsch, Markus; Surulescu, Christina

    2016-04-01

    Glioma is a broad class of brain and spinal cord tumors arising from glia cells, which are the main brain cells that can develop into neoplasms. They are highly invasive and lead to irregular tumor margins which are not precisely identifiable by medical imaging, thus rendering a precise enough resection very difficult. The understanding of glioma spread patterns is hence essential for both radiological therapy as well as surgical treatment. In this paper we propose a multiscale model for glioma growth including interactions of the cells with the underlying tissue network, along with proliferative effects. Our current accounting for two subpopulations of cells to accomodate proliferation according to the go-or-grow dichtomoty is an extension of the setting in [16]. As in that paper, we assume that cancer cells use neuronal fiber tracts as invasive pathways. Hence, the individual structure of brain tissue seems to be decisive for the tumor spread. Diffusion tensor imaging (DTI) is able to provide such information, thus opening the way for patient specific modeling of glioma invasion. Starting from a multiscale model involving subcellular (microscopic) and individual (mesoscale) cell dynamics, we perform a parabolic scaling to obtain an approximating reaction-diffusion-transport equation on the macroscale of the tumor cell population. Numerical simulations based on DTI data are carried out in order to assess the performance of our modeling approach.

  11. Habitability of super-Earth planets around other suns: models including Red Giant Branch evolution.

    Science.gov (United States)

    von Bloh, W; Cuntz, M; Schröder, K-P; Bounama, C; Franck, S

    2009-01-01

    The unexpected diversity of exoplanets includes a growing number of super-Earth planets, i.e., exoplanets with masses of up to several Earth masses and a similar chemical and mineralogical composition as Earth. We present a thermal evolution model for a 10 Earth-mass planet orbiting a star like the Sun. Our model is based on the integrated system approach, which describes the photosynthetic biomass production and takes into account a variety of climatological, biogeochemical, and geodynamical processes. This allows us to identify a so-called photosynthesis-sustaining habitable zone (pHZ), as determined by the limits of biological productivity on the planetary surface. Our model considers solar evolution during the main-sequence stage and along the Red Giant Branch as described by the most recent solar model. We obtain a large set of solutions consistent with the principal possibility of life. The highest likelihood of habitability is found for "water worlds." Only mass-rich water worlds are able to realize pHZ-type habitability beyond the stellar main sequence on the Red Giant Branch.

  12. Networked Print Production: Does JDF Provide a Perfect Workflow?

    Directory of Open Access Journals (Sweden)

    Bernd Zipper

    2004-12-01

    Full Text Available The "networked printing works" is a well-worn slogan used by many providers in the graphics industry and for the past number of years printing-works manufacturers have been working on the goal of achieving the "networked printing works". A turning point from the concept to real implementation can now be expected at drupa 2004: JDF (Job Definition Format and thus "networked production" will form the center of interest here. The first approaches towards a complete, networked workflow between prepress, print and postpress in production are already available - the products and solutions will now be presented publicly at drupa 2004. So, drupa 2004 will undoubtedly be the "JDF-drupa" - the drupa where machines learn to communicate with each other digitally - the drupa, where the dream of general system and job communication in the printing industry can be first realized. CIP3, which has since been renamed CIP4, is an international consortium of leading manufacturers from the printing and media industry who have taken on the task of integrating processes for prepress, print and postpress. The association, to which nearly all manufacturers in the graphics industry belong, has succeeded with CIP3 in developing a first international standard for the transmission of control data in the print workflow.Further development of the CIP4 standard now includes a more extensive "system language" called JDF, which will guarantee workflow communication beyond manufacturer boundaries. However, not only data for actual print production will be communicated with JDF (Job Definition Format: planning and calculation data for MIS (Management Information systems and calculation systems will also be prepared. The German printing specialist Hans-Georg Wenke defines JDF as follows: "JDF takes over data from MIS for machines, aggregates and their control desks, data exchange within office applications, and finally ensures that data can be incorporated in the technical workflow

  13. Analysis of electronic models for solar cells including energy resolved defect densities

    Energy Technology Data Exchange (ETDEWEB)

    Glitzky, Annegret

    2010-07-01

    We introduce an electronic model for solar cells including energy resolved defect densities. The resulting drift-diffusion model corresponds to a generalized van Roosbroeck system with additional source terms coupled with ODEs containing space and energy as parameters for all defect densities. The system has to be considered in heterostructures and with mixed boundary conditions from device simulation. We give a weak formulation of the problem. If the boundary data and the sources are compatible with thermodynamic equilibrium the free energy along solutions decays monotonously. In other cases it may be increasing, but we estimate its growth. We establish boundedness and uniqueness results and prove the existence of a weak solution. This is done by considering a regularized problem, showing its solvability and the boundedness of its solutions independent of the regularization level. (orig.)

  14. Effect of including decay chains on predictions of equilibrium-type terrestrial food chain models

    International Nuclear Information System (INIS)

    Kirchner, G.

    1990-01-01

    Equilibrium-type food chain models are commonly used for assessing the radiological impact to man from environmental releases of radionuclides. Usually these do not take into account build-up of radioactive decay products during environmental transport. This may be a potential source of underprediction. For estimating consequences of this simplification, the equations of an internationally recognised terrestrial food chain model have been extended to include decay chains of variable length. Example calculations show that for releases from light water reactors as expected both during routine operation and in the case of severe accidents, the build-up of decay products during environmental transport is generally of minor importance. However, a considerable number of radionuclides of potential radiological significance have been identified which show marked contributions of decay products to calculated contamination of human food and resulting radiation dose rates. (author)

  15. CONNJUR Workflow Builder: a software integration environment for spectral reconstruction

    Energy Technology Data Exchange (ETDEWEB)

    Fenwick, Matthew; Weatherby, Gerard; Vyas, Jay; Sesanker, Colbert [UConn Health, Department of Molecular Biology and Biophysics (United States); Martyn, Timothy O. [Rensselaer at Hartford, Department of Engineering and Science (United States); Ellis, Heidi J. C. [Western New England College, Department of Computer Science and Information Technology (United States); Gryk, Michael R., E-mail: gryk@uchc.edu [UConn Health, Department of Molecular Biology and Biophysics (United States)

    2015-07-15

    CONNJUR Workflow Builder (WB) is an open-source software integration environment that leverages existing spectral reconstruction tools to create a synergistic, coherent platform for converting biomolecular NMR data from the time domain to the frequency domain. WB provides data integration of primary data and metadata using a relational database, and includes a library of pre-built workflows for processing time domain data. WB simplifies maximum entropy reconstruction, facilitating the processing of non-uniformly sampled time domain data. As will be shown in the paper, the unique features of WB provide it with novel abilities to enhance the quality, accuracy, and fidelity of the spectral reconstruction process. WB also provides features which promote collaboration, education, parameterization, and non-uniform data sets along with processing integrated with the Rowland NMR Toolkit (RNMRTK) and NMRPipe software packages. WB is available free of charge in perpetuity, dual-licensed under the MIT and GPL open source licenses.

  16. CONNJUR Workflow Builder: a software integration environment for spectral reconstruction

    International Nuclear Information System (INIS)

    Fenwick, Matthew; Weatherby, Gerard; Vyas, Jay; Sesanker, Colbert; Martyn, Timothy O.; Ellis, Heidi J. C.; Gryk, Michael R.

    2015-01-01

    CONNJUR Workflow Builder (WB) is an open-source software integration environment that leverages existing spectral reconstruction tools to create a synergistic, coherent platform for converting biomolecular NMR data from the time domain to the frequency domain. WB provides data integration of primary data and metadata using a relational database, and includes a library of pre-built workflows for processing time domain data. WB simplifies maximum entropy reconstruction, facilitating the processing of non-uniformly sampled time domain data. As will be shown in the paper, the unique features of WB provide it with novel abilities to enhance the quality, accuracy, and fidelity of the spectral reconstruction process. WB also provides features which promote collaboration, education, parameterization, and non-uniform data sets along with processing integrated with the Rowland NMR Toolkit (RNMRTK) and NMRPipe software packages. WB is available free of charge in perpetuity, dual-licensed under the MIT and GPL open source licenses

  17. Staffing and Workflow of a Maturing Institutional Repository

    Directory of Open Access Journals (Sweden)

    Debora L. Madsen

    2013-02-01

    Full Text Available Institutional repositories (IRs have become established components of many academic libraries. As an IR matures it will face the challenge of how to scale up its operations to increase the amount and types of content archived. These challenges involve staffing, systems, workflows, and promotion. In the past eight years, Kansas State University's IR (K-REx has grown from a platform for student theses, dissertations, and reports to also include faculty works. The initial workforce of a single faculty member was expanded as a part of a library-wide reorganization, resulting in a cross-departmental team that is better able to accommodate the expansion of the IR. The resultant need to define staff responsibilities and develop resources to manage the workflows has led to the innovations described here, which may prove useful to the greater library community as other IRs mature.

  18. Multilevel Workflow System in the ATLAS Experiment

    International Nuclear Information System (INIS)

    Borodin, M; De, K; Navarro, J Garcia; Golubkov, D; Klimentov, A; Maeno, T; Vaniachine, A

    2015-01-01

    The ATLAS experiment is scaling up Big Data processing for the next LHC run using a multilevel workflow system comprised of many layers. In Big Data processing ATLAS deals with datasets, not individual files. Similarly a task (comprised of many jobs) has become a unit of the ATLAS workflow in distributed computing, with about 0.8M tasks processed per year. In order to manage the diversity of LHC physics (exceeding 35K physics samples per year), the individual data processing tasks are organized into workflows. For example, the Monte Carlo workflow is composed of many steps: generate or configure hard-processes, hadronize signal and minimum-bias (pileup) events, simulate energy deposition in the ATLAS detector, digitize electronics response, simulate triggers, reconstruct data, convert the reconstructed data into ROOT ntuples for physics analysis, etc. Outputs are merged and/or filtered as necessary to optimize the chain. The bi-level workflow manager - ProdSys2 - generates actual workflow tasks and their jobs are executed across more than a hundred distributed computing sites by PanDA - the ATLAS job-level workload management system. On the outer level, the Database Engine for Tasks (DEfT) empowers production managers with templated workflow definitions. On the next level, the Job Execution and Definition Interface (JEDI) is integrated with PanDA to provide dynamic job definition tailored to the sites capabilities. We report on scaling up the production system to accommodate a growing number of requirements from main ATLAS areas: Trigger, Physics and Data Preparation. (paper)

  19. Impact of Diabetes E-Consults on Outpatient Clinic Workflow.

    Science.gov (United States)

    Zoll, Brian; Parikh, Pratik J; Gallimore, Jennie; Harrell, Stephen; Burke, Brian

    2015-08-01

    An e-consult is an electronic communication system between clinicians, usually a primary care physician (PCP) and a medical or surgical specialist, regarding general or patient-specific, low complexity questions that would not need an in-person consultation. The objectives of this study were to understand and quantify the impact of the e-consult initiative on outpatient clinic workflow and outcomes. We collected data from 5 different Veterans Affairs (VA) outpatient clinics and interviewed several physicians and staff members. We then developed a simulation model for a primary care team at an outpatient clinic. A detailed experimental study was conducted to determine the effects of factors, such as e-consult demand, view-alert notification arrivals, walk-in patient arrivals, and PCP unavailability, on e-consult cycle time. Statistical tests indicated that 4 factors related to outpatient clinic workflow were significant, and levels within each of the 4 significant factors resulted in statistically different e-consult cycle times. The arrival rate of electronic notifications, along with patient walk-ins, had a considerable effect on cycle time. Splitting the workload of an unavailable PCP among the other PCPs, instead of the current practice of allocating it to a single PCP, increases the system's ability to handle a much larger e-consult demand. The full potential of e-consults can only be realized if the workflow at the outpatient clinics is designed or modified to support this initiative. This study furthers our understanding of how e-consult systems can be analyzed and alternative workflows tested using statistical and simulation modeling to improve care delivery and outcomes. © The Author(s) 2014.

  20. Including sugar cane in the agro-ecosystem model ORCHIDEE-STICS

    Science.gov (United States)

    Valade, A.; Vuichard, N.; Ciais, P.; Viovy, N.

    2010-12-01

    With 4 million ha currently grown for ethanol in Brazil only, approximately half the global bioethanol production in 2005 (Smeets 2008), and a devoted land area expected to expand globally in the years to come, sugar cane is at the heart of the biofuel debate. Indeed, ethanol made from biomass is currently the most widespread option for alternative transportation fuels. It was originally promoted as a carbon neutral energy resource that could bring energy independence to countries and local opportunities to farmers, until attention was drawn to its environmental and socio-economical drawbacks. It is still not clear to which extent it is a solution or a contributor to climate change mitigation. Dynamic Global Vegetation models can help address these issues and quantify the potential impacts of biofuels on ecosystems at scales ranging from on-site to global. The global agro-ecosystem model ORCHIDEE describes water, carbon and energy exchanges at the soil-atmosphere interface for a limited number of natural and agricultural vegetation types. In order to integrate agricultural management to the simulations and to capture more accurately the specificity of crops' phenology, ORCHIDEE has been coupled with the agronomical model STICS. The resulting crop-oriented vegetation model ORCHIDEE-STICS has been used so far to simulate temperate crops such as wheat, corn and soybean. As a generic ecosystem model, each grid cell can include several vegetation types with their own phenology and management practices, making it suitable to spatial simulations. Here, ORCHIDEE-STICS is altered to include sugar cane as a new agricultural Plant functional Type, implemented and parametrized using the STICS approach. An on-site calibration and validation is then performed based on biomass and flux chamber measurements in several sites in Australia and variables such as LAI, dry weight, heat fluxes and respiration are used to evaluate the ability of the model to simulate the specific

  1. Workflow management in large distributed systems

    International Nuclear Information System (INIS)

    Legrand, I; Newman, H; Voicu, R; Dobre, C; Grigoras, C

    2011-01-01

    The MonALISA (Monitoring Agents using a Large Integrated Services Architecture) framework provides a distributed service system capable of controlling and optimizing large-scale, data-intensive applications. An essential part of managing large-scale, distributed data-processing facilities is a monitoring system for computing facilities, storage, networks, and the very large number of applications running on these systems in near realtime. All this monitoring information gathered for all the subsystems is essential for developing the required higher-level services—the components that provide decision support and some degree of automated decisions—and for maintaining and optimizing workflow in large-scale distributed systems. These management and global optimization functions are performed by higher-level agent-based services. We present several applications of MonALISA's higher-level services including optimized dynamic routing, control, data-transfer scheduling, distributed job scheduling, dynamic allocation of storage resource to running jobs and automated management of remote services among a large set of grid facilities.

  2. Workflow management in large distributed systems

    Science.gov (United States)

    Legrand, I.; Newman, H.; Voicu, R.; Dobre, C.; Grigoras, C.

    2011-12-01

    The MonALISA (Monitoring Agents using a Large Integrated Services Architecture) framework provides a distributed service system capable of controlling and optimizing large-scale, data-intensive applications. An essential part of managing large-scale, distributed data-processing facilities is a monitoring system for computing facilities, storage, networks, and the very large number of applications running on these systems in near realtime. All this monitoring information gathered for all the subsystems is essential for developing the required higher-level services—the components that provide decision support and some degree of automated decisions—and for maintaining and optimizing workflow in large-scale distributed systems. These management and global optimization functions are performed by higher-level agent-based services. We present several applications of MonALISA's higher-level services including optimized dynamic routing, control, data-transfer scheduling, distributed job scheduling, dynamic allocation of storage resource to running jobs and automated management of remote services among a large set of grid facilities.

  3. Web-accessible molecular modeling with Rosetta: The Rosetta Online Server that Includes Everyone (ROSIE).

    Science.gov (United States)

    Moretti, Rocco; Lyskov, Sergey; Das, Rhiju; Meiler, Jens; Gray, Jeffrey J

    2018-01-01

    The Rosetta molecular modeling software package provides a large number of experimentally validated tools for modeling and designing proteins, nucleic acids, and other biopolymers, with new protocols being added continually. While freely available to academic users, external usage is limited by the need for expertise in the Unix command line environment. To make Rosetta protocols available to a wider audience, we previously created a web server called Rosetta Online Server that Includes Everyone (ROSIE), which provides a common environment for hosting web-accessible Rosetta protocols. Here we describe a simplification of the ROSIE protocol specification format, one that permits easier implementation of Rosetta protocols. Whereas the previous format required creating multiple separate files in different locations, the new format allows specification of the protocol in a single file. This new, simplified protocol specification has more than doubled the number of Rosetta protocols available under ROSIE. These new applications include pK a determination, lipid accessibility calculation, ribonucleic acid redesign, protein-protein docking, protein-small molecule docking, symmetric docking, antibody docking, cyclic toxin docking, critical binding peptide determination, and mapping small molecule binding sites. ROSIE is freely available to academic users at http://rosie.rosettacommons.org. © 2017 The Protein Society.

  4. Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow

    DEFF Research Database (Denmark)

    Brunk, Elizabeth; George, Kevin W.; Alonso-Gutierrez, Jorge

    2016-01-01

    Understanding the complex interactions that occur between heterologous and native biochemical pathways represents a major challenge in metabolic engineering and synthetic biology. We present a workflow that integrates metabolomics, proteomics, and genome-scale models of Escherichia coli metabolism...... to study the effects of introducing a heterologous pathway into a microbial host. This workflow incorporates complementary approaches from computational systems biology, metabolic engineering, and synthetic biology; provides molecular insight into how the host organism microenvironment changes due....... Application of this workflow identified the roles of candidate genes, pathways, and biochemical reactions in observed experimental phenomena and facilitated the construction of a mutant strain with improved productivity. The contributed workflow is available as an open-source tool in the form of i...

  5. A curved multi-component aerosol hygroscopicity model framework: 2 Including organics

    Science.gov (United States)

    Topping, D. O.; McFiggans, G. B.; Coe, H.

    2004-12-01

    This paper describes the inclusion of organic particulate material within the Aerosol Diameter Dependent Equilibrium Model (ADDEM) framework described in the companion paper applied to inorganic aerosol components. The performance of ADDEM is analysed in terms of its capability to reproduce the behaviour of various organic and mixed inorganic/organic systems using recently published bulk data. Within the modelling architecture already described two separate thermodynamic models are coupled in an additive approach and combined with a method for solving the Köhler equation in order to develop a tool for predicting the water content associated with an aerosol of known inorganic/organic composition and dry size. For development of the organic module, the widely used group contribution method UNIFAC is employed to explicitly deal with the non-ideality in solution. The UNIFAC predictions for components of atmospheric importance were improved considerably by using revised interaction parameters derived from electro-dynamic balance studies. Using such parameters, the model was found to adequately describe mixed systems including 5-6 dicarboxylic acids, down to low relative humidity conditions. The additive approach for modelling mixed inorganic/organic systems worked well for a variety of mixtures. As expected, deviations between predicted and measured data increase with increasing concentration. Available surface tension models, used in evaluating the Kelvin term, were found to reproduce measured data with varying success. Deviations from experimental data increased with increased organic compound complexity. For components only slightly soluble in water, significant deviations from measured surface tension depression behaviour were predicted with both model formalisms tested. A Sensitivity analysis showed that such variation is likely to lead to predicted growth factors within the measurement uncertainty for growth factor taken in the sub-saturated regime. Greater

  6. A Hydrological Concept including Lateral Water Flow Compatible with the Biogeochemical Model ForSAFE

    Directory of Open Access Journals (Sweden)

    Giuliana Zanchi

    2016-03-01

    Full Text Available The study presents a hydrology concept developed to include lateral water flow in the biogeochemical model ForSAFE. The hydrology concept was evaluated against data collected at Svartberget in the Vindeln Research Forest in Northern Sweden. The results show that the new concept allows simulation of a saturated and an unsaturated zone in the soil as well as water flow that reaches the stream comparable to measurements. The most relevant differences compared to streamflow measurements are that the model simulates a higher base flow in winter and lower flow peaks after snowmelt. These differences are mainly caused by the assumptions made to regulate the percolation at the bottom of the simulated soil columns. The capability for simulating lateral flows and a saturated zone in ForSAFE can greatly improve the simulation of chemical exchange in the soil and export of elements from the soil to watercourses. Such a model can help improve the understanding of how environmental changes in the forest landscape will influence chemical loads to surface waters.

  7. Integrated Sachs-Wolfe effect in a quintessence cosmological model: Including anisotropic stress of dark energy

    International Nuclear Information System (INIS)

    Wang, Y. T.; Xu, L. X.; Gui, Y. X.

    2010-01-01

    In this paper, we investigate the integrated Sachs-Wolfe effect in the quintessence cold dark matter model with constant equation of state and constant speed of sound in dark energy rest frame, including dark energy perturbation and its anisotropic stress. Comparing with the ΛCDM model, we find that the integrated Sachs-Wolfe (ISW)-power spectrums are affected by different background evolutions and dark energy perturbation. As we change the speed of sound from 1 to 0 in the quintessence cold dark matter model with given state parameters, it is found that the inclusion of dark energy anisotropic stress makes the variation of magnitude of the ISW source uncertain due to the anticorrelation between the speed of sound and the ratio of dark energy density perturbation contrast to dark matter density perturbation contrast in the ISW-source term. Thus, the magnitude of the ISW-source term is governed by the competition between the alterant multiple of (1+3/2xc-circumflex s 2 ) and that of δ de /δ m with the variation of c-circumflex s 2 .

  8. Expanded rock blast modeling capabilities of DMC{_}BLAST, including buffer blasting

    Energy Technology Data Exchange (ETDEWEB)

    Preece, D.S. [Sandia National Labs., Albuquerque, NM (United States); Tidman, J.P.; Chung, S.H. [ICI Explosives (Canada)

    1996-12-31

    A discrete element computer program named DMC{_}BLAST (Distinct Motion Code) has been under development since 1987 for modeling rock blasting. This program employs explicit time integration and uses spherical or cylindrical elements that are represented as circles in 2-D. DMC{_}BLAST calculations compare favorably with data from actual bench blasts. The blast modeling capabilities of DMC{_}BLAST have been expanded to include independently dipping geologic layers, top surface, bottom surface and pit floor. The pit can also now be defined using coordinates based on the toe of the bench. A method for modeling decked explosives has been developed which allows accurate treatment of the inert materials (stemming) in the explosive column and approximate treatment of different explosives in the same blasthole. A DMC{_}BLAST user can specify decking through a specific geologic layer with either inert material or a different explosive. Another new feature of DMC{_}BLAST is specification of an uplift angle which is the angle between the normal to the blasthole and a vector defining the direction of explosive loading on particles adjacent to the blasthole. A buffer (choke) blast capability has been added for situations where previously blasted material is adjacent to the free face of the bench preventing any significant lateral motion during the blast.

  9. Workflow in clinical trial sites & its association with near miss events for data quality: ethnographic, workflow & systems simulation.

    Directory of Open Access Journals (Sweden)

    Elias Cesar Araujo de Carvalho

    Full Text Available BACKGROUND: With the exponential expansion of clinical trials conducted in (Brazil, Russia, India, and China and VISTA (Vietnam, Indonesia, South Africa, Turkey, and Argentina countries, corresponding gains in cost and enrolment efficiency quickly outpace the consonant metrics in traditional countries in North America and European Union. However, questions still remain regarding the quality of data being collected in these countries. We used ethnographic, mapping and computer simulation studies to identify/address areas of threat to near miss events for data quality in two cancer trial sites in Brazil. METHODOLOGY/PRINCIPAL FINDINGS: Two sites in Sao Paolo and Rio Janeiro were evaluated using ethnographic observations of workflow during subject enrolment and data collection. Emerging themes related to threats to near miss events for data quality were derived from observations. They were then transformed into workflows using UML-AD and modeled using System Dynamics. 139 tasks were observed and mapped through the ethnographic study. The UML-AD detected four major activities in the workflow evaluation of potential research subjects prior to signature of informed consent, visit to obtain subject́s informed consent, regular data collection sessions following study protocol and closure of study protocol for a given project. Field observations pointed to three major emerging themes: (a lack of standardized process for data registration at source document, (b multiplicity of data repositories and (c scarcity of decision support systems at the point of research intervention. Simulation with policy model demonstrates a reduction of the rework problem. CONCLUSIONS/SIGNIFICANCE: Patterns of threats to data quality at the two sites were similar to the threats reported in the literature for American sites. The clinical trial site managers need to reorganize staff workflow by using information technology more efficiently, establish new standard procedures and

  10. Workflow in clinical trial sites & its association with near miss events for data quality: ethnographic, workflow & systems simulation.

    Science.gov (United States)

    de Carvalho, Elias Cesar Araujo; Batilana, Adelia Portero; Claudino, Wederson; Reis, Luiz Fernando Lima; Schmerling, Rafael A; Shah, Jatin; Pietrobon, Ricardo

    2012-01-01

    With the exponential expansion of clinical trials conducted in (Brazil, Russia, India, and China) and VISTA (Vietnam, Indonesia, South Africa, Turkey, and Argentina) countries, corresponding gains in cost and enrolment efficiency quickly outpace the consonant metrics in traditional countries in North America and European Union. However, questions still remain regarding the quality of data being collected in these countries. We used ethnographic, mapping and computer simulation studies to identify/address areas of threat to near miss events for data quality in two cancer trial sites in Brazil. Two sites in Sao Paolo and Rio Janeiro were evaluated using ethnographic observations of workflow during subject enrolment and data collection. Emerging themes related to threats to near miss events for data quality were derived from observations. They were then transformed into workflows using UML-AD and modeled using System Dynamics. 139 tasks were observed and mapped through the ethnographic study. The UML-AD detected four major activities in the workflow evaluation of potential research subjects prior to signature of informed consent, visit to obtain subject́s informed consent, regular data collection sessions following study protocol and closure of study protocol for a given project. Field observations pointed to three major emerging themes: (a) lack of standardized process for data registration at source document, (b) multiplicity of data repositories and (c) scarcity of decision support systems at the point of research intervention. Simulation with policy model demonstrates a reduction of the rework problem. Patterns of threats to data quality at the two sites were similar to the threats reported in the literature for American sites. The clinical trial site managers need to reorganize staff workflow by using information technology more efficiently, establish new standard procedures and manage professionals to reduce near miss events and save time/cost. Clinical trial

  11. Enhancing and Customizing Laboratory Information Systems to Improve/Enhance Pathologist Workflow.

    Science.gov (United States)

    Hartman, Douglas J

    2015-06-01

    Optimizing pathologist workflow can be difficult because it is affected by many variables. Surgical pathologists must complete many tasks that culminate in a final pathology report. Several software systems can be used to enhance/improve pathologist workflow. These include voice recognition software, pre-sign-out quality assurance, image utilization, and computerized provider order entry. Recent changes in the diagnostic coding and the more prominent role of centralized electronic health records represent potential areas for increased ways to enhance/improve the workflow for surgical pathologists. Additional unforeseen changes to the pathologist workflow may accompany the introduction of whole-slide imaging technology to the routine diagnostic work. Copyright © 2015 Elsevier Inc. All rights reserved.

  12. Visual Workflows for Oil and Gas Exploration

    KAUST Repository

    Hollt, Thomas

    2013-04-14

    The most important resources to fulfill today’s energy demands are fossil fuels, such as oil and natural gas. When exploiting hydrocarbon reservoirs, a detailed and credible model of the subsurface structures to plan the path of the borehole, is crucial in order to minimize economic and ecological risks. Before that, the placement, as well as the operations of oil rigs need to be planned carefully, as off-shore oil exploration is vulnerable to hazards caused by strong currents. The oil and gas industry therefore relies on accurate ocean forecasting systems for planning their operations. This thesis presents visual workflows for creating subsurface models as well as planning the placement and operations of off-shore structures. Creating a credible subsurface model poses two major challenges: First, the structures in highly ambiguous seismic data are interpreted in the time domain. Second, a velocity model has to be built from this interpretation to match the model to depth measurements from wells. If it is not possible to obtain a match at all positions, the interpretation has to be updated, going back to the first step. This results in a lengthy back and forth between the different steps, or in an unphysical velocity model in many cases. We present a novel, integrated approach to interactively creating subsurface models from reflection seismics, by integrating the interpretation of the seismic data using an interactive horizon extraction technique based on piecewise global optimization with velocity modeling. Computing and visualizing the effects of changes to the interpretation and velocity model on the depth-converted model, on the fly enables an integrated feedback loop that enables a completely new connection of the seismic data in time domain, and well data in depth domain. For planning the operations of off-shore structures we present a novel integrated visualization system that enables interactive visual analysis of ensemble simulations used in ocean

  13. Modelling and control of a microgrid including photovoltaic and wind generation

    Science.gov (United States)

    Hussain, Mohammed Touseef

    Extensive increase of distributed generation (DG) penetration and the existence of multiple DG units at distribution level have introduced the notion of micro-grid. This thesis develops a detailed non-linear and small-signal dynamic model of a microgrid that includes PV, wind and conventional small scale generation along with their power electronics interfaces and the filters. The models developed evaluate the amount of generation mix from various DGs for satisfactory steady state operation of the microgrid. In order to understand the interaction of the DGs on microgrid system initially two simpler configurations were considered. The first one consists of microalternator, PV and their electronics, and the second system consists of microalternator and wind system each connected to the power system grid. Nonlinear and linear state space model of each microgrid are developed. Small signal analysis showed that the large participation of PV/wind can drive the microgrid to the brink of unstable region without adequate control. Non-linear simulations are carried out to verify the results obtained through small-signal analysis. The role of the extent of generation mix of a composite microgrid consisting of wind, PV and conventional generation was investigated next. The findings of the smaller systems were verified through nonlinear and small signal modeling. A central supervisory capacitor energy storage controller interfaced through a STATCOM was proposed to monitor and enhance the microgrid operation. The potential of various control inputs to provide additional damping to the system has been evaluated through decomposition techniques. The signals identified to have damping contents were employed to design the supervisory control system. The controller gains were tuned through an optimal pole placement technique. Simulation studies demonstrate that the STATCOM voltage phase angle and PV inverter phase angle were the best inputs for enhanced stability boundaries.

  14. An analytical method for well-formed workflow/Petri net verification of classical soundness

    Directory of Open Access Journals (Sweden)

    Clempner Julio

    2014-12-01

    Full Text Available In this paper we consider workflow nets as dynamical systems governed by ordinary difference equations described by a particular class of Petri nets. Workflow nets are a formal model of business processes. Well-formed business processes correspond to sound workflow nets. Even if it seems necessary to require the soundness of workflow nets, there exist business processes with conditional behavior that will not necessarily satisfy the soundness property. In this sense, we propose an analytical method for showing that a workflow net satisfies the classical soundness property using a Petri net. To present our statement, we use Lyapunov stability theory to tackle the classical soundness verification problem for a class of dynamical systems described by Petri nets. This class of Petri nets allows a dynamical model representation that can be expressed in terms of difference equations. As a result, by applying Lyapunov theory, the classical soundness property for workflow nets is solved proving that the Petri net representation is stable. We show that a finite and non-blocking workflow net satisfies the sound property if and only if its corresponding PN is stable, i.e., given the incidence matrix A of the corresponding PN, there exists a Փ strictly positive m vector such that AՓ≤ 0. The key contribution of the paper is the analytical method itself that satisfies part of the definition of the classical soundness requirements. The method is designed for practical applications, guarantees that anomalies can be detected without domain knowledge, and can be easily implemented into existing commercial systems that do not support the verification of workflows. The validity of the proposed method is successfully demonstrated by application examples.

  15. Logical provenance in data-oriented workflows?

    KAUST Repository

    Ikeda, R.

    2013-04-01

    We consider the problem of defining, generating, and tracing provenance in data-oriented workflows, in which input data sets are processed by a graph of transformations to produce output results. We first give a new general definition of provenance for general transformations, introducing the notions of correctness, precision, and minimality. We then determine when properties such as correctness and minimality carry over from the individual transformations\\' provenance to the workflow provenance. We describe a simple logical-provenance specification language consisting of attribute mappings and filters. We provide an algorithm for provenance tracing in workflows where logical provenance for each transformation is specified using our language. We consider logical provenance in the relational setting, observing that for a class of Select-Project-Join (SPJ) transformations, logical provenance specifications encode minimal provenance. We have built a prototype system supporting the features and algorithms presented in the paper, and we report a few preliminary experimental results. © 2013 IEEE.

  16. SwinDeW-C: A Peer-to-Peer Based Cloud Workflow System

    Science.gov (United States)

    Liu, Xiao; Yuan, Dong; Zhang, Gaofeng; Chen, Jinjun; Yang, Yun

    Workflow systems are designed to support the process automation of large scale business and scientific applications. In recent years, many workflow systems have been deployed on high performance computing infrastructures such as cluster, peer-to-peer (p2p), and grid computing (Moore, 2004; Wang, Jie, & Chen, 2009; Yang, Liu, Chen, Lignier, & Jin, 2007). One of the driving forces is the increasing demand of large scale instance and data/computation intensive workflow applications (large scale workflow applications for short) which are common in both eBusiness and eScience application areas. Typical examples (will be detailed in Section 13.2.1) include such as the transaction intensive nation-wide insurance claim application process; the data and computation intensive pulsar searching process in Astrophysics. Generally speaking, instance intensive applications are those processes which need to be executed for a large number of times sequentially within a very short period or concurrently with a large number of instances (Liu, Chen, Yang, & Jin, 2008; Liu et al., 2010; Yang et al., 2008). Therefore, large scale workflow applications normally require the support of high performance computing infrastructures (e.g. advanced CPU units, large memory space and high speed network), especially when workflow activities are of data and computation intensive themselves. In the real world, to accommodate such a request, expensive computing infrastructures including such as supercomputers and data servers are bought, installed, integrated and maintained with huge cost by system users

  17. Deconstruction of Interhospital Transfer Workflow in Large Vessel Occlusion: Real-World Data in the Thrombectomy Era.

    Science.gov (United States)

    Ng, Felix C; Low, Essie; Andrew, Emily; Smith, Karen; Campbell, Bruce C V; Hand, Peter J; Crompton, Douglas E; Wijeratne, Tissa; Dewey, Helen M; Choi, Philip M

    2017-07-01

    Interhospital transfer is a critical component in the treatment of acute anterior circulation large vessel occlusive stroke transferred for mechanical thrombectomy. Real-world data for benchmarking and theoretical modeling are limited. We sought to characterize transfer workflow from primary stroke center (PSC) to comprehensive stroke center after the publication of positive thrombectomy trials. Consecutive patients transferred from 3 high-volume PSCs to a single comprehensive stroke center between January 2015 and August 2016 were included in a retrospective study. Factors associated with key time metrics were analyzed with emphasis on PSC intrahospital workflow. Sixty-seven patients were identified. Median age was 74 years (interquartile range [IQR], 63.5-78) and National Institutes of Health Stroke Scale 17 (IQR, 12-21). Median transfer time measured by PSC-door-to-comprehensive stroke center-door was 128 minutes (IQR, 107-164), of which 82.8% was spent at PSCs (door-in-door-out [DIDO]; 106 minutes; IQR, 86-143). The lengthiest component of DIDO was computed-tomography-to-retrieval-request (median 59.5 minutes; IQR, 44-83). The 37.3% had DIDO exceeding 120 minutes. DIDO times differed significantly between PSCs ( P =0.01). In multivariate analyses, rerecruiting the initial ambulance crew for transfer ( P workflow represents a major opportunity to expedite mechanical thrombectomy and improve patient outcomes. © 2017 American Heart Association, Inc.

  18. Palliative Care Processes Embedded in the ICU Workflow May Reserve Palliative Care Teams for Refractory Cases.

    Science.gov (United States)

    Mun, Eluned; Umbarger, Lillian; Ceria-Ulep, Clementina; Nakatsuka, Craig

    2018-01-01

    Palliative Care Teams have been shown to be instrumental in the early identification of multiple aspects of advanced care planning. Despite an increased number of services to meet the rising consultation demand, it is conceivable that the numbers of palliative care consultations generated from an ICU alone could become overwhelming for an existing palliative care team. Improve end-of-life care in the ICU by incorporating basic palliative care processes into the daily routine ICU workflow, thereby reserving the palliative care team for refractory situations. A structured, palliative care, quality-improvement program was implemented and evaluated in the ICU at Kaiser Permanente Medical Center in Hawaii. This included selecting trigger criteria, a care model, forming guidelines, and developing evaluation criteria. These included the early identification of the multiple features of advanced care planning, numbers of proactive ICU and palliative care family meetings, and changes in code status and treatment upon completion of either meeting. Early identification of Goals-of-Care, advance directives, and code status by the ICU staff led to a proactive ICU family meeting with resultant increases in changes in code status and treatment. The numbers of palliative care consultations also rose, but not significantly. Palliative care processes could be incorporated into a daily ICU workflow allowing for integration of aspects of advanced care planning to be identified in a systematic and proactive manner. This reserved the palliative care team for situations when palliative care efforts performed by the ICU staff were ineffective.

  19. Exergoeconomic performance optimization for a steady-flow endoreversible refrigeration model including six typical cycles

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Lingen; Kan, Xuxian; Sun, Fengrui; Wu, Feng [College of Naval Architecture and Power, Naval University of Engineering, Wuhan 430033 (China)

    2013-07-01

    The operation of a universal steady flow endoreversible refrigeration cycle model consisting of a constant thermal-capacity heating branch, two constant thermal-capacity cooling branches and two adiabatic branches is viewed as a production process with exergy as its output. The finite time exergoeconomic performance optimization of the refrigeration cycle is investigated by taking profit rate optimization criterion as the objective. The relations between the profit rate and the temperature ratio of working fluid, between the COP (coefficient of performance) and the temperature ratio of working fluid, as well as the optimal relation between profit rate and the COP of the cycle are derived. The focus of this paper is to search the compromised optimization between economics (profit rate) and the utilization factor (COP) for endoreversible refrigeration cycles, by searching the optimum COP at maximum profit, which is termed as the finite-time exergoeconomic performance bound. Moreover, performance analysis and optimization of the model are carried out in order to investigate the effect of cycle process on the performance of the cycles using numerical example. The results obtained herein include the performance characteristics of endoreversible Carnot, Diesel, Otto, Atkinson, Dual and Brayton refrigeration cycles.

  20. Intestinal bacterial overgrowth includes potential pathogens in the carbohydrate overload models of equine acute laminitis.

    Science.gov (United States)

    Onishi, Janet C; Park, Joong-Wook; Prado, Julio; Eades, Susan C; Mirza, Mustajab H; Fugaro, Michael N; Häggblom, Max M; Reinemeyer, Craig R

    2012-10-12

    Carbohydrate overload models of equine acute laminitis are used to study the development of lameness. It is hypothesized that a diet-induced shift in cecal bacterial communities contributes to the development of the pro-inflammatory state that progresses to laminar failure. It is proposed that vasoactive amines, protease activators and endotoxin, all bacterial derived bioactive metabolites, play a role in disease development. Questions regarding the oral bioavailability of many of the bacterial derived bioactive metabolites remain. This study evaluates the possibility that a carbohydrate-induced overgrowth of potentially pathogenic cecal bacteria occurs and that bacterial translocation contributes toward the development of the pro-inflammatory state. Two groups of mixed-breed horses were used, those with laminitis induced by cornstarch (n=6) or oligofructan (n=6) and non-laminitic controls (n=8). Cecal fluid and tissue homogenates of extra-intestinal sites including the laminae were used to enumerate Gram-negative and -positive bacteria. Horses that developed Obel grade2 lameness, revealed a significant overgrowth of potentially pathogenic Gram-positive and Gram-negative intestinal bacteria within the cecal fluid. Although colonization of extra-intestinal sites with potentially pathogenic bacteria was not detected, results of this study indicate that cecal/colonic lymphadenopathy and eosinophilia develop in horses progressing to lameness. It is hypothesized that the pro-inflammatory state in carbohydrate overload models of equine acute laminitis is driven by an immune response to the rapid overgrowth of Gram-positive and Gram-negative cecal bacterial communities in the gut. Further equine research is indicated to study the immunological response, involving the lymphatic system that develops in the model. Copyright © 2012 Elsevier B.V. All rights reserved.

  1. CFD simulations and reduced order modeling of a refrigerator compartment including radiation effects

    International Nuclear Information System (INIS)

    Bayer, Ozgur; Oskay, Ruknettin; Paksoy, Akin; Aradag, Selin

    2013-01-01

    Highlights: ► Free convection in a refrigerator is simulated including radiation effects. ► Heat rates are affected drastically when radiation effects are considered. ► 95% of the flow energy can be represented by using one spatial POD mode. - Abstract: Considering the engineering problem of natural convection in domestic refrigerator applications, this study aims to simulate the fluid flow and temperature distribution in a single commercial refrigerator compartment by using the experimentally determined temperature values as the specified constant wall temperature boundary conditions. The free convection in refrigerator applications is evaluated as a three-dimensional (3D), turbulent, transient and coupled non-linear flow problem. Radiation heat transfer mode is also included in the analysis. According to the results, taking radiation effects into consideration does not change the temperature distribution inside the refrigerator significantly; however the heat rates are affected drastically. The flow inside the compartment is further analyzed with a reduced order modeling method called Proper Orthogonal Decomposition (POD) and the energy contents of several spatial and temporal modes that exist in the flow are examined. The results show that approximately 95% of all the flow energy can be represented by only using one spatial mode

  2. Improved Screening Mammogram Workflow by Maximizing PACS Streamlining Capabilities in an Academic Breast Center.

    Science.gov (United States)

    Pham, Ramya; Forsberg, Daniel; Plecha, Donna

    2017-04-01

    The aim of this study was to perform an operational improvement project targeted at the breast imaging reading workflow of mammography examinations at an academic medical center with its associated breast centers and satellite sites. Through careful analysis of the current workflow, two major issues were identified: stockpiling of paperwork and multiple worklists. Both issues were considered to cause significant delays to the start of interpreting screening mammograms. Four workflow changes were suggested (scanning of paperwork, worklist consolidation, use of chat functionality, and tracking of case distribution among trainees) and implemented in July 2015. Timestamp data was collected 2 months before (May-Jun) and after (Aug-Sep) the implemented changes. Generalized linear models were used to analyze the data. The results showed significant improvements for the interpretation of screening mammograms. The average time elapsed for time to open a case reduced from 70 to 28 min (60 % decrease, p workflow for diagnostic mammograms at large unaltered even with increased volume of mammography examinations (31 % increase of 4344 examinations for May-Jun to 5678 examinations for Aug-Sep). In conclusion, targeted efforts to improve the breast imaging reading workflow for screening mammograms in a teaching environment provided significant performance improvements without affecting the workflow of diagnostic mammograms.

  3. An iterative expanding and shrinking process for processor allocation in mixed-parallel workflow scheduling.

    Science.gov (United States)

    Huang, Kuo-Chan; Wu, Wei-Ya; Wang, Feng-Jian; Liu, Hsiao-Ching; Hung, Chun-Hao

    2016-01-01

    Parallel computation has been widely applied in a variety of large-scale scientific and engineering applications. Many studies indicate that exploiting both task and data parallelisms, i.e. mixed-parallel workflows, to solve large computational problems can get better efficacy compared with either pure task parallelism or pure data parallelism. Scheduling traditional workflows of pure task parallelism on parallel systems has long been known to be an NP-complete problem. Mixed-parallel workflow scheduling has to deal with an additional challenging issue of processor allocation. In this paper, we explore the processor allocation issue in scheduling mixed-parallel workflows of moldable tasks, called M-task, and propose an Iterative Allocation Expanding and Shrinking (IAES) approach. Compared to previous approaches, our IAES has two distinguishing features. The first is allocating more processors to the tasks on allocated critical paths for effectively reducing the makespan of workflow execution. The second is allowing the processor allocation of an M-task to shrink during the iterative procedure, resulting in a more flexible and effective process for finding better allocation. The proposed IAES approach has been evaluated with a series of simulation experiments and compared to several well-known previous methods, including CPR, CPA, MCPA, and MCPA2. The experimental results indicate that our IAES approach outperforms those previous methods significantly in most situations, especially when nodes of the same layer in a workflow might have unequal workloads.

  4. Impact of workflow on the use of the Surgical Safety Checklist: a qualitative study.

    Science.gov (United States)

    Gillespie, Brigid M; Marshall, Andrea P; Gardiner, Therese; Lavin, Joanne; Withers, Teresa K

    2016-11-01

    Regardless of the benefits associated of the Surgical Safety Checklist, adherence across its three phases remains inconsistent. The aim of this study was to systematically identify issues around workflow that impact on surgical teams' ability to use the Surgical Safety Checklist in a large tertiary facility in Queensland, Australia. Observational audit of 10 surgical teams and 33 semi-structured interviews with 70 participants from nursing, medicine and the community were conducted. Data were collected during 2014-2015. Inductive and deductive approaches were used to analyse field observations and interview transcripts. The domain, impact of workflow on checklist utilization, was identified. Within this domain, seven categories illustrated the causal conditions which determined the ways in which workflow influenced checklist use. These categories included: 'busy doing the task'; 'clashing task priorities'; 'being pressured, running out of time'; 'adapting processes to work patterns'; 'doubling up on work'; 'a domino effect, leading to delays' and 'reality of the workflow'. One of the greatest systemic challenges to checklist use in surgery is workflow. Process changes in the way that surgical safety checklists are used need to incorporate the temporal demands of the workflow. Any changes made must ensure the process is reliable, is easily embedded into existing work routines and is not disruptive. © 2016 Royal Australasian College of Surgeons.

  5. Evolution of the continental upper mantle : numerical modelling of thermo-chemical convection including partial melting

    NARCIS (Netherlands)

    de Smet, J.H.

    1999-01-01

    This thesis elaborates on the evolution of the continental upper mantle based on numerical modelling results. The descriptive and explanatory basis is formed by a numerical thermo-chemical convection model. The model evolution starts in the early Archaean about 4 billion years ago. The model follows

  6. Evolution of the continental upper mantle : numerical modelling of thermo-chemical convection including partial melting

    NARCIS (Netherlands)

    Smet, J.H. de

    1999-01-01

    This thesis elaborates on the evolution of the continental upper mantle based on numerical modelling results. The descriptive and explanatory basis is formed by a numerical thermo-chemical convection model. The model evolution starts in the early Archaean about 4 billion years ago. The model

  7. A Thermal Evolution Model of the Earth Including the Biosphere, Continental Growth and Mantle Hydration

    Science.gov (United States)

    Höning, D.; Spohn, T.

    2014-12-01

    By harvesting solar energy and converting it to chemical energy, photosynthetic life plays an important role in the energy budget of Earth [2]. This leads to alterations of chemical reservoirs eventually affecting the Earth's interior [4]. It further has been speculated [3] that the formation of continents may be a consequence of the evolution life. A steady state model [1] suggests that the Earth without its biosphere would evolve to a steady state with a smaller continent coverage and a dryer mantle than is observed today. We present a model including (i) parameterized thermal evolution, (ii) continental growth and destruction, and (iii) mantle water regassing and outgassing. The biosphere enhances the production rate of sediments which eventually are subducted. These sediments are assumed to (i) carry water to depth bound in stable mineral phases and (ii) have the potential to suppress shallow dewatering of the underlying sediments and crust due to their low permeability. We run a Monte Carlo simulation for various initial conditions and treat all those parameter combinations as success which result in the fraction of continental crust coverage observed for present day Earth. Finally, we simulate the evolution of an abiotic Earth using the same set of parameters but a reduced rate of continental weathering and erosion. Our results suggest that the origin and evolution of life could have stabilized the large continental surface area of the Earth and its wet mantle, leading to the relatively low mantle viscosity we observe at present. Without photosynthetic life on our planet, the Earth would be geodynamical less active due to a dryer mantle, and would have a smaller fraction of continental coverage than observed today. References[1] Höning, D., Hansen-Goos, H., Airo, A., Spohn, T., 2014. Biotic vs. abiotic Earth: A model for mantle hydration and continental coverage. Planetary and Space Science 98, 5-13. [2] Kleidon, A., 2010. Life, hierarchy, and the

  8. CSPBuilder - CSP based Scientific Workflow Modelling

    DEFF Research Database (Denmark)

    Friborg, Rune Møllegaard; Vinter, Brian

    2008-01-01

    This paper introduces a framework for building CSP based applications, targeted for clusters and next generation CPU designs. CPUs are produced with several cores today and every future CPU generation will feature increasingly more cores, resulting in a requirement for concurrency that has not pr...

  9. Introducing students to digital geological mapping: A workflow based on cheap hardware and free software

    Science.gov (United States)

    Vrabec, Marko; Dolžan, Erazem

    2016-04-01

    The undergraduate field course in Geological Mapping at the University of Ljubljana involves 20-40 students per year, which precludes the use of specialized rugged digital field equipment as the costs would be way beyond the capabilities of the Department. A different mapping area is selected each year with the aim to provide typical conditions that a professional geologist might encounter when doing fieldwork in Slovenia, which includes rugged relief, dense tree cover, and moderately-well- to poorly-exposed bedrock due to vegetation and urbanization. It is therefore mandatory that the digital tools and workflows are combined with classical methods of fieldwork, since, for example, full-time precise GNSS positioning is not viable under such circumstances. Additionally, due to the prevailing combination of complex geological structure with generally poor exposure, students cannot be expected to produce line (vector) maps of geological contacts on the go, so there is no need for such functionality in hardware and software that we use in the field. Our workflow therefore still relies on paper base maps, but is strongly complemented with digital tools to provide robust positioning, track recording, and acquisition of various point-based data. Primary field hardware are students' Android-based smartphones and optionally tablets. For our purposes, the built-in GNSS chips provide adequate positioning precision most of the time, particularly if they are GLONASS-capable. We use Oruxmaps, a powerful free offline map viewer for the Android platform, which facilitates the use of custom-made geopositioned maps. For digital base maps, which we prepare in free Windows QGIS software, we use scanned topographic maps provided by the National Geodetic Authority, but also other maps such as aerial imagery, processed Digital Elevation Models, scans of existing geological maps, etc. Point data, like important outcrop locations or structural measurements, are entered into Oruxmaps as

  10. Verification of Timed Healthcare Workflows Using Component Timed-Arc Petri Nets

    DEFF Research Database (Denmark)

    Bertolini, Cristiano; Liu, Zhiming; Srba, Jiri

    2013-01-01

    Workflows in modern healthcare systems are becoming increasingly complex and their execution involves concurrency and sharing of resources. The definition, analysis and management of collaborative healthcare workflows requires abstract model notations with a precisely defined semantics and a supp......Workflows in modern healthcare systems are becoming increasingly complex and their execution involves concurrency and sharing of resources. The definition, analysis and management of collaborative healthcare workflows requires abstract model notations with a precisely defined semantics...... and a support for compositional reasoning. We use the formalism of component-based timed-arc Petri Nets (CTAPN) for modular modelling of collaborative healthcare workflows and demonstrate how the model checker TAPAAL supports the verification of their functional and non-functional requirements. To this end, we...... use CTAPN to define the semantics of the healthcare domain specific graphical notation Little-JIL, extended with timing constrains, and apply it to the case study of blood transfusion. The value added in general, and to Little-JIL in particular, is the formal support for compositional modelling...

  11. Numerical modelling of seawater intrusion in Shenzhen (China) using a 3D density-dependent model including tidal effects

    Science.gov (United States)

    Lu, Wei; Yang, Qingchun; Martín, Jordi D.; Juncosa, Ricardo

    2013-04-01

    During the 1990s, groundwater overexploitation has resulted in seawater intrusion in the coastal aquifer of the Shenzhen city, China. Although water supply facilities have been improved and alleviated seawater intrusion in recent years, groundwater overexploitation is still of great concern in some local areas. In this work we present a three-dimensional density-dependent numerical model developed with the FEFLOW code, which is aimed at simulating the extent of seawater intrusion while including tidal effects and different groundwater pumping scenarios. Model calibration, using waterheads and reported chloride concentration, has been performed based on the data from 14 boreholes, which were monitored from May 2008 to December 2009. A fairly good fitness between the observed and computed values was obtained by a manual trial-and-error method. Model prediction has been carried out forward 3 years with the calibrated model taking into account high, medium and low tide levels and different groundwater exploitation schemes. The model results show that tide-induced seawater intrusion significantly affects the groundwater levels and concentrations near the estuarine of the Dasha river, which implies that an important hydraulic connection exists between this river and groundwater, even considering that some anti-seepage measures were taken in the river bed. Two pumping scenarios were considered in the calibrated model in order to predict the future changes in the water levels and chloride concentration. The numerical results reveal a decreased tendency of seawater intrusion if groundwater exploitation does not reach an upper bound of about 1.32 × 104 m3/d. The model results provide also insights for controlling seawater intrusion in such coastal aquifer systems.

  12. Workflows and performances in the ranking prediction of 2016 D3R Grand Challenge 2: lessons learned from a collaborative effort

    Science.gov (United States)

    Gao, Ying-Duo; Hu, Yuan; Crespo, Alejandro; Wang, Deping; Armacost, Kira A.; Fells, James I.; Fradera, Xavier; Wang, Hongwu; Wang, Huijun; Sherborne, Brad; Verras, Andreas; Peng, Zhengwei

    2018-01-01

    The 2016 D3R Grand Challenge 2 includes both pose and affinity or ranking predictions. This article is focused exclusively on affinity predictions submitted to the D3R challenge from a collaborative effort of the modeling and informatics group. Our submissions include ranking of 102 ligands covering 4 different chemotypes against the FXR ligand binding domain structure, and the relative binding affinity predictions of the two designated free energy subsets of 15 and 18 compounds. Using all the complex structures prepared in the same way allowed us to cover many types of workflows and compare their performances effectively. We evaluated typical workflows used in our daily structure-based design modeling support, which include docking scores, force field-based scores, QM/MM, MMGBSA, MD-MMGBSA, and MacroModel interaction energy estimations. The best performing methods for the two free energy subsets are discussed. Our results suggest that affinity ranking still remains very challenging; that the knowledge of more structural information does not necessarily yield more accurate predictions; and that visual inspection and human intervention are considerably important for ranking. Knowledge of the mode of action and protein flexibility along with visualization tools that depict polar and hydrophobic maps are very useful for visual inspection. QM/MM-based workflows were found to be powerful in affinity ranking and are encouraged to be applied more often. The standardized input and output enable systematic analysis and support methodology development and improvement for high level blinded predictions.

  13. Beyond Scientific Workflows: Networked Open Processes

    NARCIS (Netherlands)

    Cushing, R.; Bubak, M.; Belloum, A.; de Laat, C.

    2013-01-01

    The multitude of scientific services and processes being developed brings about challenges for future in silico distributed experiments. Choosing the correct service from an expanding body of processes means that the the task of manually building workflows is becoming untenable. In this paper we

  14. Workflow Management for Complex HEP Analyses

    Science.gov (United States)

    Erdmann, M.; Fischer, R.; Rieger, M.; von Cube, R. F.

    2017-10-01

    We present the novel Analysis Workflow Management (AWM) that provides users with the tools and competences of professional large scale workflow systems, e.g. Apache’s Airavata[1]. The approach presents a paradigm shift from executing parts of the analysis to defining the analysis. Within AWM an analysis consists of steps. For example, a step defines to run a certain executable for multiple files of an input data collection. Each call to the executable for one of those input files can be submitted to the desired run location, which could be the local computer or a remote batch system. An integrated software manager enables automated user installation of dependencies in the working directory at the run location. Each execution of a step item creates one report for bookkeeping purposes containing error codes and output data or file references. Required files, e.g. created by previous steps, are retrieved automatically. Since data storage and run locations are exchangeable from the steps perspective, computing resources can be used opportunistically. A visualization of the workflow as a graph of the steps in the web browser provides a high-level view on the analysis. The workflow system is developed and tested alongside of a ttbb cross section measurement where, for instance, the event selection is represented by one step and a Bayesian statistical inference is performed by another. The clear interface and dependencies between steps enables a make-like execution of the whole analysis.

  15. Using workflow for projects in higher education

    NARCIS (Netherlands)

    van der Veen, Johan (CTIT); Jones, Valerie M.; Collis, Betty

    2000-01-01

    The WWW is increasingly used as a medium to support education and training. A course at the University of Twente in which groups of students collaborate in the design and production of multimedia instructional materials has now been supported by a website since 1995. Workflow was integrated with

  16. Workflow Automation: A Collective Case Study

    Science.gov (United States)

    Harlan, Jennifer

    2013-01-01

    Knowledge management has proven to be a sustainable competitive advantage for many organizations. Knowledge management systems are abundant, with multiple functionalities. The literature reinforces the use of workflow automation with knowledge management systems to benefit organizations; however, it was not known if process automation yielded…

  17. On Secure Workflow Decentralisation on the Internet

    Directory of Open Access Journals (Sweden)

    Petteri Kaskenpalo

    2010-06-01

    Full Text Available Decentralised workflow management systems are a new research area, where most work to-date has focused on the system's overall architecture. As little attention has been given to the security aspects in such systems, we follow a security driven approach, and consider, from the perspective of available security building blocks, how security can be implemented and what new opportunities are presented when empowering the decentralised environment with modern distributed security protocols. Our research is motivated by a more general question of how to combine the positive enablers that email exchange enjoys, with the general benefits of workflow systems, and more specifically with the benefits that can be introduced in a decentralised environment. This aims to equip email users with a set of tools to manage the semantics of a message exchange, contents, participants and their roles in the exchange in an environment that provides inherent assurances of security and privacy. This work is based on a survey of contemporary distributed security protocols, and considers how these protocols could be used in implementing a distributed workflow management system with decentralised control . We review a set of these protocols, focusing on the required message sequences in reviewing the protocols, and discuss how these security protocols provide the foundations for implementing core control-flow, data, and resource patterns in a distributed workflow environment.

  18. Adaptive workflow simulation of emergency response

    NARCIS (Netherlands)

    Bruinsma, Guido Wybe Jan

    2010-01-01

    Recent incidents and major training exercises in and outside the Netherlands have persistently shown that not having or not sharing information during emergency response are major sources of emergency response inefficiency and error, and affect incident mitigation outcomes through workflow planning

  19. Complete digital workflow for the production of implant-supported single-unit monolithic crowns.

    Science.gov (United States)

    Joda, Tim; Brägger, Urs

    2014-11-01

    The aim of this case series was to introduce a complete digital workflow for the production of monolithic implant crowns. Six patients were treated with implant-supported crowns made of resin nano ceramic (RNC). Starting with an intraoral optical scan (IOS), and following a CAD/CAM process, the monolithic crowns were bonded either to a novel prefabricated titanium abutment base (group A) or to a CAD/CAM-generated individualized titanium abutment (group B) in premolar or molar sites on a soft tissue level dental implant. Economic analyses included clinical and laboratory steps. An esthetic evaluation was performed to compare the two abutment-crown combinations. None of the digitally constructed RNC crowns required any clinical adaptation. Overall mean work time calculations revealed obvious differences for group A (65.3 min) compared with group B (86.5 min). Esthetic analysis demonstrated a more favorable outcome for the prefabricated bonding bases. Prefabricated or individualized abutments on monolithic RNC crowns using CAD/CAM technology in a model-free workflow seem to provide a feasible and streamlined treatment approach for single-edentulous space rehabilitation in the posterior region. However, RNC as full-contour material has to be considered experimental, and further large-scale clinical investigations with long-term follow-up observation are necessary. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  20. Achieving Coordination through Dynamic Construction of Open Workflows

    Science.gov (United States)

    Thomas, Louis; Wilson, Justin; Roman, Gruia-Catalin; Gill, Christopher

    Workflow middleware executes tasks orchestrated by rules defined in a carefully handcrafted static graph. Workflow management systems have proved effective for service-oriented business automation in stable, wired infrastructures. We introduce a radically new paradigm for workflow construction and execution called open workflow to support goal-directed coordination among physically mobile people and devices that form a transient community over an ad hoc wireless network. The quintessential feature of the open workflow paradigm is dynamic construction of custom, context-specific workflows in response to unpredictable and evolving circumstances by exploiting the knowledge and services available within a given spatiotemporal context. This paper introduces the open workflow approach, surveys open research challenges in this promising new field, and presents algorithmic, architectural, and evaluation results for the first practical realization of an open workflow management system.

  1. Including Overweight or Obese Students in Physical Education: A Social Ecological Constraint Model

    Science.gov (United States)

    Li, Weidong; Rukavina, Paul

    2012-01-01

    In this review, we propose a social ecological constraint model to study inclusion of overweight or obese students in physical education by integrating key concepts and assumptions from ecological constraint theory in motor development and social ecological models in health promotion and behavior. The social ecological constraint model proposes…

  2. ETM documentation update – including modelling conventions and manual for software tools

    DEFF Research Database (Denmark)

    Grohnheit, Poul Erik

    , it summarises the work done during 2013, and it also contains presentations for promotion of fusion as a future element in the electricity generation mix and presentations for the modelling community concerning model development and model documentation – in particular for TIAM collaboration workshops....

  3. Serverification of Molecular Modeling Applications: The Rosetta Online Server That Includes Everyone (ROSIE)

    Science.gov (United States)

    Conchúir, Shane Ó.; Der, Bryan S.; Drew, Kevin; Kuroda, Daisuke; Xu, Jianqing; Weitzner, Brian D.; Renfrew, P. Douglas; Sripakdeevong, Parin; Borgo, Benjamin; Havranek, James J.; Kuhlman, Brian; Kortemme, Tanja; Bonneau, Richard; Gray, Jeffrey J.; Das, Rhiju

    2013-01-01

    The Rosetta molecular modeling software package provides experimentally tested and rapidly evolving tools for the 3D structure prediction and high-resolution design of proteins, nucleic acids, and a growing number of non-natural polymers. Despite its free availability to academic users and improving documentation, use of Rosetta has largely remained confined to developers and their immediate collaborators due to the code’s difficulty of use, the requirement for large computational resources, and the unavailability of servers for most of the Rosetta applications. Here, we present a unified web framework for Rosetta applications called ROSIE (Rosetta Online Server that Includes Everyone). ROSIE provides (a) a common user interface for Rosetta protocols, (b) a stable application programming interface for developers to add additional protocols, (c) a flexible back-end to allow leveraging of computer cluster resources shared by RosettaCommons member institutions, and (d) centralized administration by the RosettaCommons to ensure continuous maintenance. This paper describes the ROSIE server infrastructure, a step-by-step ‘serverification’ protocol for use by Rosetta developers, and the deployment of the first nine ROSIE applications by six separate developer teams: Docking, RNA de novo, ERRASER, Antibody, Sequence Tolerance, Supercharge, Beta peptide design, NCBB design, and VIP redesign. As illustrated by the number and diversity of these applications, ROSIE offers a general and speedy paradigm for serverification of Rosetta applications that incurs negligible cost to developers and lowers barriers to Rosetta use for the broader biological community. ROSIE is available at http://rosie.rosettacommons.org. PMID:23717507

  4. LHCb: LHCbDirac is a DIRAC extension to support LHCb specific workflows

    CERN Multimedia

    Stagni, Federico

    2012-01-01

    We present LHCbDIRAC, an extension of the DIRAC community Grid solution to handle the LHCb specificities. The DIRAC software has been developed for many years within LHCb only. Nowadays it is a generic software, used by many scientific communities worldwide. Each community wanting to take advantage of DIRAC has to develop an extension, containing all the necessary code for handling their specific cases. LHCbDIRAC is an actively developed extension, implementing the LHCb computing model and workflows. LHCbDIRAC extends DIRAC to handle all the distributed computing activities of LHCb. Such activities include real data processing (reconstruction, stripping and streaming), Monte-Carlo simulation and data replication. Other activities are groups and user analysis, data management, resources management and monitoring, data provenance, accounting for user and production jobs. LHCbDIRAC also provides extensions of the DIRAC interfaces, including a secure web client, python APIs and CLIs. While DIRAC and LHCbDIRAC f...

  5. Database Support for Workflow Management: The WIDE Project

    NARCIS (Netherlands)

    Grefen, P.W.P.J.; Pernici, B; Sánchez, G.; Unknown, [Unknown

    1999-01-01

    Database Support for Workflow Management: The WIDE Project presents the results of the ESPRIT WIDE project on advanced database support for workflow management. The book discusses the state of the art in combining database management and workflow management technology, especially in the areas of

  6. Construction of biological networks from unstructured information based on a semi-automated curation workflow.

    Science.gov (United States)

    Szostak, Justyna; Ansari, Sam; Madan, Sumit; Fluck, Juliane; Talikka, Marja; Iskandar, Anita; De Leon, Hector; Hofmann-Apitius, Martin; Peitsch, Manuel C; Hoeng, Julia

    2015-06-17

    Capture and representation of scientific knowledge in a structured format are essential to improve the understanding of biological mechanisms involved in complex diseases. Biological knowledge and knowledge about standardized terminologies are difficult to capture from literature in a usable form. A semi-automated knowledge extraction workflow is presented that was developed to allow users to extract causal and correlative relationships from scientific literature and to transcribe them into the computable and human readable Biological Expression Language (BEL). The workflow combines state-of-the-art linguistic tools for recognition of various entities and extraction of knowledge from literature sources. Unlike most other approaches, the workflow outputs the results to a curation interface for manual curation and converts them into BEL documents that can be compiled to form biological networks. We developed a new semi-automated knowledge extraction workflow that was designed to capture and organize scientific knowledge and reduce the required curation skills and effort for this task. The workflow was used to build a network that represents the cellular and molecular mechanisms implicated in atherosclerotic plaque destabilization in an apolipoprotein-E-deficient (ApoE(-/-)) mouse model. The network was generated using knowledge extracted from the primary literature. The resultant atherosclerotic plaque destabilization network contains 304 nodes and 743 edges supported by 33 PubMed referenced articles. A comparison between the semi-automated and conventional curation processes showed similar results, but significantly reduced curation effort for the semi-automated process. Creating structured knowledge from unstructured text is an important step for the mechanistic interpretation and reusability of knowledge. Our new semi-automated knowledge extraction workflow reduced the curation skills and effort required to capture and organize scientific knowledge. The

  7. Integration of implant planning workflows into the PACS infrastructure

    Science.gov (United States)

    Gessat, Michael; Strauß, Gero; Burgert, Oliver

    2008-03-01

    The integration of imaging devices, diagnostic workstations, and image servers into Picture Archiving and Communication Systems (PACS) has had an enormous effect on the efficiency of radiology workflows. The standardization of the information exchange between the devices with the DICOM standard has been an essential precondition for that development. For surgical procedures, no such infrastructure exists. With the increasingly important role computerized planning and assistance systems play in the surgical domain, an infrastructure that unifies the communication between devices becomes necessary. In recent publications, the need for a modularized system design has been established. A reference architecture for a Therapy Imaging and Model Management System (TIMMS) has been proposed. It was accepted by the DICOM Working Group 6 as the reference architecture for DICOM developments for surgery. In this paper we propose the inclusion of implant planning systems into the PACS infrastructure. We propose a generic information model for the patient specific selection and positioning of implants from a repository according to patient image data. The information models are based on clinical workflows from ENT, cardiac, and orthopedic surgery as well as technical requirements derived from different use cases and systems. We show an exemplary implementation of the model for application in ENT surgery: the selection and positioning of an ossicular implant in the middle ear. An implant repository is stored in the PACS. It makes use of an experimental implementation of the Surface Mesh Module that is currently being developed as extension to the DICOM standard.

  8. Transverse Crack Modeling and Validation in Rotor Systems, Including Thermal Effects

    Directory of Open Access Journals (Sweden)

    N. Bachschmid

    2003-01-01

    Full Text Available This article describes a model that allows the simulation of the static behavior of a transverse crack in a horizontal rotor under the action of weight and other possible static loads and the dynamic behavior of cracked rotating shaft. The crack breathes—that is, the mechanism of the crack's opening and closing is ruled by the stress on the cracked section exerted by the external loads. In a rotor, the stresses are time-dependent and have a period equal to the period of rotation; thus, the crack periodically breathes. An original, simplified model allows cracks of various shapes to be modeled and thermal stresses to be taken into account, as they may influence the opening and closing mechanism. The proposed method was validated by using two criteria. First the crack's breathing mechanism, simulated by the model, was compared with the results obtained by a nonlinear, threedimensional finite element model calculation, and a good agreement in the results was observed. Then the proposed model allowed the development of the equivalent cracked beam. The results of this model were compared with those obtained by the three-dimensional finite element model. Also in this case, there was a good agreement in the results.

  9. A model for firm-specific strategic wisdom : including illustrations and 49 guiding questions

    NARCIS (Netherlands)

    van Straten, Roeland Peter

    2017-01-01

    This PhD thesis provides an answer to the question ‘How may one think strategically’. It does so by presenting a new prescriptive ‘Model for Firm-Specific Strategic Wisdom’. This Model aims to guide any individual strategist in his or her thinking from a state of firm-specific ‘ignorance’ to a state

  10. Complete Loss and Thermal Model of Power Semiconductors Including Device Rating Information

    DEFF Research Database (Denmark)

    Ma, Ke; Bahman, Amir Sajjad; Beczkowski, Szymon

    2015-01-01

    models, only the electrical loadings are focused and treated as design variables, while the device rating is normally pre-defined by experience with limited design flexibility. Consequently, a more complete loss and thermal model is proposed in this paper, which takes into account not only the electrical...

  11. Numerical models of single- and double-negative metamaterials including viscous and thermal losses

    DEFF Research Database (Denmark)

    Cutanda Henriquez, Vicente; Sánchez-Dehesa, José

    2017-01-01

    detailed understanding on how viscous and thermal losses affect the setups at different frequencies. The modeling of a simpler single-negative metamaterial also broadens this overview. Both setups have been modeled with quadratic BEM meshes. Each sample, scaled at two different sizes, has been represented...

  12. Gasification of biomass in a fixed bed downdraft gasifier--a realistic model including tar.

    Science.gov (United States)

    Barman, Niladri Sekhar; Ghosh, Sudip; De, Sudipta

    2012-03-01

    This study presents a model for fixed bed downdraft biomass gasifiers considering tar also as one of the gasification products. A representative tar composition along with its mole fractions, as available in the literature was used as an input parameter within the model. The study used an equilibrium approach for the applicable gasification reactions and also considered possible deviations from equilibrium to further upgrade the equilibrium model to validate a range of reported experimental results. Heat balance was applied to predict the gasification temperature and the predicted values were compared with reported results in literature. A comparative study was made with some reference models available in the literature and also with experimental results reported in the literature. Finally a predicted variation of performance of the gasifier by this validated model for different air-fuel ratio and moisture content was also discussed. Copyright © 2011 Elsevier Ltd. All rights reserved.

  13. A viscoplastic model including anisotropic damage for the time dependent behaviour of rock

    Science.gov (United States)

    Pellet, F.; Hajdu, A.; Deleruyelle, F.; Besnus, F.

    2005-08-01

    This paper presents a new constitutive model for the time dependent mechanical behaviour of rock which takes into account both viscoplastic behaviour and evolution of damage with respect to time. This model is built by associating a viscoplastic constitutive law to the damage theory. The main characteristics of this model are the account of a viscoplastic volumetric strain (i.e. contractancy and dilatancy) as well as the anisotropy of damage. The latter is described by a second rank tensor. Using this model, it is possible to predict delayed rupture by determining time to failure, in creep tests for example. The identification of the model parameters is based on experiments such as creep tests, relaxation tests and quasi-static tests. The physical meaning of these parameters is discussed and comparisons with lab tests are presented. The ability of the model to reproduce the delayed failure observed in tertiary creep is demonstrated as well as the sensitivity of the mechanical response to the rate of loading. The model could be used to simulate the evolution of the excavated damage zone around underground openings.

  14. Potential transformation of trace species including aircraft exhaust in a cloud environment. The `Chedrom model`

    Energy Technology Data Exchange (ETDEWEB)

    Ozolin, Y.E.; Karol, I.L. [Main Geophysical Observatory, St. Petersburg (Russian Federation); Ramaroson, R. [Office National d`Etudes et de Recherches Aerospatiales (ONERA), 92 - Chatillon (France)

    1997-12-31

    Box model for coupled gaseous and aqueous phases is used for sensitivity study of potential transformation of trace gases in a cloud environment. The rate of this transformation decreases with decreasing of pH in droplets, with decreasing of photodissociation rates inside the cloud and with increasing of the droplet size. Model calculations show the potential formation of H{sub 2}O{sub 2} in aqueous phase and transformation of gaseous HNO{sub 3} into NO{sub x} in a cloud. This model is applied for exploration of aircraft exhausts evolution in plume inside a cloud. (author) 10 refs.

  15. A Two-Dimensional Modeling Procedure to Estimate the Loss Equivalent Resistance Including the Saturation Effect

    Directory of Open Access Journals (Sweden)

    Rosa Ana Salas

    2013-11-01

    Full Text Available We propose a modeling procedure specifically designed for a ferrite inductor excited by a waveform in time domain. We estimate the loss resistance in the core (parameter of the electrical model of the inductor by means of a Finite Element Method in 2D which leads to significant computational advantages over the 3D model. The methodology is validated for an RM (rectangular modulus ferrite core working in the linear and the saturation regions. Excellent agreement is found between the experimental data and the computational results.

  16. A Two-Account Life Insurance Model for Scenario-Based Valuation Including Event Risk

    DEFF Research Database (Denmark)

    Jensen, Ninna Reitzel; Schomacker, Kristian Juul

    2015-01-01

    Using a two-account model with event risk, we model life insurance contracts taking into account both guaranteed and non-guaranteed payments in participating life insurance as well as in unit-linked insurance. Here, event risk is used as a generic term for life insurance events, such as death......, disability, etc. In our treatment of participating life insurance, we have special focus on the bonus schemes “consolidation” and “additional benefits”, and one goal is to formalize how these work and interact. Another goal is to describe similarities and differences between participating life insurance...... and unit-linked insurance. By use of a two-account model, we are able to illustrate general concepts without making the model too abstract. To allow for complicated financial markets without dramatically increasing the mathematical complexity, we focus on economic scenarios. We illustrate the use of our...

  17. A Lumped Thermal Model Including Thermal Coupling and Thermal Boundary Conditions for High Power IGBT Modules

    DEFF Research Database (Denmark)

    Bahman, Amir Sajjad; Ma, Ke; Blaabjerg, Frede

    2018-01-01

    Detailed thermal dynamics of high power IGBT modules are important information for the reliability analysis and thermal design of power electronic systems. However, the existing thermal models have their limits to correctly predict these complicated thermal behavior in the IGBTs: The typically used...... thermal model based on one-dimensional RC lumps have limits to provide temperature distributions inside the device, moreover some variable factors in the real-field applications like the cooling and heating conditions of the converter cannot be adapted. On the other hand, the more advanced three......-dimensional thermal models based on Finite Element Method (FEM) need massive computations, which make the long-term thermal dynamics difficult to calculate. In this paper, a new lumped three-dimensional thermal model is proposed, which can be easily characterized from FEM simulations and can acquire the critical...

  18. Advanced Modeling of Ramp Operations including Departure Status at Secondary Airports, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — This project addresses three modeling elements relevant to NASA's IADS research and ATD-2 project, two related to ramp operations at primary airports and one related...

  19. Extending the Scope of the Acculturation/Pidginization Model to Include Cognition.

    Science.gov (United States)

    Schumann, John H.

    1990-01-01

    Examines five cognitive models for second-language acquisition (SLA) and assesses how each might account for the Pidginized interlanguage found in the early stages of second-language acquisition. (23 references) (JL)

  20. An integrated computable general equilibrium model including multiple types and uses of water

    OpenAIRE

    Luckmann, Jonas Jens

    2015-01-01

    Water is a scarce resource in many regions of the world and competition for water is an increasing problem. To countervail this trend policies are needed regulating supply and demand for water. As water is used in many economic activities, water related management decisions usually have complex implications. Economic simulation models have been proven useful to ex-ante assess the consequences of policy changes. Specifically, Computable General Equilibrium (CGE) models are very suitable to ana...

  1. Transverse Crack Modeling and Validation in Rotor Systems Including Thermal Effects

    Directory of Open Access Journals (Sweden)

    N. Bachschmid

    2004-01-01

    Full Text Available In this article, a model is described that allows one to simulate the static behavior of a transversal crack in a horizontal rotor, under the action of the weight and other possible static loads and the dynamical behavior of the rotating cracked shaft. The crack “breaths,” i.e., the mechanism of opening and closing of the crack, is ruled by the stress acting on the cracked section due to the external loads; in a rotor the stress is time-depending with a period equal to the period of rotation, thus the crack “periodically breaths.” An original simplified model is described that allows cracks of different shape to be modeled and thermal stresses to be taken into account, since they may influence the opening and closing mechanism. The proposed method has been validated using two criteria. Firstly, the crack “breathing” mechanism, simulated with the model, has been compared with the results obtained by a nonlinear 3-D FEM calculation and a good agreement in the results has been observed. Secondly, the proposed model allows the development of the equivalent cracked beam. The results of this model are compared with those obtained by the above-mentioned 3-D FEM. There is a good agreement in the results, of this case as well.

  2. Including sugar cane in the agro-ecosystem model ORCHIDEE-STICS: calibration and validation

    Science.gov (United States)

    Valade, A.; Vuichard, N.; Ciais, P.; Viovy, N.

    2011-12-01

    Sugarcane is currently the most efficient bioenergy crop with regards to the energy produced per hectare. With approximately half the global bioethanol production in 2005, and a devoted land area expected to expand globally in the years to come, sugar cane is at the heart of the biofuel debate. Dynamic global vegetation models coupled with agronomical models are powerful and novel tools to tackle many of the environmental issues related to biofuels if they are carefully calibrated and validated against field observations. Here we adapt the agro-terrestrial model ORCHIDEE-STICS for sugar cane simulations. Observation data of LAI are used to evaluate the sensitivity of the model to parameters of nitrogen absorption and phenology, which are calibrated in a systematic way for six sites in Australia and La Reunion. We find that the optimal set of parameters is highly dependent on the sites' characteristics and that the model can reproduce satisfactorily the evolution of LAI. This careful calibration of ORCHIDEE-STICS for sugar cane biomass production for different locations and technical itineraries provides a strong basis for further analysis of the impacts of bioenergy-related land use change on carbon cycle budgets. As a next step, a sensitivity analysis is carried out to estimate the uncertainty of the model in biomass and carbon flux simulation due to its parameterization.

  3. Simplification and Validation of a Spectral-Tensor Model for Turbulence Including Atmospheric Stability

    Science.gov (United States)

    Chougule, Abhijit; Mann, Jakob; Kelly, Mark; Larsen, Gunner C.

    2018-02-01

    A spectral-tensor model of non-neutral, atmospheric-boundary-layer turbulence is evaluated using Eulerian statistics from single-point measurements of the wind speed and temperature at heights up to 100 m, assuming constant vertical gradients of mean wind speed and temperature. The model has been previously described in terms of the dissipation rate ɛ , the length scale of energy-containing eddies L , a turbulence anisotropy parameter Γ, the Richardson number Ri, and the normalized rate of destruction of temperature variance η _θ ≡ ɛ _θ /ɛ . Here, the latter two parameters are collapsed into a single atmospheric stability parameter z / L using Monin-Obukhov similarity theory, where z is the height above the Earth's surface, and L is the Obukhov length corresponding to Ri,η _θ. Model outputs of the one-dimensional velocity spectra, as well as cospectra of the streamwise and/or vertical velocity components, and/or temperature, and cross-spectra for the spatial separation of all three velocity components and temperature, are compared with measurements. As a function of the four model parameters, spectra and cospectra are reproduced quite well, but horizontal temperature fluxes are slightly underestimated in stable conditions. In moderately unstable stratification, our model reproduces spectra only up to a scale ˜ 1 km. The model also overestimates coherences for vertical separations, but is less severe in unstable than in stable cases.

  4. A Novel Mean-Value Model of the Cardiovascular System Including a Left Ventricular Assist Device.

    Science.gov (United States)

    Ochsner, Gregor; Amacher, Raffael; Schmid Daners, Marianne

    2017-06-01

    Time-varying elastance models (TVEMs) are often used for simulation studies of the cardiovascular system with a left ventricular assist device (LVAD). Because these models are computationally expensive, they cannot be used for long-term simulation studies. In addition, their equilibria are periodic solutions, which prevent the extraction of a linear time-invariant model that could be used e.g. for the design of a physiological controller. In the current paper, we present a new type of model to overcome these problems: the mean-value model (MVM). The MVM captures the behavior of the cardiovascular system by representative mean values that do not change within the cardiac cycle. For this purpose, each time-varying element is manually converted to its mean-value counterpart. We compare the derived MVM to a similar TVEM in two simulation experiments. In both cases, the MVM is able to fully capture the inter-cycle dynamics of the TVEM. We hope that the new MVM will become a useful tool for researchers working on physiological control algorithms. This paper provides a plant model that enables for the first time the use of tools from classical control theory in the field of physiological LVAD control.

  5. Including crystal structure attributes in machine learning models of formation energies via Voronoi tessellations

    Science.gov (United States)

    Ward, Logan; Liu, Ruoqian; Krishna, Amar; Hegde, Vinay I.; Agrawal, Ankit; Choudhary, Alok; Wolverton, Chris

    2017-07-01

    While high-throughput density functional theory (DFT) has become a prevalent tool for materials discovery, it is limited by the relatively large computational cost. In this paper, we explore using DFT data from high-throughput calculations to create faster, surrogate models with machine learning (ML) that can be used to guide new searches. Our method works by using decision tree models to map DFT-calculated formation enthalpies to a set of attributes consisting of two distinct types: (i) composition-dependent attributes of elemental properties (as have been used in previous ML models of DFT formation energies), combined with (ii) attributes derived from the Voronoi tessellation of the compound's crystal structure. The ML models created using this method have half the cross-validation error and similar training and evaluation speeds to models created with the Coulomb matrix and partial radial distribution function methods. For a dataset of 435 000 formation energies taken from the Open Quantum Materials Database (OQMD), our model achieves a mean absolute error of 80 meV/atom in cross validation, which is lower than the approximate error between DFT-computed and experimentally measured formation enthalpies and below 15% of the mean absolute deviation of the training set. We also demonstrate that our method can accurately estimate the formation energy of materials outside of the training set and be used to identify materials with especially large formation enthalpies. We propose that our models can be used to accelerate the discovery of new materials by identifying the most promising materials to study with DFT at little additional computational cost.

  6. Managing Evolving Business Workflows through the Capture of Descriptive Information

    CERN Document Server

    Gaspard, S; Dindeleux, R; McClatchey, R; Gaspard, Sebastien; Estrella, Florida

    2003-01-01

    Business systems these days need to be agile to address the needs of a changing world. In particular the discipline of Enterprise Application Integration requires business process management to be highly reconfigurable with the ability to support dynamic workflows, inter-application integration and process reconfiguration. Basing EAI systems on model-resident or on a so-called description-driven approach enables aspects of flexibility, distribution, system evolution and integration to be addressed in a domain-independent manner. Such a system called CRISTAL is described in this paper with particular emphasis on its application to EAI problem domains. A practical example of the CRISTAL technology in the domain of manufacturing systems, called Agilium, is described to demonstrate the principles of model-driven system evolution and integration. The approach is compared to other model-driven development approaches such as the Model-Driven Architecture of the OMG and so-called Adaptive Object Models.

  7. Including fluid shear viscosity in a structural acoustic finite element model using a scalar fluid representation

    Science.gov (United States)

    Cheng, Lei; Li, Yizeng; Grosh, Karl

    2013-01-01

    An approximate boundary condition is developed in this paper to model fluid shear viscosity at boundaries of coupled fluid-structure system. The effect of shear viscosity is approximated by a correction term to the inviscid boundary condition, written in terms of second order in-plane derivatives of pressure. Both thin and thick viscous boundary layer approximations are formulated; the latter subsumes the former. These approximations are used to develop a variational formation, upon which a viscous finite element method (FEM) model is based, requiring only minor modifications to the boundary integral contributions of an existing inviscid FEM model. Since this FEM formulation has only one degree of freedom for pressure, it holds a great computational advantage over the conventional viscous FEM formulation which requires discretization of the full set of linearized Navier-Stokes equations. The results from thick viscous boundary layer approximation are found to be in good agreement with the prediction from a Navier-Stokes model. When applicable, thin viscous boundary layer approximation also gives accurate results with computational simplicity compared to the thick boundary layer formulation. Direct comparison of simulation results using the boundary layer approximations and a full, linearized Navier-Stokes model are made and used to evaluate the accuracy of the approximate technique. Guidelines are given for the parameter ranges over which the accurate application of the thick and thin boundary approximations can be used for a fluid-structure interaction problem. PMID:23729844

  8. Kinetic modelling of anaerobic hydrolysis of solid wastes, including disintegration processes

    Energy Technology Data Exchange (ETDEWEB)

    García-Gen, Santiago [Department of Chemical Engineering, Institute of Technology, University of Santiago de Compostela, 15782 Santiago de Compostela (Spain); Sousbie, Philippe; Rangaraj, Ganesh [INRA, UR50, Laboratoire de Biotechnologie de l’Environnement, Avenue des Etangs, Narbonne F-11100 (France); Lema, Juan M. [Department of Chemical Engineering, Institute of Technology, University of Santiago de Compostela, 15782 Santiago de Compostela (Spain); Rodríguez, Jorge, E-mail: jrodriguez@masdar.ac.ae [Department of Chemical Engineering, Institute of Technology, University of Santiago de Compostela, 15782 Santiago de Compostela (Spain); Institute Centre for Water and Environment (iWater), Masdar Institute of Science and Technology, PO Box 54224 Abu Dhabi (United Arab Emirates); Steyer, Jean-Philippe; Torrijos, Michel [INRA, UR50, Laboratoire de Biotechnologie de l’Environnement, Avenue des Etangs, Narbonne F-11100 (France)

    2015-01-15

    Highlights: • Fractionation of solid wastes into readily and slowly biodegradable fractions. • Kinetic coefficients estimation from mono-digestion batch assays. • Validation of kinetic coefficients with a co-digestion continuous experiment. • Simulation of batch and continuous experiments with an ADM1-based model. - Abstract: A methodology to estimate disintegration and hydrolysis kinetic parameters of solid wastes and validate an ADM1-based anaerobic co-digestion model is presented. Kinetic parameters of the model were calibrated from batch reactor experiments treating individually fruit and vegetable wastes (among other residues) following a new protocol for batch tests. In addition, decoupled disintegration kinetics for readily and slowly biodegradable fractions of solid wastes was considered. Calibrated parameters from batch assays of individual substrates were used to validate the model for a semi-continuous co-digestion operation treating simultaneously 5 fruit and vegetable wastes. The semi-continuous experiment was carried out in a lab-scale CSTR reactor for 15 weeks at organic loading rate ranging between 2.0 and 4.7 g VS/L d. The model (built in Matlab/Simulink) fit to a large extent the experimental results in both batch and semi-continuous mode and served as a powerful tool to simulate the digestion or co-digestion of solid wastes.

  9. Results of including geometric nonlinearities in an aeroelastic model of an F/A-18

    Science.gov (United States)

    Buttrill, Carey S.

    1989-01-01

    An integrated, nonlinear simulation model suitable for aeroelastic modeling of fixed-wing aircraft has been developed. While the author realizes that the subject of modeling rotating, elastic structures is not closed, it is believed that the equations of motion developed and applied herein are correct to second order and are suitable for use with typical aircraft structures. The equations are not suitable for large elastic deformation. In addition, the modeling framework generalizes both the methods and terminology of non-linear rigid-body airplane simulation and traditional linear aeroelastic modeling. Concerning the importance of angular/elastic inertial coupling in the dynamic analysis of fixed-wing aircraft, the following may be said. The rigorous inclusion of said coupling is not without peril and must be approached with care. In keeping with the same engineering judgment that guided the development of the traditional aeroelastic equations, the effect of non-linear inertial effects for most airplane applications is expected to be small. A parameter does not tell the whole story, however, and modes flagged by the parameter as significant also need to be checked to see if the coupling is not a one-way path, i.e., the inertially affected modes can influence other modes.

  10. HIV Model Parameter Estimates from Interruption Trial Data including Drug Efficacy and Reservoir Dynamics

    Science.gov (United States)

    Luo, Rutao; Piovoso, Michael J.; Martinez-Picado, Javier; Zurakowski, Ryan

    2012-01-01

    Mathematical models based on ordinary differential equations (ODE) have had significant impact on understanding HIV disease dynamics and optimizing patient treatment. A model that characterizes the essential disease dynamics can be used for prediction only if the model parameters are identifiable from clinical data. Most previous parameter identification studies for HIV have used sparsely sampled data from the decay phase following the introduction of therapy. In this paper, model parameters are identified from frequently sampled viral-load data taken from ten patients enrolled in the previously published AutoVac HAART interruption study, providing between 69 and 114 viral load measurements from 3–5 phases of viral decay and rebound for each patient. This dataset is considerably larger than those used in previously published parameter estimation studies. Furthermore, the measurements come from two separate experimental conditions, which allows for the direct estimation of drug efficacy and reservoir contribution rates, two parameters that cannot be identified from decay-phase data alone. A Markov-Chain Monte-Carlo method is used to estimate the model parameter values, with initial estimates obtained using nonlinear least-squares methods. The posterior distributions of the parameter estimates are reported and compared for all patients. PMID:22815727

  11. Modelling of bypass transition including the pseudolaminar part of the boundary layer

    Energy Technology Data Exchange (ETDEWEB)

    Prihoda, J.; Hlava, T. [Ceska Akademie Ved, Prague (Czech Republic). Inst. of Thermomechanics; Kozel, K. [Ceske Vysoke Uceni Technicke, Prague (Czech Republic). Faculty of Mechanical Engineering

    1999-12-01

    The boundary-layer transition in turbomachinery is accelerated by a number of parameters, especially by the free-stream turbulence. This so-called bypass transition is usually modelled by means of one-equation or two-equation turbulence models based on turbulent viscosity. Using of transport equations for turbulent energy and for dissipation rate in these models is questionable before the onset of the last stage of the transition, i.e. before the formation of turbulent spots. Used approximations of production and turbulent diffusion are the weak points of turbulence models with turbulent viscosity in the pseudolaminar boundary layer, as the Boussinesq assumption on turbulent viscosity is not fulfilled in this part of the boundary layer. In order to obtain a more reliable prediction of the transitional boundary layer, Mayle and Schulz (1997) proposed for the solution of pseudolaminar boundary layer a special `laminar-kinetic-energy` equation based on the analysis of laminar boundary layer in flows with velocity fluctuations. The effect of production and turbulent diffusion on the development of turbulent energy in the pseudolaminar boundary layer was tested using a two-layer turbulence model. (orig.)

  12. Modelling of bypass transition including the pseudolaminar part of the boundary layer

    Energy Technology Data Exchange (ETDEWEB)

    Prihoda, J.; Hlava, T. (Ceska Akademie Ved, Prague (Czech Republic). Inst. of Thermomechanics); Kozel, K. (Ceske Vysoke Uceni Technicke, Prague (Czech Republic). Faculty of Mechanical Engineering)

    1999-01-01

    The boundary-layer transition in turbomachinery is accelerated by a number of parameters, especially by the free-stream turbulence. This so-called bypass transition is usually modelled by means of one-equation or two-equation turbulence models based on turbulent viscosity. Using of transport equations for turbulent energy and for dissipation rate in these models is questionable before the onset of the last stage of the transition, i.e. before the formation of turbulent spots. Used approximations of production and turbulent diffusion are the weak points of turbulence models with turbulent viscosity in the pseudolaminar boundary layer, as the Boussinesq assumption on turbulent viscosity is not fulfilled in this part of the boundary layer. In order to obtain a more reliable prediction of the transitional boundary layer, Mayle and Schulz (1997) proposed for the solution of pseudolaminar boundary layer a special 'laminar-kinetic-energy' equation based on the analysis of laminar boundary layer in flows with velocity fluctuations. The effect of production and turbulent diffusion on the development of turbulent energy in the pseudolaminar boundary layer was tested using a two-layer turbulence model. (orig.)

  13. Beam dynamics in high intensity cyclotrons including neighboring bunch effects: Model, implementation, and application

    Directory of Open Access Journals (Sweden)

    J. J. Yang (杨建俊

    2010-06-01

    Full Text Available Space-charge effects, being one of the most significant collective effects, play an important role in high intensity cyclotrons. However, for cyclotrons with small turn separation, other existing effects are of equal importance. Interactions of radially neighboring bunches are also present, but their combined effects have not yet been investigated in any great detail. In this paper, a new particle in the cell-based self-consistent numerical simulation model is presented for the first time. The model covers neighboring bunch effects and is implemented in the three-dimensional object-oriented parallel code OPAL-cycl, a flavor of the OPAL framework. We discuss this model together with its implementation and validation. Simulation results are presented from the PSI 590 MeV ring cyclotron in the context of the ongoing high intensity upgrade program, which aims to provide a beam power of 1.8 MW (CW at the target destination.

  14. Finding practical phenomenological models that include both photoresist behavior and etch process effects

    Science.gov (United States)

    Jung, Sunwook; Do, Thuy; Sturtevant, John

    2015-03-01

    For more than five decades, the semiconductor industry has overcome technology challenges with innovative ideas that have continued to enable Moore's Law. It is clear that multi-patterning lithography is vital for 20nm half pitch using 193i. Multi-patterning exposure sequences and pattern multiplication processes can create complicated tolerance accounting due to the variability associated with the component processes. It is essential to ensure good predictive accuracy of compact etch models used in multipatterning simulation. New modelforms have been developed to account for etch bias behavior at 20 nm and below. The new modeling components show good results in terms of global fitness and some improved predication capability for specific features. We've also investigated a new methodology to make the etch model aware of 3D resist profiles.

  15. A Simple Model of Fields Including the Strong or Nuclear Force and a Cosmological Speculation

    Directory of Open Access Journals (Sweden)

    David L. Spencer

    2016-10-01

    Full Text Available Reexamining the assumptions underlying the General Theory of Relativity and calling an object's gravitational field its inertia, and acceleration simply resistance to that inertia, yields a simple field model where the potential (kinetic energy of a particle at rest is its capacity to move itself when its inertial field becomes imbalanced. The model then attributes electromagnetic and strong forces to the effects of changes in basic particle shape. Following up on the model's assumption that the relative intensity of a particle's gravitational field is always inversely related to its perceived volume and assuming that all black holes spin, may create the possibility of a cosmic rebound where a final spinning black hole ends with a new Big Bang.

  16. Modeling of the dynamics of wind to power conversion including high wind speed behavior

    DEFF Research Database (Denmark)

    Litong-Palima, Marisciel; Bjerge, Martin Huus; Cutululis, Nicolaos Antonio

    2016-01-01

    This paper proposes and validates an efficient, generic and computationally simple dynamic model for the conversion of the wind speed at hub height into the electrical power by a wind turbine. This proposed wind turbine model was developed as a first step to simulate wind power time series...... speed shutdowns and restarts are represented as on–off switching rules that govern the output of the wind turbine at extreme wind speed conditions. The model uses the concept of equivalent wind speed, estimated from the single point (hub height) wind speed using a second-order dynamic filter...... measurements available from the DONG Energy offshore wind farm Horns Rev 2. Copyright © 2015 John Wiley & Sons, Ltd....

  17. Workflow optimization beyond RIS and PACS

    International Nuclear Information System (INIS)

    Treitl, M.; Wirth, S.; Lucke, A.; Nissen-Meyer, S.; Trumm, C.; Rieger, J.; Pfeifer, K.-J.; Reiser, M.; Villain, S.

    2005-01-01

    Technological progress and the rising cost pressure on the healthcare system have led to a drastic change in the work environment of radiologists today. The pervasive demand for workflow optimization and increased efficiency of its activities raises the question of whether by employment of electronic systems, such as RIS and PACS, the potentials of digital technology are sufficiently used to fulfil this demand. This report describes the tasks and structures in radiology departments, which so far are only insufficiently supported by commercially available electronic systems but are nevertheless substantial. We developed and employed a web-based, integrated workplace system, which simplifies many daily tasks of departmental organization and administration apart from well-established tasks of documentation. Furthermore, we analyzed the effects exerted on departmental workflow by employment of this system for 3 years. (orig.) [de

  18. Grid workflow job execution service 'Pilot'

    Science.gov (United States)

    Shamardin, Lev; Kryukov, Alexander; Demichev, Andrey; Ilyin, Vyacheslav

    2011-12-01

    'Pilot' is a grid job execution service for workflow jobs. The main goal for the service is to automate computations with multiple stages since they can be expressed as simple workflows. Each job is a directed acyclic graph of tasks and each task is an execution of something on a grid resource (or 'computing element'). Tasks may be submitted to any WS-GRAM (Globus Toolkit 4) service. The target resources for the tasks execution are selected by the Pilot service from the set of available resources which match the specific requirements from the task and/or job definition. Some simple conditional execution logic is also provided. The 'Pilot' service is built on the REST concepts and provides a simple API through authenticated HTTPS. This service is deployed and used in production in a Russian national grid project GridNNN.

  19. Grid workflow job execution service 'Pilot'

    International Nuclear Information System (INIS)

    Shamardin, Lev; Kryukov, Alexander; Demichev, Andrey; Ilyin, Vyacheslav

    2011-01-01

    'Pilot' is a grid job execution service for workflow jobs. The main goal for the service is to automate computations with multiple stages since they can be expressed as simple workflows. Each job is a directed acyclic graph of tasks and each task is an execution of something on a grid resource (or 'computing element'). Tasks may be submitted to any WS-GRAM (Globus Toolkit 4) service. The target resources for the tasks execution are selected by the Pilot service from the set of available resources which match the specific requirements from the task and/or job definition. Some simple conditional execution logic is also provided. The 'Pilot' service is built on the REST concepts and provides a simple API through authenticated HTTPS. This service is deployed and used in production in a Russian national grid project GridNNN.

  20. An extended TRANSCAR model including ionospheric convection: simulation of EISCAT observations using inputs from AMIE

    Directory of Open Access Journals (Sweden)

    P.-L. Blelly

    2005-02-01

    Full Text Available The TRANSCAR ionospheric model was extended to account for the convection of the magnetic field lines in the auroral and polar ionosphere. A mixed Eulerian-Lagrangian 13-moment approach was used to describe the dynamics of an ionospheric plasma tube. In the present study, one focuses on large scale transports in the polar ionosphere. The model was used to simulate a 35-h period of EISCAT-UHF observations on 16-17 February 1993. The first day was magnetically quiet, and characterized by elevated electron concentrations: the diurnal F2 layer reached as much as 1012m-3, which is unusual for a winter and moderate solar activity (F10.7=130 period. An intense geomagnetic event occurred on the second day, seen in the data as a strong intensification of the ionosphere convection velocities in the early afternoon (with the northward electric field reaching 150mVm-1 and corresponding frictional heating of the ions up to 2500K. The simulation used time-dependent AMIE outputs to infer flux-tube transports in the polar region, and to provide magnetospheric particle and energy inputs to the ionosphere. The overall very good agreement, obtained between the model and the observations, demonstrates the high ability of the extended TRANSCAR model for quantitative modelling of the high-latitude ionosphere; however, some differences are found which are attributed to the precipitation of electrons with very low energy. All these results are finally discussed in the frame of modelling the auroral ionosphere with space weather applications in mind.

  1. An extended TRANSCAR model including ionospheric convection: simulation of EISCAT observations using inputs from AMIE

    Directory of Open Access Journals (Sweden)

    P.-L. Blelly

    2005-02-01

    Full Text Available The TRANSCAR ionospheric model was extended to account for the convection of the magnetic field lines in the auroral and polar ionosphere. A mixed Eulerian-Lagrangian 13-moment approach was used to describe the dynamics of an ionospheric plasma tube. In the present study, one focuses on large scale transports in the polar ionosphere. The model was used to simulate a 35-h period of EISCAT-UHF observations on 16-17 February 1993. The first day was magnetically quiet, and characterized by elevated electron concentrations: the diurnal F2 layer reached as much as 1012m-3, which is unusual for a winter and moderate solar activity (F10.7=130 period. An intense geomagnetic event occurred on the second day, seen in the data as a strong intensification of the ionosphere convection velocities in the early afternoon (with the northward electric field reaching 150mVm-1 and corresponding frictional heating of the ions up to 2500K. The simulation used time-dependent AMIE outputs to infer flux-tube transports in the polar region, and to provide magnetospheric particle and energy inputs to the ionosphere. The overall very good agreement, obtained between the model and the observations, demonstrates the high ability of the extended TRANSCAR model for quantitative modelling of the high-latitude ionosphere; however, some differences are found which are attributed to the precipitation of electrons with very low energy. All these results are finally discussed in the frame of modelling the auroral ionosphere with space weather applications in mind.

  2. Evaluation of European air quality modelled by CAMx including the volatility basis set scheme

    Directory of Open Access Journals (Sweden)

    G. Ciarelli

    2016-08-01

    Full Text Available Four periods of EMEP (European Monitoring and Evaluation Programme intensive measurement campaigns (June 2006, January 2007, September–October 2008 and February–March 2009 were modelled using the regional air quality model CAMx with VBS (volatility basis set approach for the first time in Europe within the framework of the EURODELTA-III model intercomparison exercise. More detailed analysis and sensitivity tests were performed for the period of February–March 2009 and June 2006 to investigate the uncertainties in emissions as well as to improve the modelling of organic aerosol (OA. Model performance for selected gas phase species and PM2.5 was evaluated using the European air quality database AirBase. Sulfur dioxide (SO2 and ozone (O3 were found to be overestimated for all the four periods, with O3 having the largest mean bias during June 2006 and January–February 2007 periods (8.9 pbb and 12.3 ppb mean biases respectively. In contrast, nitrogen dioxide (NO2 and carbon monoxide (CO were found to be underestimated for all the four periods. CAMx reproduced both total concentrations and monthly variations of PM2.5 for all the four periods with average biases ranging from −2.1 to 1.0 µg m−3. Comparisons with AMS (aerosol mass spectrometer measurements at different sites in Europe during February–March 2009 showed that in general the model overpredicts the inorganic aerosol fraction and underpredicts the organic one, such that the good agreement for PM2.5 is partly due to compensation of errors. The effect of the choice of VBS scheme on OA was investigated as well. Two sensitivity tests with volatility distributions based on previous chamber and ambient measurements data were performed. For February–March 2009 the chamber case reduced the total OA concentrations by about 42 % on average. In contrast, a test based on ambient measurement data increased OA concentrations by about 42 % for the same period bringing

  3. Molecular Modeling of Aerospace Polymer Matrices Including Carbon Nanotube-Enhanced Epoxy

    Science.gov (United States)

    Radue, Matthew S.

    Carbon fiber (CF) composites are increasingly replacing metals used in major structural parts of aircraft, spacecraft, and automobiles. The current limitations of carbon fiber composites are addressed through computational material design by modeling the salient aerospace matrix materials. Molecular Dynamics (MD) models of epoxies with and without carbon nanotube (CNT) reinforcement and models of pure bismaleimides (BMIs) were developed to elucidate structure-property relationships for improved selection and tailoring of matrices. The influence of monomer functionality on the mechanical properties of epoxies is studied using the Reax Force Field (ReaxFF). From deformation simulations, the Young's modulus, yield point, and Poisson's ratio are calculated and analyzed. The results demonstrate an increase in stiffness and yield strength with increasing resin functionality. Comparison between the network structures of distinct epoxies is further advanced by the Monomeric Degree Index (MDI). Experimental validation demonstrates the MD results correctly predict the relationship in Young's moduli for all epoxies modeled. Therefore, the ReaxFF is confirmed to be a useful tool for studying the mechanical behavior of epoxies. While epoxies have been well-studied using MD, there has been no concerted effort to model cured BMI polymers due to the complexity of the network-forming reactions. A novel, adaptable crosslinking framework is developed for implementing 5 distinct cure reactions of Matrimid-5292 (a BMI resin) and investigating the network structure using MD simulations. The influence of different cure reactions and extent of curing are analyzed on the several thermo-mechanical properties such as mass density, glass transition temperature, coefficient of thermal expansion, elastic moduli, and thermal conductivity. The developed crosslinked models correctly predict experimentally observed trends for various properties. Finally, the epoxies modeled (di-, tri-, and tetra

  4. Modelling of safety barriers including human and organisational factors to improve process safety

    DEFF Research Database (Denmark)

    Markert, Frank; Duijm, Nijs Jan; Thommesen, Jacob

    2013-01-01

    Assessment Methodology for IndustrieS, see Salvi et al 2006). ARAMIS employs the bow-tie approach to modelling hazardous scenarios, and it suggests the outcome of auditing safety management to be connected to a semi-quantitative assessment of the quality of safety barriers. ARAMIS discriminates a number...... of safety barrier (passive, automated, or involving human action). Such models are valuable for many purposes, but are difficult to apply to more complex situations, as the influences are to be set individually for each barrier. The approach described in this paper is trying to improve the state...

  5. Implementation of a blockchain workflow management prototype

    OpenAIRE

    Fridgen, Gilbert; Sablowsky, Bernd; Urbach, Nils

    2017-01-01

    Blockchain technology offers huge potential to various industries and application areas. In a joint applied research project, Fraunhofer Institute for Applied Information Technology (FIT) together with Norddeutsche Landesbank (NORD/LB) identified (inter-company) workflow management as a promising application area and developed a Blockchain prototype for a documentary letter of credit in the international shipping business. In addition to the projects explicit outcome a Blockchain prototype an...

  6. SPECT/CT workflow and imaging protocols

    International Nuclear Information System (INIS)

    Beckers, Catherine; Hustinx, Roland

    2014-01-01

    Introducing a hybrid imaging method such as single photon emission computed tomography (SPECT)/CT greatly alters the routine in the nuclear medicine department. It requires designing new workflow processes and the revision of original scheduling process and imaging protocols. In addition, the imaging protocol should be adapted for each individual patient, so that performing CT is fully justified and the CT procedure is fully tailored to address the clinical issue. Such refinements often occur before the procedure is started but may be required at some intermediate stage of the procedure. Furthermore, SPECT/CT leads in many instances to a new partnership with the radiology department. This article presents practical advice and highlights the key clinical elements which need to be considered to help understand the workflow process of SPECT/CT and optimise imaging protocols. The workflow process using SPECT/CT is complex in particular because of its bimodal character, the large spectrum of stakeholders, the multiplicity of their activities at various time points and the need for real-time decision-making. With help from analytical tools developed for quality assessment, the workflow process using SPECT/CT may be separated into related, but independent steps, each with its specific human and material resources to use as inputs or outputs. This helps identify factors that could contribute to failure in routine clinical practice. At each step of the process, practical aspects to optimise imaging procedure and protocols are developed. A decision-making algorithm for justifying each CT indication as well as the appropriateness of each CT protocol is the cornerstone of routine clinical practice using SPECT/CT. In conclusion, implementing hybrid SPECT/CT imaging requires new ways of working. It is highly rewarding from a clinical perspective, but it also proves to be a daily challenge in terms of management. (orig.)

  7. Workflow and cost analysis on MODULAR ANALYTICS.

    Science.gov (United States)

    Stolz, Herbert; Dossler, Bettina; Keller, Franz; Steigerwald, Udo

    2003-01-01

    Four stand-alone analyzers in a centralized laboratory were replaced by two modular analytical systems processing 45 methods of the general chemistry and specific protein segment. This consolidation led to a reduction of the daily workflow and operational costs. The cost saving with 1.3 million reported results per year was 53,000 Euro, which can be assessed as an important contribution to cost reduction in the health care system.

  8. SPECT/CT workflow and imaging protocols

    Energy Technology Data Exchange (ETDEWEB)

    Beckers, Catherine [University Hospital of Liege, Division of Nuclear Medicine and Oncological Imaging, Department of Medical Physics, Liege (Belgium); Hustinx, Roland [University Hospital of Liege, Division of Nuclear Medicine and Oncological Imaging, Department of Medical Physics, Liege (Belgium); Domaine Universitaire du Sart Tilman, Service de Medecine Nucleaire et Imagerie Oncologique, CHU de Liege, Liege (Belgium)

    2014-05-15

    Introducing a hybrid imaging method such as single photon emission computed tomography (SPECT)/CT greatly alters the routine in the nuclear medicine department. It requires designing new workflow processes and the revision of original scheduling process and imaging protocols. In addition, the imaging protocol should be adapted for each individual patient, so that performing CT is fully justified and the CT procedure is fully tailored to address the clinical issue. Such refinements often occur before the procedure is started but may be required at some intermediate stage of the procedure. Furthermore, SPECT/CT leads in many instances to a new partnership with the radiology department. This article presents practical advice and highlights the key clinical elements which need to be considered to help understand the workflow process of SPECT/CT and optimise imaging protocols. The workflow process using SPECT/CT is complex in particular because of its bimodal character, the large spectrum of stakeholders, the multiplicity of their activities at various time points and the need for real-time decision-making. With help from analytical tools developed for quality assessment, the workflow process using SPECT/CT may be separated into related, but independent steps, each with its specific human and material resources to use as inputs or outputs. This helps identify factors that could contribute to failure in routine clinical practice. At each step of the process, practical aspects to optimise imaging procedure and protocols are developed. A decision-making algorithm for justifying each CT indication as well as the appropriateness of each CT protocol is the cornerstone of routine clinical practice using SPECT/CT. In conclusion, implementing hybrid SPECT/CT imaging requires new ways of working. It is highly rewarding from a clinical perspective, but it also proves to be a daily challenge in terms of management. (orig.)

  9. IDD Archival Hardware Architecture and Workflow

    Energy Technology Data Exchange (ETDEWEB)

    Mendonsa, D; Nekoogar, F; Martz, H

    2008-10-09

    This document describes the functionality of every component in the DHS/IDD archival and storage hardware system shown in Fig. 1. The document describes steps by step process of image data being received at LLNL then being processed and made available to authorized personnel and collaborators. Throughout this document references will be made to one of two figures, Fig. 1 describing the elements of the architecture and the Fig. 2 describing the workflow and how the project utilizes the available hardware.

  10. The economic production lot size model extended to include more than one production rate

    DEFF Research Database (Denmark)

    Larsen, Christian

    2005-01-01

    We study an extension of the economic production lot size model, where more than one production rate can be used during a cycle. Moreover, the production rates, as well as their corresponding runtimes are decision variables. We decompose the problem into two subproblems. First, we show that all...

  11. The economic production lot size model extended to include more than one production rate

    DEFF Research Database (Denmark)

    Larsen, Christian

    2001-01-01

    We study an extension of the economic production lot size model, where more than one production rate can be used during a cycle. Moreover, the production rates, as well as their corresponding runtimes are decision variables. First, we show that all production rates should be choosen in the interval...

  12. Static aeroelastic analysis including geometric nonlinearities based on reduced order model

    Directory of Open Access Journals (Sweden)

    Changchuan Xie

    2017-04-01

    Full Text Available This paper describes a method proposed for modeling large deflection of aircraft in nonlinear aeroelastic analysis by developing reduced order model (ROM. The method is applied for solving the static aeroelastic and static aeroel