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....

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

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 not natu......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...... not naturally support dynamic change, is used as a target for implementation. The WS-BPEL recovery framework is here exploited to implement the reconfiguration using principles derived from previous research in process algebra and two mappings from BPMN to WS-BPEL are presented, one automatic and only mostly...

Improving adherence to the Epic Beacon ambulatory workflow.

Science.gov (United States)

Chackunkal, Ellen; Dhanapal Vogel, Vishnuprabha; Grycki, Meredith; Kostoff, Diana

2017-06-01

Computerized physician order entry has been shown to significantly improve chemotherapy safety by reducing the number of prescribing errors. Epic's Beacon Oncology Information System of computerized physician order entry and electronic medication administration was implemented in Henry Ford Health System's ambulatory oncology infusion centers on 9 November 2013. Since that time, compliance to the infusion workflow had not been assessed. The objective of this study was to optimize the current workflow and improve the compliance to this workflow in the ambulatory oncology setting. This study was a retrospective, quasi-experimental study which analyzed the composite workflow compliance rate of patient encounters from 9 to 23 November 2014. Based on this analysis, an intervention was identified and implemented in February 2015 to improve workflow compliance. The primary endpoint was to compare the composite compliance rate to the Beacon workflow before and after a pharmacy-initiated intervention. The intervention, which was education of infusion center staff, was initiated by ambulatory-based, oncology pharmacists and implemented by a multi-disciplinary team of pharmacists and nurses. The composite compliance rate was then reassessed for patient encounters from 2 to 13 March 2015 in order to analyze the effects of the determined intervention on compliance. The initial analysis in November 2014 revealed a composite compliance rate of 38%, and data analysis after the intervention revealed a statistically significant increase in the composite compliance rate to 83% ( p < 0.001). This study supports a pharmacist-initiated educational intervention can improve compliance to an ambulatory, oncology infusion workflow.

Workflow Support for Advanced Grid-Enabled Computing

OpenAIRE

Xu, Fenglian; Eres, M.H.; Tao, Feng; Cox, Simon J.

2004-01-01

The Geodise project brings computer scientists and engineer's skills together to build up a service-oriented computing environmnet for engineers to perform complicated computations in a distributed system. The workflow tool is a front GUI to provide a full life cycle of workflow functions for Grid-enabled computing. The full life cycle of workflow functions have been enhanced based our initial research and development. The life cycle starts with a composition of a workflow, followed by an ins...

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.

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...... 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....

Worklist handling in workflow-enabled radiological application systems

Science.gov (United States)

Wendler, Thomas; Meetz, Kirsten; Schmidt, Joachim; von Berg, Jens

2000-05-01

For the next generation integrated information systems for health care applications, more emphasis has to be put on systems which, by design, support the reduction of cost, the increase inefficiency and the improvement of the quality of services. A substantial contribution to this will be the modeling. optimization, automation and enactment of processes in health care institutions. One of the perceived key success factors for the system integration of processes will be the application of workflow management, with workflow management systems as key technology components. In this paper we address workflow management in radiology. We focus on an important aspect of workflow management, the generation and handling of worklists, which provide workflow participants automatically with work items that reflect tasks to be performed. The display of worklists and the functions associated with work items are the visible part for the end-users of an information system using a workflow management approach. Appropriate worklist design and implementation will influence user friendliness of a system and will largely influence work efficiency. Technically, in current imaging department information system environments (modality-PACS-RIS installations), a data-driven approach has been taken: Worklist -- if present at all -- are generated from filtered views on application data bases. In a future workflow-based approach, worklists will be generated by autonomous workflow services based on explicit process models and organizational models. This process-oriented approach will provide us with an integral view of entire health care processes or sub- processes. The paper describes the basic mechanisms of this approach and summarizes its benefits.

Automatic support for product based workflow design : generation of process models from a product data model

NARCIS (Netherlands)

Vanderfeesten, I.T.P.; Reijers, H.A.; Aalst, van der W.M.P.; Vogelaar, J.J.C.L.; Meersman, R.; Dillon, T.; Herrero, P.

2010-01-01

Product Based Workflow Design (PBWD) is one of the few scientific methodologies for the (re)design of workflow processes. It is based on an analysis of the product that is produced in the workflow process and derives a process model from the product structure. Until now this derivation has been a

Integrated workflows for spiking neuronal network simulations

Directory of Open Access Journals (Sweden)

Ján eAntolík

2013-12-01

Full Text Available The increasing availability of computational resources is enabling more detailed, realistic modelling in computational neuroscience, resulting in a shift towards more heterogeneous models of neuronal circuits, and employment of complex experimental protocols. This poses a challenge for existing tool chains, as the set of tools involved in a typical modeller's workflow is expanding concomitantly, with growing complexity in the metadata flowing between them. For many parts of the workflow, a range of tools is available; however, numerous areas lack dedicated tools, while integration of existing tools is limited. This forces modellers to either handle the workflow manually, leading to errors, or to write substantial amounts of code to automate parts of the workflow, in both cases reducing their productivity.To address these issues, we have developed Mozaik: a workflow system for spiking neuronal network simulations written in Python. Mozaik integrates model, experiment and stimulation specification, simulation execution, data storage, data analysis and visualisation into a single automated workflow, ensuring that all relevant metadata are available to all workflow components. It is based on several existing tools, including PyNN, Neo and Matplotlib. It offers a declarative way to specify models and recording configurations using hierarchically organised configuration files. Mozaik automatically records all data together with all relevant metadata about the experimental context, allowing automation of the analysis and visualisation stages. Mozaik has a modular architecture, and the existing modules are designed to be extensible with minimal programming effort. Mozaik increases the productivity of running virtual experiments on highly structured neuronal networks by automating the entire experimental cycle, while increasing the reliability of modelling studies by relieving the user from manual handling of the flow of metadata between the individual

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.

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.

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.

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

Extension of specification language for soundness and completeness of service workflow

Science.gov (United States)

Viriyasitavat, Wattana; Xu, Li Da; Bi, Zhuming; Sapsomboon, Assadaporn

2018-05-01

A Service Workflow is an aggregation of distributed services to fulfill specific functionalities. With ever increasing available services, the methodologies for the selections of the services against the given requirements become main research subjects in multiple disciplines. A few of researchers have contributed to the formal specification languages and the methods for model checking; however, existing methods have the difficulties to tackle with the complexity of workflow compositions. In this paper, we propose to formalize the specification language to reduce the complexity of the workflow composition. To this end, we extend a specification language with the consideration of formal logic, so that some effective theorems can be derived for the verification of syntax, semantics, and inference rules in the workflow composition. The logic-based approach automates compliance checking effectively. The Service Workflow Specification (SWSpec) has been extended and formulated, and the soundness, completeness, and consistency of SWSpec applications have been verified; note that a logic-based SWSpec is mandatory for the development of model checking. The application of the proposed SWSpec has been demonstrated by the examples with the addressed soundness, completeness, and consistency.

Provenance-Based Debugging and Drill-Down in Data-Oriented Workflows

KAUST Repository

Ikeda, Robert

2012-04-01

Panda (for Provenance and Data) is a system that supports the creation and execution of data-oriented workflows, with automatic provenance generation and built-in provenance tracing operations. Workflows in Panda are arbitrary a cyclic graphs containing both relational (SQL) processing nodes and opaque processing nodes programmed in Python. For both types of nodes, Panda generates logical provenance - provenance information stored at the processing-node level - and uses the generated provenance to support record-level backward tracing and forward tracing operations. In our demonstration we use Panda to integrate, process, and analyze actual education data from multiple sources. We specifically demonstrate how Panda\\'s provenance generation and tracing capabilities can be very useful for workflow debugging, and for drilling down on specific results of interest. © 2012 IEEE.

Analyzing the Gap between Workflows and their Natural Language Descriptions

NARCIS (Netherlands)

Groth, P.T.; Gil, Y

2009-01-01

Scientists increasingly use workflows to represent and share their computational experiments. Because of their declarative nature, focus on pre-existing component composition and the availability of visual editors, workflows provide a valuable start for creating user-friendly environments for end

Child vocalization composition as discriminant information for automatic autism detection.

Science.gov (United States)

Xu, Dongxin; Gilkerson, Jill; Richards, Jeffrey; Yapanel, Umit; Gray, Sharmi

2009-01-01

Early identification is crucial for young children with autism to access early intervention. The existing screens require either a parent-report questionnaire and/or direct observation by a trained practitioner. Although an automatic tool would benefit parents, clinicians and children, there is no automatic screening tool in clinical use. This study reports a fully automatic mechanism for autism detection/screening for young children. This is a direct extension of the LENA (Language ENvironment Analysis) system, which utilizes speech signal processing technology to analyze and monitor a child's natural language environment and the vocalizations/speech of the child. It is discovered that child vocalization composition contains rich discriminant information for autism detection. By applying pattern recognition and machine learning approaches to child vocalization composition data, accuracy rates of 85% to 90% in cross-validation tests for autism detection have been achieved at the equal-error-rate (EER) point on a data set with 34 children with autism, 30 language delayed children and 76 typically developing children. Due to its easy and automatic procedure, it is believed that this new tool can serve a significant role in childhood autism screening, especially in regards to population-based or universal screening.

Deploying and sharing U-Compare workflows as web services.

Science.gov (United States)

Kontonatsios, Georgios; Korkontzelos, Ioannis; Kolluru, Balakrishna; Thompson, Paul; Ananiadou, Sophia

2013-02-18

U-Compare is a text mining platform that allows the construction, evaluation and comparison of text mining workflows. U-Compare contains a large library of components that are tuned to the biomedical domain. Users can rapidly develop biomedical text mining workflows by mixing and matching U-Compare's components. Workflows developed using U-Compare can be exported and sent to other users who, in turn, can import and re-use them. However, the resulting workflows are standalone applications, i.e., software tools that run and are accessible only via a local machine, and that can only be run with the U-Compare platform. We address the above issues by extending U-Compare to convert standalone workflows into web services automatically, via a two-click process. The resulting web services can be registered on a central server and made publicly available. Alternatively, users can make web services available on their own servers, after installing the web application framework, which is part of the extension to U-Compare. We have performed a user-oriented evaluation of the proposed extension, by asking users who have tested the enhanced functionality of U-Compare to complete questionnaires that assess its functionality, reliability, usability, efficiency and maintainability. The results obtained reveal that the new functionality is well received by users. The web services produced by U-Compare are built on top of open standards, i.e., REST and SOAP protocols, and therefore, they are decoupled from the underlying platform. Exported workflows can be integrated with any application that supports these open standards. We demonstrate how the newly extended U-Compare enhances the cross-platform interoperability of workflows, by seamlessly importing a number of text mining workflow web services exported from U-Compare into Taverna, i.e., a generic scientific workflow construction platform.

Integration Of Externalized Decision Models In The Definition Of Workflows For Digital Pathology

Directory of Open Access Journals (Sweden)

J. van Leeuwen

2016-06-01

We proposed a workflow solution enabling the representation of decision models as externalized executable tasks in the process definition. Our approach separates the task implementations from the workflow model, ensuring scalability and allowing for the inclusion of complex decision logic in the workflow execution. In we depict a simplified model of a pathology diagnosis workflow (starting with the digitization of the slides, represented according to the BPMN modeling conventions. The example shows a workflow sequence that automatically orders a HER2 FISH when IHC is borderline according to defined customizable thresholds. The process model integrates an image analysis algorithm that scores images. Based on the score and the thresholds the decision model evaluates the condition and recommends the pre-ordering of an additional test when the score falls between the two thresholds. This leads to faster diagnosis and allows balancing the costs of an additional test versus the overhead of the pathologist by choosing the values of the thresholds.  

Developing a Workflow Composite Score to Measure Clinical Information Logistics. A Top-down Approach.

Science.gov (United States)

Liebe, J D; Hübner, U; Straede, M C; Thye, J

2015-01-01

Availability and usage of individual IT applications have been studied intensively in the past years. Recently, IT support of clinical processes is attaining increasing attention. The underlying construct that describes the IT support of clinical workflows is clinical information logistics. This construct needs to be better understood, operationalised and measured. It is therefore the aim of this study to propose and develop a workflow composite score (WCS) for measuring clinical information logistics and to examine its quality based on reliability and validity analyses. We largely followed the procedural model of MacKenzie and colleagues (2011) for defining and conceptualising the construct domain, for developing the measurement instrument, assessing the content validity, pretesting the instrument, specifying the model, capturing the data and computing the WCS and testing the reliability and validity. Clinical information logistics was decomposed into the descriptors data and information, function, integration and distribution, which embraced the framework validated by an analysis of the international literature. This framework was refined selecting representative clinical processes. We chose ward rounds, pre- and post-surgery processes and discharge as sample processes that served as concrete instances for the measurements. They are sufficiently complex, represent core clinical processes and involve different professions, departments and settings. The score was computed on the basis of data from 183 hospitals of different size, ownership, location and teaching status. Testing the reliability and validity yielded encouraging results: the reliability was high with r(split-half) = 0.89, the WCS discriminated between groups; the WCS correlated significantly and moderately with two EHR models and the WCS received good evaluation results by a sample of chief information officers (n = 67). These findings suggest the further utilisation of the WCS. As the WCS does not

Support for Taverna workflows in the VPH-Share cloud platform.

Science.gov (United States)

Kasztelnik, Marek; Coto, Ernesto; Bubak, Marian; Malawski, Maciej; Nowakowski, Piotr; Arenas, Juan; Saglimbeni, Alfredo; Testi, Debora; Frangi, Alejandro F

2017-07-01

To address the increasing need for collaborative endeavours within the Virtual Physiological Human (VPH) community, the VPH-Share collaborative cloud platform allows researchers to expose and share sequences of complex biomedical processing tasks in the form of computational workflows. The Taverna Workflow System is a very popular tool for orchestrating complex biomedical & bioinformatics processing tasks in the VPH community. This paper describes the VPH-Share components that support the building and execution of Taverna workflows, and explains how they interact with other VPH-Share components to improve the capabilities of the VPH-Share platform. Taverna workflow support is delivered by the Atmosphere cloud management platform and the VPH-Share Taverna plugin. These components are explained in detail, along with the two main procedures that were developed to enable this seamless integration: workflow composition and execution. 1) Seamless integration of VPH-Share with other components and systems. 2) Extended range of different tools for workflows. 3) Successful integration of scientific workflows from other VPH projects. 4) Execution speed improvement for medical applications. The presented workflow integration provides VPH-Share users with a wide range of different possibilities to compose and execute workflows, such as desktop or online composition, online batch execution, multithreading, remote execution, etc. The specific advantages of each supported tool are presented, as are the roles of Atmosphere and the VPH-Share plugin within the VPH-Share project. The combination of the VPH-Share plugin and Atmosphere engenders the VPH-Share infrastructure with far more flexible, powerful and usable capabilities for the VPH-Share community. As both components can continue to evolve and improve independently, we acknowledge that further improvements are still to be developed and will be described. Copyright © 2017 Elsevier B.V. All rights reserved.

AWSCS-A System to Evaluate Different Approaches for the Automatic Composition and Execution of Web Services Flows.

Science.gov (United States)

Tardiole Kuehne, Bruno; Estrella, Julio Cezar; Nunes, Luiz Henrique; Martins de Oliveira, Edvard; Hideo Nakamura, Luis; Gomes Ferreira, Carlos Henrique; Carlucci Santana, Regina Helena; Reiff-Marganiec, Stephan; Santana, Marcos José

2015-01-01

This paper proposes a system named AWSCS (Automatic Web Service Composition System) to evaluate different approaches for automatic composition of Web services, based on QoS parameters that are measured at execution time. The AWSCS is a system to implement different approaches for automatic composition of Web services and also to execute the resulting flows from these approaches. Aiming at demonstrating the results of this paper, a scenario was developed, where empirical flows were built to demonstrate the operation of AWSCS, since algorithms for automatic composition are not readily available to test. The results allow us to study the behaviour of running composite Web services, when flows with the same functionality but different problem-solving strategies were compared. Furthermore, we observed that the influence of the load applied on the running system as the type of load submitted to the system is an important factor to define which approach for the Web service composition can achieve the best performance in production.

AWSCS-A System to Evaluate Different Approaches for the Automatic Composition and Execution of Web Services Flows.

Directory of Open Access Journals (Sweden)

Bruno Tardiole Kuehne

Full Text Available This paper proposes a system named AWSCS (Automatic Web Service Composition System to evaluate different approaches for automatic composition of Web services, based on QoS parameters that are measured at execution time. The AWSCS is a system to implement different approaches for automatic composition of Web services and also to execute the resulting flows from these approaches. Aiming at demonstrating the results of this paper, a scenario was developed, where empirical flows were built to demonstrate the operation of AWSCS, since algorithms for automatic composition are not readily available to test. The results allow us to study the behaviour of running composite Web services, when flows with the same functionality but different problem-solving strategies were compared. Furthermore, we observed that the influence of the load applied on the running system as the type of load submitted to the system is an important factor to define which approach for the Web service composition can achieve the best performance in production.

A Tool Supporting Collaborative Data Analytics Workflow Design and Management

Science.gov (United States)

Zhang, J.; Bao, Q.; Lee, T. J.

2016-12-01

Collaborative experiment design could significantly enhance the sharing and adoption of the data analytics algorithms and models emerged in Earth science. Existing data-oriented workflow tools, however, are not suitable to support collaborative design of such a workflow, to name a few, to support real-time co-design; to track how a workflow evolves over time based on changing designs contributed by multiple Earth scientists; and to capture and retrieve collaboration knowledge on workflow design (discussions that lead to a design). To address the aforementioned challenges, we have designed and developed a technique supporting collaborative data-oriented workflow composition and management, as a key component toward supporting big data collaboration through the Internet. Reproducibility and scalability are two major targets demanding fundamental infrastructural support. One outcome of the project os a software tool, supporting an elastic number of groups of Earth scientists to collaboratively design and compose data analytics workflows through the Internet. Instead of recreating the wheel, we have extended an existing workflow tool VisTrails into an online collaborative environment as a proof of concept.

Supporting the annotation of chronic obstructive pulmonary disease (COPD) phenotypes with text mining workflows.

Science.gov (United States)

Fu, Xiao; Batista-Navarro, Riza; Rak, Rafal; Ananiadou, Sophia

2015-01-01

Chronic obstructive pulmonary disease (COPD) is a life-threatening lung disorder whose recent prevalence has led to an increasing burden on public healthcare. Phenotypic information in electronic clinical records is essential in providing suitable personalised treatment to patients with COPD. However, as phenotypes are often "hidden" within free text in clinical records, clinicians could benefit from text mining systems that facilitate their prompt recognition. This paper reports on a semi-automatic methodology for producing a corpus that can ultimately support the development of text mining tools that, in turn, will expedite the process of identifying groups of COPD patients. A corpus of 30 full-text papers was formed based on selection criteria informed by the expertise of COPD specialists. We developed an annotation scheme that is aimed at producing fine-grained, expressive and computable COPD annotations without burdening our curators with a highly complicated task. This was implemented in the Argo platform by means of a semi-automatic annotation workflow that integrates several text mining tools, including a graphical user interface for marking up documents. When evaluated using gold standard (i.e., manually validated) annotations, the semi-automatic workflow was shown to obtain a micro-averaged F-score of 45.70% (with relaxed matching). Utilising the gold standard data to train new concept recognisers, we demonstrated that our corpus, although still a work in progress, can foster the development of significantly better performing COPD phenotype extractors. We describe in this work the means by which we aim to eventually support the process of COPD phenotype curation, i.e., by the application of various text mining tools integrated into an annotation workflow. Although the corpus being described is still under development, our results thus far are encouraging and show great potential in stimulating the development of further automatic COPD phenotype extractors.

Automatic Creation of Machine Learning Workflows with Strongly Typed Genetic Programming

Czech Academy of Sciences Publication Activity Database

Křen, T.; Pilát, M.; Neruda, Roman

2017-01-01

Roč. 26, č. 5 (2017), č. článku 1760020. ISSN 0218-2130 R&D Projects: GA ČR GA15-19877S Grant - others:GA MŠk(CZ) LM2015042 Institutional support: RVO:67985807 Keywords : genetic programming * machine learning workflows * asynchronous evolutionary algorithm Subject RIV: IN - Informatics, Computer Science OBOR OECD: Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8) Impact factor: 0.778, year: 2016

From Data to Knowledge to Discoveries: Artificial Intelligence and Scientific Workflows

Directory of Open Access Journals (Sweden)

Yolanda Gil

2009-01-01

Full Text Available Scientific computing has entered a new era of scale and sharing with the arrival of cyberinfrastructure facilities for computational experimentation. A key emerging concept is scientific workflows, which provide a declarative representation of complex scientific applications that can be automatically managed and executed in distributed shared resources. In the coming decades, computational experimentation will push the boundaries of current cyberinfrastructure in terms of inter-disciplinary scope and integrative models of scientific phenomena under study. This paper argues that knowledge-rich workflow environments will provide necessary capabilities for that vision by assisting scientists to validate and vet complex analysis processes and by automating important aspects of scientific exploration and discovery.

Cloud-based bioinformatics workflow platform for large-scale next-generation sequencing analyses.

Science.gov (United States)

Liu, Bo; Madduri, Ravi K; Sotomayor, Borja; Chard, Kyle; Lacinski, Lukasz; Dave, Utpal J; Li, Jianqiang; Liu, Chunchen; Foster, Ian T

2014-06-01

Due to the upcoming data deluge of genome data, the need for storing and processing large-scale genome data, easy access to biomedical analyses tools, efficient data sharing and retrieval has presented significant challenges. The variability in data volume results in variable computing and storage requirements, therefore biomedical researchers are pursuing more reliable, dynamic and convenient methods for conducting sequencing analyses. This paper proposes a Cloud-based bioinformatics workflow platform for large-scale next-generation sequencing analyses, which enables reliable and highly scalable execution of sequencing analyses workflows in a fully automated manner. Our platform extends the existing Galaxy workflow system by adding data management capabilities for transferring large quantities of data efficiently and reliably (via Globus Transfer), domain-specific analyses tools preconfigured for immediate use by researchers (via user-specific tools integration), automatic deployment on Cloud for on-demand resource allocation and pay-as-you-go pricing (via Globus Provision), a Cloud provisioning tool for auto-scaling (via HTCondor scheduler), and the support for validating the correctness of workflows (via semantic verification tools). Two bioinformatics workflow use cases as well as performance evaluation are presented to validate the feasibility of the proposed approach. Copyright © 2014 Elsevier Inc. All rights reserved.

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

Using workflows to explore and optimise named entity recognition for chemistry.

Directory of Open Access Journals (Sweden)

Balakrishna Kolluru

Full Text Available Chemistry text mining tools should be interoperable and adaptable regardless of system-level implementation, installation or even programming issues. We aim to abstract the functionality of these tools from the underlying implementation via reconfigurable workflows for automatically identifying chemical names. To achieve this, we refactored an established named entity recogniser (in the chemistry domain, OSCAR and studied the impact of each component on the net performance. We developed two reconfigurable workflows from OSCAR using an interoperable text mining framework, U-Compare. These workflows can be altered using the drag-&-drop mechanism of the graphical user interface of U-Compare. These workflows also provide a platform to study the relationship between text mining components such as tokenisation and named entity recognition (using maximum entropy Markov model (MEMM and pattern recognition based classifiers. Results indicate that, for chemistry in particular, eliminating noise generated by tokenisation techniques lead to a slightly better performance than others, in terms of named entity recognition (NER accuracy. Poor tokenisation translates into poorer input to the classifier components which in turn leads to an increase in Type I or Type II errors, thus, lowering the overall performance. On the Sciborg corpus, the workflow based system, which uses a new tokeniser whilst retaining the same MEMM component, increases the F-score from 82.35% to 84.44%. On the PubMed corpus, it recorded an F-score of 84.84% as against 84.23% by OSCAR.

Automatic multimodal real-time tracking for image plane alignment in interventional Magnetic Resonance Imaging

International Nuclear Information System (INIS)

Neumann, Markus

2014-01-01

Interventional magnetic resonance imaging (MRI) aims at performing minimally invasive percutaneous interventions, such as tumor ablations and biopsies, under MRI guidance. During such interventions, the acquired MR image planes are typically aligned to the surgical instrument (needle) axis and to surrounding anatomical structures of interest in order to efficiently monitor the advancement in real-time of the instrument inside the patient's body. Object tracking inside the MRI is expected to facilitate and accelerate MR-guided interventions by allowing to automatically align the image planes to the surgical instrument. In this PhD thesis, an image-based work-flow is proposed and refined for automatic image plane alignment. An automatic tracking work-flow was developed, performing detection and tracking of a passive marker directly in clinical real-time images. This tracking work-flow is designed for fully automated image plane alignment, with minimization of tracking-dedicated time. Its main drawback is its inherent dependence on the slow clinical MRI update rate. First, the addition of motion estimation and prediction with a Kalman filter was investigated and improved the work-flow tracking performance. Second, a complementary optical sensor was used for multi-sensor tracking in order to decouple the tracking update rate from the MR image acquisition rate. Performance of the work-flow was evaluated with both computer simulations and experiments using an MR compatible test bed. Results show a high robustness of the multi-sensor tracking approach for dynamic image plane alignment, due to the combination of the individual strengths of each sensor. (author)

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

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

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.

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

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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

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

NARCIS (Netherlands)

Iochpe, Cirano; Chiao, Carolina; Hess, Guillermo; Nascimento, Gleison; Thom, Lucinéia; Reichert, Manfred

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

Using UML to Model Web Services for Automatic Composition

OpenAIRE

Amal Elgammal; Mohamed El-Sharkawi

2010-01-01

There is a great interest paid to the web services paradigm nowadays. One of the most important problems related to the web service paradigm is the automatic composition of web services. Several frameworks have been proposed to achieve this novel goal. The most recent and richest framework (model) is the Colombo model. However, even for experienced developers, working with Colombo formalisms is low-level, very complex and timeconsuming. We propose to use UML (Unified Modeling Language) to mod...

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

Evaluation of an automatic MR-based gold fiducial marker localisation method for MR-only prostate radiotherapy

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Maspero, Matteo; van den Berg, Cornelis A. T.; Zijlstra, Frank; Sikkes, Gonda G.; de Boer, Hans C. J.; Meijer, Gert J.; Kerkmeijer, Linda G. W.; Viergever, Max A.; Lagendijk, Jan J. W.; Seevinck, Peter R.

2017-10-01

An MR-only radiotherapy planning (RTP) workflow would reduce the cost, radiation exposure and uncertainties introduced by CT-MRI registrations. In the case of prostate treatment, one of the remaining challenges currently holding back the implementation of an RTP workflow is the MR-based localisation of intraprostatic gold fiducial markers (FMs), which is crucial for accurate patient positioning. Currently, MR-based FM localisation is clinically performed manually. This is sub-optimal, as manual interaction increases the workload. Attempts to perform automatic FM detection often rely on being able to detect signal voids induced by the FMs in magnitude images. However, signal voids may not always be sufficiently specific, hampering accurate and robust automatic FM localisation. Here, we present an approach that aims at automatic MR-based FM localisation. This method is based on template matching using a library of simulated complex-valued templates, and exploiting the behaviour of the complex MR signal in the vicinity of the FM. Clinical evaluation was performed on seventeen prostate cancer patients undergoing external beam radiotherapy treatment. Automatic MR-based FM localisation was compared to manual MR-based and semi-automatic CT-based localisation (the current gold standard) in terms of detection rate and the spatial accuracy and precision of localisation. The proposed method correctly detected all three FMs in 15/17 patients. The spatial accuracy (mean) and precision (STD) were 0.9 mm and 0.5 mm respectively, which is below the voxel size of 1.1 × 1.1 × 1.2 mm3 and comparable to MR-based manual localisation. FM localisation failed (3/51 FMs) in the presence of bleeding or calcifications in the direct vicinity of the FM. The method was found to be spatially accurate and precise, which is essential for clinical use. To overcome any missed detection, we envision the use of the proposed method along with verification by an observer. This will result in a

Evaluation of an automatic MR-based gold fiducial marker localisation method for MR-only prostate radiotherapy.

Science.gov (United States)

Maspero, Matteo; van den Berg, Cornelis A T; Zijlstra, Frank; Sikkes, Gonda G; de Boer, Hans C J; Meijer, Gert J; Kerkmeijer, Linda G W; Viergever, Max A; Lagendijk, Jan J W; Seevinck, Peter R

2017-10-03

An MR-only radiotherapy planning (RTP) workflow would reduce the cost, radiation exposure and uncertainties introduced by CT-MRI registrations. In the case of prostate treatment, one of the remaining challenges currently holding back the implementation of an RTP workflow is the MR-based localisation of intraprostatic gold fiducial markers (FMs), which is crucial for accurate patient positioning. Currently, MR-based FM localisation is clinically performed manually. This is sub-optimal, as manual interaction increases the workload. Attempts to perform automatic FM detection often rely on being able to detect signal voids induced by the FMs in magnitude images. However, signal voids may not always be sufficiently specific, hampering accurate and robust automatic FM localisation. Here, we present an approach that aims at automatic MR-based FM localisation. This method is based on template matching using a library of simulated complex-valued templates, and exploiting the behaviour of the complex MR signal in the vicinity of the FM. Clinical evaluation was performed on seventeen prostate cancer patients undergoing external beam radiotherapy treatment. Automatic MR-based FM localisation was compared to manual MR-based and semi-automatic CT-based localisation (the current gold standard) in terms of detection rate and the spatial accuracy and precision of localisation. The proposed method correctly detected all three FMs in 15/17 patients. The spatial accuracy (mean) and precision (STD) were 0.9 mm and 0.5 mm respectively, which is below the voxel size of [Formula: see text] mm 3 and comparable to MR-based manual localisation. FM localisation failed (3/51 FMs) in the presence of bleeding or calcifications in the direct vicinity of the FM. The method was found to be spatially accurate and precise, which is essential for clinical use. To overcome any missed detection, we envision the use of the proposed method along with verification by an observer. This will result in a

Observing health professionals' workflow patterns for diabetes care - First steps towards an ontology for EHR services.

Science.gov (United States)

Schweitzer, M; Lasierra, N; Hoerbst, A

2015-01-01

Increasing the flexibility from a user-perspective and enabling a workflow based interaction, facilitates an easy user-friendly utilization of EHRs for healthcare professionals' daily work. To offer such versatile EHR-functionality, our approach is based on the execution of clinical workflows by means of a composition of semantic web-services. The backbone of such architecture is an ontology which enables to represent clinical workflows and facilitates the selection of suitable services. In this paper we present the methods and results after running observations of diabetes routine consultations which were conducted in order to identify those workflows and the relation among the included tasks. Mentioned workflows were first modeled by BPMN and then generalized. As a following step in our study, interviews will be conducted with clinical personnel to validate modeled workflows.

Flexible Early Warning Systems with Workflows and Decision Tables

Science.gov (United States)

Riedel, F.; Chaves, F.; Zeiner, H.

2012-04-01

are usually only suited for rigid processes. We show how improvements can be achieved by using decision tables and rule-based adaptive workflows. Decision tables have been shown to be an intuitive tool that can be used by domain experts to express rule sets that can be interpreted automatically at runtime. Adaptive workflows use a rule-based approach to increase the flexibility of workflows by providing mechanisms to adapt workflows based on context changes, human intervention and availability of services. The combination of workflows, decision tables and rule-based adaption creates a framework that opens up new possibilities for flexible and adaptable workflows, especially, for use in early warning and crisis management systems.

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)

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.

Visual mismatch negativity indicates automatic, task-independent detection of artistic image composition in abstract artworks.

Science.gov (United States)

Menzel, Claudia; Kovács, Gyula; Amado, Catarina; Hayn-Leichsenring, Gregor U; Redies, Christoph

2018-05-06

In complex abstract art, image composition (i.e., the artist's deliberate arrangement of pictorial elements) is an important aesthetic feature. We investigated whether the human brain detects image composition in abstract artworks automatically (i.e., independently of the experimental task). To this aim, we studied whether a group of 20 original artworks elicited a visual mismatch negativity when contrasted with a group of 20 images that were composed of the same pictorial elements as the originals, but in shuffled arrangements, which destroy artistic composition. We used a passive oddball paradigm with parallel electroencephalogram recordings to investigate the detection of image type-specific properties. We observed significant deviant-standard differences for the shuffled and original images, respectively. Furthermore, for both types of images, differences in amplitudes correlated with the behavioral ratings of the images. In conclusion, we show that the human brain can detect composition-related image properties in visual artworks in an automatic fashion. Copyright © 2018 Elsevier B.V. All rights reserved.

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.

Structuring research methods and data with the research object model: genomics workflows as a case study.

Science.gov (United States)

Hettne, Kristina M; Dharuri, Harish; Zhao, Jun; Wolstencroft, Katherine; Belhajjame, Khalid; Soiland-Reyes, Stian; Mina, Eleni; Thompson, Mark; Cruickshank, Don; Verdes-Montenegro, Lourdes; Garrido, Julian; de Roure, David; Corcho, Oscar; Klyne, Graham; van Schouwen, Reinout; 't Hoen, Peter A C; Bechhofer, Sean; Goble, Carole; Roos, Marco

2014-01-01

One of the main challenges for biomedical research lies in the computer-assisted integrative study of large and increasingly complex combinations of data in order to understand molecular mechanisms. The preservation of the materials and methods of such computational experiments with clear annotations is essential for understanding an experiment, and this is increasingly recognized in the bioinformatics community. Our assumption is that offering means of digital, structured aggregation and annotation of the objects of an experiment will provide necessary meta-data for a scientist to understand and recreate the results of an experiment. To support this we explored a model for the semantic description of a workflow-centric Research Object (RO), where an RO is defined as a resource that aggregates other resources, e.g., datasets, software, spreadsheets, text, etc. We applied this model to a case study where we analysed human metabolite variation by workflows. We present the application of the workflow-centric RO model for our bioinformatics case study. Three workflows were produced following recently defined Best Practices for workflow design. By modelling the experiment as an RO, we were able to automatically query the experiment and answer questions such as "which particular data was input to a particular workflow to test a particular hypothesis?", and "which particular conclusions were drawn from a particular workflow?". Applying a workflow-centric RO model to aggregate and annotate the resources used in a bioinformatics experiment, allowed us to retrieve the conclusions of the experiment in the context of the driving hypothesis, the executed workflows and their input data. The RO model is an extendable reference model that can be used by other systems as well. The Research Object is available at http://www.myexperiment.org/packs/428 The Wf4Ever Research Object Model is available at http://wf4ever.github.io/ro.

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.

BioMoby extensions to the Taverna workflow management and enactment software

Directory of Open Access Journals (Sweden)

Senger Martin

2006-11-01

Full Text Available Abstract Background As biology becomes an increasingly computational science, it is critical that we develop software tools that support not only bioinformaticians, but also bench biologists in their exploration of the vast and complex data-sets that continue to build from international genomic, proteomic, and systems-biology projects. The BioMoby interoperability system was created with the goal of facilitating the movement of data from one Web-based resource to another to fulfill the requirements of non-expert bioinformaticians. In parallel with the development of BioMoby, the European myGrid project was designing Taverna, a bioinformatics workflow design and enactment tool. Here we describe the marriage of these two projects in the form of a Taverna plug-in that provides access to many of BioMoby's features through the Taverna interface. Results The exposed BioMoby functionality aids in the design of "sensible" BioMoby workflows, aids in pipelining BioMoby and non-BioMoby-based resources, and ensures that end-users need only a minimal understanding of both BioMoby, and the Taverna interface itself. Users are guided through the construction of syntactically and semantically correct workflows through plug-in calls to the Moby Central registry. Moby Central provides a menu of only those BioMoby services capable of operating on the data-type(s that exist at any given position in the workflow. Moreover, the plug-in automatically and correctly connects a selected service into the workflow such that users are not required to understand the nature of the inputs or outputs for any service, leaving them to focus on the biological meaning of the workflow they are constructing, rather than the technical details of how the services will interoperate. Conclusion With the availability of the BioMoby plug-in to Taverna, we believe that BioMoby-based Web Services are now significantly more useful and accessible to bench scientists than are more traditional

Workflows in bioinformatics: meta-analysis and prototype implementation of a workflow generator

Directory of Open Access Journals (Sweden)

Thoraval Samuel

2005-04-01

Full Text Available Abstract Background Computational methods for problem solving need to interleave information access and algorithm execution in a problem-specific workflow. The structures of these workflows are defined by a scaffold of syntactic, semantic and algebraic objects capable of representing them. Despite the proliferation of GUIs (Graphic User Interfaces in bioinformatics, only some of them provide workflow capabilities; surprisingly, no meta-analysis of workflow operators and components in bioinformatics has been reported. Results We present a set of syntactic components and algebraic operators capable of representing analytical workflows in bioinformatics. Iteration, recursion, the use of conditional statements, and management of suspend/resume tasks have traditionally been implemented on an ad hoc basis and hard-coded; by having these operators properly defined it is possible to use and parameterize them as generic re-usable components. To illustrate how these operations can be orchestrated, we present GPIPE, a prototype graphic pipeline generator for PISE that allows the definition of a pipeline, parameterization of its component methods, and storage of metadata in XML formats. This implementation goes beyond the macro capacities currently in PISE. As the entire analysis protocol is defined in XML, a complete bioinformatic experiment (linked sets of methods, parameters and results can be reproduced or shared among users. Availability: http://if-web1.imb.uq.edu.au/Pise/5.a/gpipe.html (interactive, ftp://ftp.pasteur.fr/pub/GenSoft/unix/misc/Pise/ (download. Conclusion From our meta-analysis we have identified syntactic structures and algebraic operators common to many workflows in bioinformatics. The workflow components and algebraic operators can be assimilated into re-usable software components. GPIPE, a prototype implementation of this framework, provides a GUI builder to facilitate the generation of workflows and integration of heterogeneous

Insightful Workflow For Grid Computing

Energy Technology Data Exchange (ETDEWEB)

Dr. Charles Earl

2008-10-09

We developed a workflow adaptation and scheduling system for Grid workflow. The system currently interfaces with and uses the Karajan workflow system. We developed machine learning agents that provide the planner/scheduler with information needed to make decisions about when and how to replan. The Kubrick restructures workflow at runtime, making it unique among workflow scheduling systems. The existing Kubrick system provides a platform on which to integrate additional quality of service constraints and in which to explore the use of an ensemble of scheduling and planning algorithms. This will be the principle thrust of our Phase II work.

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

Covariance among milking frequency, milk yield, and milk composition from automatically milked cows

DEFF Research Database (Denmark)

Løvendahl, Peter; Chagunda, G G

2011-01-01

Automatic milking systems allow cows voluntary access to milking and concentrates within set limits. This leads to large variation in milking intervals, both within and between cows, which further affects yield per milking and composition of milk. This study aimed to describe the degree to which ...

Application of industrial robots in automatic disassembly line of waste LCD displays

Science.gov (United States)

Wang, Sujuan

2017-11-01

In the automatic disassembly line of waste LCD displays, LCD displays are disassembled into plastic shells, metal shields, circuit boards, and LCD panels. Two industrial robots are used to cut metal shields and remove circuit boards in this automatic disassembly line. The functions of these two industrial robots, and the solutions to the critical issues of model selection, the interfaces with PLCs and the workflows were described in detail in this paper.

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.

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

Development of a data independent acquisition mass spectrometry workflow to enable glycopeptide analysis without predefined glycan compositional knowledge.

Science.gov (United States)

Lin, Chi-Hung; Krisp, Christoph; Packer, Nicolle H; Molloy, Mark P

2018-02-10

Glycoproteomics investigates glycan moieties in a site specific manner to reveal the functional roles of protein glycosylation. Identification of glycopeptides from data-dependent acquisition (DDA) relies on high quality MS/MS spectra of glycopeptide precursors and often requires manual validation to ensure confident assignments. In this study, we investigated pseudo-MRM (MRM-HR) and data-independent acquisition (DIA) as alternative acquisition strategies for glycopeptide analysis. These approaches allow data acquisition over the full MS/MS scan range allowing data re-analysis post-acquisition, without data re-acquisition. The advantage of MRM-HR over DDA for N-glycopeptide detection was demonstrated from targeted analysis of bovine fetuin where all three N-glycosylation sites were detected, which was not the case with DDA. To overcome the duty cycle limitation of MRM-HR acquisition needed for analysis of complex samples such as plasma we trialed DIA. This allowed development of a targeted DIA method to identify N-glycopeptides without pre-defined knowledge of the glycan composition, thus providing the potential to identify N-glycopeptides with unexpected structures. This workflow was demonstrated by detection of 59 N-glycosylation sites from 41 glycoproteins from a HILIC enriched human plasma tryptic digest. 21 glycoforms of IgG1 glycopeptides were identified including two truncated structures that are rarely reported. We developed a data-independent mass spectrometry workflow to identify specific glycopeptides from complex biological mixtures. The novelty is that this approach does not require glycan composition to be pre-defined, thereby allowing glycopeptides carrying unexpected glycans to be identified. This is demonstrated through the analysis of immunoglobulins in human plasma where we detected two IgG1 glycoforms that are rarely observed. Copyright © 2017 Elsevier B.V. All rights reserved.

geoKepler Workflow Module for Computationally Scalable and Reproducible Geoprocessing and Modeling

Science.gov (United States)

Cowart, C.; Block, J.; Crawl, D.; Graham, J.; Gupta, A.; Nguyen, M.; de Callafon, R.; Smarr, L.; Altintas, I.

2015-12-01

The NSF-funded WIFIRE project has developed an open-source, online geospatial workflow platform for unifying geoprocessing tools and models for for fire and other geospatially dependent modeling applications. It is a product of WIFIRE's objective to build an end-to-end cyberinfrastructure for real-time and data-driven simulation, prediction and visualization of wildfire behavior. geoKepler includes a set of reusable GIS components, or actors, for the Kepler Scientific Workflow System (https://kepler-project.org). Actors exist for reading and writing GIS data in formats such as Shapefile, GeoJSON, KML, and using OGC web services such as WFS. The actors also allow for calling geoprocessing tools in other packages such as GDAL and GRASS. Kepler integrates functions from multiple platforms and file formats into one framework, thus enabling optimal GIS interoperability, model coupling, and scalability. Products of the GIS actors can be fed directly to models such as FARSITE and WRF. Kepler's ability to schedule and scale processes using Hadoop and Spark also makes geoprocessing ultimately extensible and computationally scalable. The reusable workflows in geoKepler can be made to run automatically when alerted by real-time environmental conditions. Here, we show breakthroughs in the speed of creating complex data for hazard assessments with this platform. We also demonstrate geoKepler workflows that use Data Assimilation to ingest real-time weather data into wildfire simulations, and for data mining techniques to gain insight into environmental conditions affecting fire behavior. Existing machine learning tools and libraries such as R and MLlib are being leveraged for this purpose in Kepler, as well as Kepler's Distributed Data Parallel (DDP) capability to provide a framework for scalable processing. geoKepler workflows can be executed via an iPython notebook as a part of a Jupyter hub at UC San Diego for sharing and reporting of the scientific analysis and results from

A Network Inference Workflow Applied to Virulence-Related Processes in Salmonella typhimurium

Energy Technology Data Exchange (ETDEWEB)

Taylor, Ronald C.; Singhal, Mudita; Weller, Jennifer B.; Khoshnevis, Saeed; Shi, Liang; McDermott, Jason E.

2009-04-20

Inference of the structure of mRNA transcriptional regulatory networks, protein regulatory or interaction networks, and protein activation/inactivation-based signal transduction networks are critical tasks in systems biology. In this article we discuss a workflow for the reconstruction of parts of the transcriptional regulatory network of the pathogenic bacterium Salmonella typhimurium based on the information contained in sets of microarray gene expression data now available for that organism, and describe our results obtained by following this workflow. The primary tool is one of the network inference algorithms deployed in the Software Environment for BIological Network Inference (SEBINI). Specifically, we selected the algorithm called Context Likelihood of Relatedness (CLR), which uses the mutual information contained in the gene expression data to infer regulatory connections. The associated analysis pipeline automatically stores the inferred edges from the CLR runs within SEBINI and, upon request, transfers the inferred edges into either Cytoscape or the plug-in Collective Analysis of Biological of Biological Interaction Networks (CABIN) tool for further post-analysis of the inferred regulatory edges. The following article presents the outcome of this workflow, as well as the protocols followed for microarray data collection, data cleansing, and network inference. Our analysis revealed several interesting interactions, functional groups, metabolic pathways, and regulons in S. typhimurium.

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.

Characterizing chaotic melodies in automatic music composition

Science.gov (United States)

Coca, Andrés E.; Tost, Gerard O.; Zhao, Liang

2010-09-01

In this paper, we initially present an algorithm for automatic composition of melodies using chaotic dynamical systems. Afterward, we characterize chaotic music in a comprehensive way as comprising three perspectives: musical discrimination, dynamical influence on musical features, and musical perception. With respect to the first perspective, the coherence between generated chaotic melodies (continuous as well as discrete chaotic melodies) and a set of classical reference melodies is characterized by statistical descriptors and melodic measures. The significant differences among the three types of melodies are determined by discriminant analysis. Regarding the second perspective, the influence of dynamical features of chaotic attractors, e.g., Lyapunov exponent, Hurst coefficient, and correlation dimension, on melodic features is determined by canonical correlation analysis. The last perspective is related to perception of originality, complexity, and degree of melodiousness (Euler's gradus suavitatis) of chaotic and classical melodies by nonparametric statistical tests.

Unidirectional high fiber content composites: Automatic 3D FE model generation and damage simulation

DEFF Research Database (Denmark)

Qing, Hai; Mishnaevsky, Leon

2009-01-01

A new method and a software code for the automatic generation of 3D micromechanical FE models of unidirectional long-fiber-reinforced composite (LFRC) with high fiber volume fraction with random fiber arrangement are presented. The fiber arrangement in the cross-section is generated through random...

Workflow and web application for annotating NCBI BioProject transcriptome data.

Science.gov (United States)

Vera Alvarez, Roberto; Medeiros Vidal, Newton; Garzón-Martínez, Gina A; Barrero, Luz S; Landsman, David; Mariño-Ramírez, Leonardo

2017-01-01

The volume of transcriptome data is growing exponentially due to rapid improvement of experimental technologies. In response, large central resources such as those of the National Center for Biotechnology Information (NCBI) are continually adapting their computational infrastructure to accommodate this large influx of data. New and specialized databases, such as Transcriptome Shotgun Assembly Sequence Database (TSA) and Sequence Read Archive (SRA), have been created to aid the development and expansion of centralized repositories. Although the central resource databases are under continual development, they do not include automatic pipelines to increase annotation of newly deposited data. Therefore, third-party applications are required to achieve that aim. Here, we present an automatic workflow and web application for the annotation of transcriptome data. The workflow creates secondary data such as sequencing reads and BLAST alignments, which are available through the web application. They are based on freely available bioinformatics tools and scripts developed in-house. The interactive web application provides a search engine and several browser utilities. Graphical views of transcript alignments are available through SeqViewer, an embedded tool developed by NCBI for viewing biological sequence data. The web application is tightly integrated with other NCBI web applications and tools to extend the functionality of data processing and interconnectivity. We present a case study for the species Physalis peruviana with data generated from BioProject ID 67621. URL: http://www.ncbi.nlm.nih.gov/projects/physalis/. Published by Oxford University Press 2017. This work is written by US Government employees and is in the public domain in the US.

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.

Perti Net-Based Workflow Access Control Model

Institute of Scientific and Technical Information of China (English)

陈卓; 骆婷; 石磊; 洪帆

2004-01-01

Access control is an important protection mechanism for information systems. This paper shows how to make access control in workflow system. We give a workflow access control model (WACM) based on several current access control models. The model supports roles assignment and dynamic authorization. The paper defines the workflow using Petri net. It firstly gives the definition and description of the workflow, and then analyzes the architecture of the workflow access control model (WACM). Finally, an example of an e-commerce workflow access control model is discussed in detail.

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 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......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...

Real-Time Electronic Dashboard Technology and Its Use to Improve Pediatric Radiology Workflow.

Science.gov (United States)

Shailam, Randheer; Botwin, Ariel; Stout, Markus; Gee, Michael S

The purpose of our study was to create a real-time electronic dashboard in the pediatric radiology reading room providing a visual display of updated information regarding scheduled and in-progress radiology examinations that could help radiologists to improve clinical workflow and efficiency. To accomplish this, a script was set up to automatically send real-time HL7 messages from the radiology information system (Epic Systems, Verona, WI) to an Iguana Interface engine, with relevant data regarding examinations stored in an SQL Server database for visual display on the dashboard. Implementation of an electronic dashboard in the reading room of a pediatric radiology academic practice has led to several improvements in clinical workflow, including decreasing the time interval for radiologist protocol entry for computed tomography or magnetic resonance imaging examinations as well as fewer telephone calls related to unprotocoled examinations. Other advantages include enhanced ability of radiologists to anticipate and attend to examinations requiring radiologist monitoring or scanning, as well as to work with technologists and operations managers to optimize scheduling in radiology resources. We foresee increased utilization of electronic dashboard technology in the future as a method to improve radiology workflow and quality of patient care. Copyright © 2017 Elsevier Inc. All rights reserved.

Automatic geospatial information Web service composition based on ontology interface matching

Science.gov (United States)

Xu, Xianbin; Wu, Qunyong; Wang, Qinmin

2008-10-01

With Web services technology the functions of WebGIS can be presented as a kind of geospatial information service, and helped to overcome the limitation of the information-isolated situation in geospatial information sharing field. Thus Geospatial Information Web service composition, which conglomerates outsourced services working in tandem to offer value-added service, plays the key role in fully taking advantage of geospatial information services. This paper proposes an automatic geospatial information web service composition algorithm that employed the ontology dictionary WordNet to analyze semantic distances among the interfaces. Through making matching between input/output parameters and the semantic meaning of pairs of service interfaces, a geospatial information web service chain can be created from a number of candidate services. A practice of the algorithm is also proposed and the result of it shows the feasibility of this algorithm and the great promise in the emerging demand for geospatial information web service composition.

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.

Dynamic reusable workflows for ocean science

Science.gov (United States)

Signell, Richard; Fernandez, Filipe; Wilcox, Kyle

2016-01-01

Digital catalogs of ocean data have been available for decades, but advances in standardized services and software for catalog search and data access make it now 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 enters 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 use of dynamic

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

Understanding dental CAD/CAM for restorations--the digital workflow from a mechanical engineering viewpoint.

Science.gov (United States)

Tapie, L; Lebon, N; Mawussi, B; Fron Chabouis, H; Duret, F; Attal, J-P

2015-01-01

As digital technology infiltrates every area of daily life, including the field of medicine, so it is increasingly being introduced into dental practice. Apart from chairside practice, computer-aided design/computer-aided manufacturing (CAD/CAM) solutions are available for creating inlays, crowns, fixed partial dentures (FPDs), implant abutments, and other dental prostheses. CAD/CAM dental solutions can be considered a chain of digital devices and software for the almost automatic design and creation of dental restorations. However, dentists who want to use the technology often do not have the time or knowledge to understand it. A basic knowledge of the CAD/CAM digital workflow for dental restorations can help dentists to grasp the technology and purchase a CAM/CAM system that meets the needs of their office. This article provides a computer-science and mechanical-engineering approach to the CAD/CAM digital workflow to help dentists understand the technology.

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.)

AuTom: a novel automatic platform for electron tomography reconstruction

KAUST Repository

Han, Renmin

2017-07-26

We have developed a software package towards automatic electron tomography (ET): Automatic Tomography (AuTom). The presented package has the following characteristics: accurate alignment modules for marker-free datasets containing substantial biological structures; fully automatic alignment modules for datasets with fiducial markers; wide coverage of reconstruction methods including a new iterative method based on the compressed-sensing theory that suppresses the “missing wedge” effect; and multi-platform acceleration solutions that support faster iterative algebraic reconstruction. AuTom aims to achieve fully automatic alignment and reconstruction for electron tomography and has already been successful for a variety of datasets. AuTom also offers user-friendly interface and auxiliary designs for file management and workflow management, in which fiducial marker-based datasets and marker-free datasets are addressed with totally different subprocesses. With all of these features, AuTom can serve as a convenient and effective tool for processing in electron tomography.

Integration of services into workflow applications

CERN Document Server

Czarnul, Pawel

2015-01-01

Describing state-of-the-art solutions in distributed system architectures, Integration of Services into Workflow Applications presents a concise approach to the integration of loosely coupled services into workflow applications. It discusses key challenges related to the integration of distributed systems and proposes solutions, both in terms of theoretical aspects such as models and workflow scheduling algorithms, and technical solutions such as software tools and APIs.The book provides an in-depth look at workflow scheduling and proposes a way to integrate several different types of services

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.

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...

SegMine workflows for semantic microarray data analysis in Orange4WS

Directory of Open Access Journals (Sweden)

Kulovesi Kimmo

2011-10-01

Full Text Available Abstract Background In experimental data analysis, bioinformatics researchers increasingly rely on tools that enable the composition and reuse of scientific workflows. The utility of current bioinformatics workflow environments can be significantly increased by offering advanced data mining services as workflow components. Such services can support, for instance, knowledge discovery from diverse distributed data and knowledge sources (such as GO, KEGG, PubMed, and experimental databases. Specifically, cutting-edge data analysis approaches, such as semantic data mining, link discovery, and visualization, have not yet been made available to researchers investigating complex biological datasets. Results We present a new methodology, SegMine, for semantic analysis of microarray data by exploiting general biological knowledge, and a new workflow environment, Orange4WS, with integrated support for web services in which the SegMine methodology is implemented. The SegMine methodology consists of two main steps. First, the semantic subgroup discovery algorithm is used to construct elaborate rules that identify enriched gene sets. Then, a link discovery service is used for the creation and visualization of new biological hypotheses. The utility of SegMine, implemented as a set of workflows in Orange4WS, is demonstrated in two microarray data analysis applications. In the analysis of senescence in human stem cells, the use of SegMine resulted in three novel research hypotheses that could improve understanding of the underlying mechanisms of senescence and identification of candidate marker genes. Conclusions Compared to the available data analysis systems, SegMine offers improved hypothesis generation and data interpretation for bioinformatics in an easy-to-use integrated workflow environment.

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.

Automatic Generation of Building Models with Levels of Detail 1-3

Science.gov (United States)

Nguatem, W.; Drauschke, M.; Mayer, H.

2016-06-01

We present a workflow for the automatic generation of building models with levels of detail (LOD) 1 to 3 according to the CityGML standard (Gröger et al., 2012). We start with orienting unsorted image sets employing (Mayer et al., 2012), we compute depth maps using semi-global matching (SGM) (Hirschmüller, 2008), and fuse these depth maps to reconstruct dense 3D point clouds (Kuhn et al., 2014). Based on planes segmented from these point clouds, we have developed a stochastic method for roof model selection (Nguatem et al., 2013) and window model selection (Nguatem et al., 2014). We demonstrate our workflow up to the export into CityGML.

Automatic Generation of Supervisory Control System Software Using Graph Composition

Science.gov (United States)

Nakata, Hideo; Sano, Tatsuro; Kojima, Taizo; Seo, Kazuo; Uchida, Tomoyuki; Nakamura, Yasuaki

This paper describes the automatic generation of system descriptions for SCADA (Supervisory Control And Data Acquisition) systems. The proposed method produces various types of data and programs for SCADA systems from equipment definitions using conversion rules. At first, this method makes directed graphs, which represent connections between the equipment, from equipment definitions. System descriptions are generated using the conversion rules, by analyzing these directed graphs, and finding the groups of equipment that involve similar operations. This method can make the conversion rules multi levels by using the composition of graphs, and can reduce the number of rules. The developer can define and manage these rules efficiently.

Concentrate composition for automatic milking systems - effect on milking frequency

DEFF Research Database (Denmark)

Madsen, Jørgen; Weisbjerg, Martin Riis; Hvelplund, Torben

2010-01-01

The purpose of this study was to investigate the potential of affecting milking frequency in an Automatic Milking System (AMS) by changing ingredient composition of the concentrate fed in the AMS. In six experiments, six experimental concentrates were tested against a Standard concentrate all...... supplied in the amounts of 5 kg/cow/day. Fifteen cows were fed the experimental concentrate and another 15 cows the Standard concentrate for 14 days and then for the next 14 days the cows were fed the opposite diets to be their own control. The change from one mixture to the next was done over only one day...

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.)

A practical data processing workflow for multi-OMICS projects.

Science.gov (United States)

Kohl, Michael; Megger, Dominik A; Trippler, Martin; Meckel, Hagen; Ahrens, Maike; Bracht, Thilo; Weber, Frank; Hoffmann, Andreas-Claudius; Baba, Hideo A; Sitek, Barbara; Schlaak, Jörg F; Meyer, Helmut E; Stephan, Christian; Eisenacher, Martin

2014-01-01

Multi-OMICS approaches aim on the integration of quantitative data obtained for different biological molecules in order to understand their interrelation and the functioning of larger systems. This paper deals with several data integration and data processing issues that frequently occur within this context. To this end, the data processing workflow within the PROFILE project is presented, a multi-OMICS project that aims on identification of novel biomarkers and the development of new therapeutic targets for seven important liver diseases. Furthermore, a software called CrossPlatformCommander is sketched, which facilitates several steps of the proposed workflow in a semi-automatic manner. Application of the software is presented for the detection of novel biomarkers, their ranking and annotation with existing knowledge using the example of corresponding Transcriptomics and Proteomics data sets obtained from patients suffering from hepatocellular carcinoma. Additionally, a linear regression analysis of Transcriptomics vs. Proteomics data is presented and its performance assessed. It was shown, that for capturing profound relations between Transcriptomics and Proteomics data, a simple linear regression analysis is not sufficient and implementation and evaluation of alternative statistical approaches are needed. Additionally, the integration of multivariate variable selection and classification approaches is intended for further development of the software. Although this paper focuses only on the combination of data obtained from quantitative Proteomics and Transcriptomics experiments, several approaches and data integration steps are also applicable for other OMICS technologies. Keeping specific restrictions in mind the suggested workflow (or at least parts of it) may be used as a template for similar projects that make use of different high throughput techniques. This article is part of a Special Issue entitled: Computational Proteomics in the Post

Automatic 1H-NMR Screening of Fatty Acid Composition in Edible Oils

Directory of Open Access Journals (Sweden)

David Castejón

2016-02-01

Full Text Available In this work, we introduce an NMR-based screening method for the fatty acid composition analysis of edible oils. We describe the evaluation and optimization needed for the automated analysis of vegetable oils by low-field NMR to obtain the fatty acid composition (FAC. To achieve this, two scripts, which automatically analyze and interpret the spectral data, were developed. The objective of this work was to drive forward the automated analysis of the FAC by NMR. Due to the fact that this protocol can be carried out at low field and that the complete process from sample preparation to printing the report only takes about 3 min, this approach is promising to become a fundamental technique for high-throughput screening. To demonstrate the applicability of this method, the fatty acid composition of extra virgin olive oils from various Spanish olive varieties (arbequina, cornicabra, hojiblanca, manzanilla, and picual was determined by 1H-NMR spectroscopy according to this protocol.

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

Science.gov (United States)

Venco, Francesco; Vaskin, Yuriy; Ceol, Arnaud; Muller, Heiko

2014-01-01

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). 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. 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 workflows are available

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

Design and evaluation of a multimedia electronic patient record "oncoflow" with clinical workflow assistance for head and neck tumor therapy.

Science.gov (United States)

Meier, Jens; Boehm, Andreas; Kielhorn, Anne; Dietz, Andreas; Bohn, Stefan; Neumuth, Thomas

2014-11-01

The management of patient-specific information is a challenging task for surgeons and physicians because existing clinical information systems are insufficiently integrated into daily clinical routine and contained information entities are distributed across different proprietary databases. Thus, existing information is hardly usable for further electronic processing, workflow support or clinical studies. A Web-based clinical information system has been developed that automatically imports patient-specific information from different information systems. The system is tailored to the existing workflow for the treatment of patients with head and neck cancer. In this paper, the clinical assistance functions and a quantitative as well as a qualitative system evaluation are presented. The information system has been deployed at a clinical site and is in use in daily clinical routine. Two evaluation studies show that the information integration, the structured information presentation in the Web browser and the assistance functions improve the physician's workflow. The studies also show that the usage of the new information system does not impair the time physicians need for a process step compared with the usage of the existing information system. Information integration is crucial for efficient workflow support in the clinic. The central access to information within a modern and structured user interface saves valuable time for the physician. The comprehensive database allows an instant usage of the existing information clinical workflow support or the conduction of trial studies.

All-automatic swimmer tracking system based on an optimized scaled composite JTC technique

Science.gov (United States)

Benarab, D.; Napoléon, T.; Alfalou, A.; Verney, A.; Hellard, P.

2016-04-01

In this paper, an all-automatic optimized JTC based swimmer tracking system is proposed and evaluated on real video database outcome from national and international swimming competitions (French National Championship, Limoges 2015, FINA World Championships, Barcelona 2013 and Kazan 2015). First, we proposed to calibrate the swimming pool using the DLT algorithm (Direct Linear Transformation). DLT calculates the homography matrix given a sufficient set of correspondence points between pixels and metric coordinates: i.e. DLT takes into account the dimensions of the swimming pool and the type of the swim. Once the swimming pool is calibrated, we extract the lane. Then we apply a motion detection approach to detect globally the swimmer in this lane. Next, we apply our optimized Scaled Composite JTC which consists of creating an adapted input plane that contains the predicted region and the head reference image. This latter is generated using a composite filter of fin images chosen from the database. The dimension of this reference will be scaled according to the ratio between the head's dimension and the width of the swimming lane. Finally, applying the proposed approach improves the performances of our previous tracking method by adding a detection module in order to achieve an all-automatic swimmer tracking system.

An Ontology-supported Approach for Automatic Chaining of Web Services in Geospatial Knowledge Discovery

Science.gov (United States)

di, L.; Yue, P.; Yang, W.; Yu, G.

2006-12-01

Recent developments in geospatial semantic Web have shown promise for automatic discovery, access, and use of geospatial Web services to quickly and efficiently solve particular application problems. With the semantic Web technology, it is highly feasible to construct intelligent geospatial knowledge systems that can provide answers to many geospatial application questions. A key challenge in constructing such intelligent knowledge system is to automate the creation of a chain or process workflow that involves multiple services and highly diversified data and can generate the answer to a specific question of users. This presentation discusses an approach for automating composition of geospatial Web service chains by employing geospatial semantics described by geospatial ontologies. It shows how ontology-based geospatial semantics are used for enabling the automatic discovery, mediation, and chaining of geospatial Web services. OWL-S is used to represent the geospatial semantics of individual Web services and the type of the services it belongs to and the type of the data it can handle. The hierarchy and classification of service types are described in the service ontology. The hierarchy and classification of data types are presented in the data ontology. For answering users' geospatial questions, an Artificial Intelligent (AI) planning algorithm is used to construct the service chain by using the service and data logics expressed in the ontologies. The chain can be expressed as a graph with nodes representing services and connection weights representing degrees of semantic matching between nodes. The graph is a visual representation of logical geo-processing path for answering users' questions. The graph can be instantiated to a physical service workflow for execution to generate the answer to a user's question. A prototype system, which includes real world geospatial applications, is implemented to demonstrate the concept and approach.

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

Biowep: a workflow enactment portal for bioinformatics applications.

Science.gov (United States)

Romano, Paolo; Bartocci, Ezio; Bertolini, Guglielmo; De Paoli, Flavio; Marra, Domenico; Mauri, Giancarlo; Merelli, Emanuela; Milanesi, Luciano

2007-03-08

The huge amount of biological information, its distribution over the Internet and the heterogeneity of available software tools makes the adoption of new data integration and analysis network tools a necessity in bioinformatics. ICT standards and tools, like Web Services and Workflow Management Systems (WMS), can support the creation and deployment of such systems. Many Web Services are already available and some WMS have been proposed. They assume that researchers know which bioinformatics resources can be reached through a programmatic interface and that they are skilled in programming and building workflows. Therefore, they are not viable to the majority of unskilled researchers. A portal enabling these to take profit from new technologies is still missing. We designed biowep, a web based client application that allows for the selection and execution of a set of predefined workflows. The system is available on-line. Biowep architecture includes a Workflow Manager, a User Interface and a Workflow Executor. The task of the Workflow Manager is the creation and annotation of workflows. These can be created by using either the Taverna Workbench or BioWMS. Enactment of workflows is carried out by FreeFluo for Taverna workflows and by BioAgent/Hermes, a mobile agent-based middleware, for BioWMS ones. Main workflows' processing steps are annotated on the basis of their input and output, elaboration type and application domain by using a classification of bioinformatics data and tasks. The interface supports users authentication and profiling. Workflows can be selected on the basis of users' profiles and can be searched through their annotations. Results can be saved. We developed a web system that support the selection and execution of predefined workflows, thus simplifying access for all researchers. The implementation of Web Services allowing specialized software to interact with an exhaustive set of biomedical databases and analysis software and the creation of

Biowep: a workflow enactment portal for bioinformatics applications

Directory of Open Access Journals (Sweden)

Romano Paolo

2007-03-01

Full Text Available Abstract Background The huge amount of biological information, its distribution over the Internet and the heterogeneity of available software tools makes the adoption of new data integration and analysis network tools a necessity in bioinformatics. ICT standards and tools, like Web Services and Workflow Management Systems (WMS, can support the creation and deployment of such systems. Many Web Services are already available and some WMS have been proposed. They assume that researchers know which bioinformatics resources can be reached through a programmatic interface and that they are skilled in programming and building workflows. Therefore, they are not viable to the majority of unskilled researchers. A portal enabling these to take profit from new technologies is still missing. Results We designed biowep, a web based client application that allows for the selection and execution of a set of predefined workflows. The system is available on-line. Biowep architecture includes a Workflow Manager, a User Interface and a Workflow Executor. The task of the Workflow Manager is the creation and annotation of workflows. These can be created by using either the Taverna Workbench or BioWMS. Enactment of workflows is carried out by FreeFluo for Taverna workflows and by BioAgent/Hermes, a mobile agent-based middleware, for BioWMS ones. Main workflows' processing steps are annotated on the basis of their input and output, elaboration type and application domain by using a classification of bioinformatics data and tasks. The interface supports users authentication and profiling. Workflows can be selected on the basis of users' profiles and can be searched through their annotations. Results can be saved. Conclusion We developed a web system that support the selection and execution of predefined workflows, thus simplifying access for all researchers. The implementation of Web Services allowing specialized software to interact with an exhaustive set of biomedical

ATLAS Grid Workflow Performance Optimization

CERN Document Server

Elmsheuser, Johannes; The ATLAS collaboration

2018-01-01

The CERN ATLAS experiment grid workflow system manages routinely 250 to 500 thousand concurrently running production and analysis jobs to process simulation and detector data. In total more than 300 PB of data is distributed over more than 150 sites in the WLCG. At this scale small improvements in the software and computing performance and workflows can lead to significant resource usage gains. ATLAS is reviewing together with CERN IT experts several typical simulation and data processing workloads for potential performance improvements in terms of memory and CPU usage, disk and network I/O. All ATLAS production and analysis grid jobs are instrumented to collect many performance metrics for detailed statistical studies using modern data analytics tools like ElasticSearch and Kibana. This presentation will review and explain the performance gains of several ATLAS simulation and data processing workflows and present analytics studies of the ATLAS grid workflows.

Grid infrastructure for automatic processing of SAR data for flood applications

Science.gov (United States)

Kussul, Natalia; Skakun, Serhiy; Shelestov, Andrii

2010-05-01

More and more geosciences applications are being put on to the Grids. Due to the complexity of geosciences applications that is caused by complex workflow, the use of computationally intensive environmental models, the need of management and integration of heterogeneous data sets, Grid offers solutions to tackle these problems. Many geosciences applications, especially those related to the disaster management and mitigations require the geospatial services to be delivered in proper time. For example, information on flooded areas should be provided to corresponding organizations (local authorities, civil protection agencies, UN agencies etc.) no more than in 24 h to be able to effectively allocate resources required to mitigate the disaster. Therefore, providing infrastructure and services that will enable automatic generation of products based on the integration of heterogeneous data represents the tasks of great importance. In this paper we present Grid infrastructure for automatic processing of synthetic-aperture radar (SAR) satellite images to derive flood products. In particular, we use SAR data acquired by ESA's ENVSAT satellite, and neural networks to derive flood extent. The data are provided in operational mode from ESA rolling archive (within ESA Category-1 grant). We developed a portal that is based on OpenLayers frameworks and provides access point to the developed services. Through the portal the user can define geographical region and search for the required data. Upon selection of data sets a workflow is automatically generated and executed on the resources of Grid infrastructure. For workflow execution and management we use Karajan language. The workflow of SAR data processing consists of the following steps: image calibration, image orthorectification, image processing with neural networks, topographic effects removal, geocoding and transformation to lat/long projection, and visualisation. These steps are executed by different software, and can be

Behavioral technique for workflow abstraction and matching

NARCIS (Netherlands)

Klai, K.; Ould Ahmed M'bareck, N.; Tata, S.; Dustdar, S.; Fiadeiro, J.L.; Sheth, A.

2006-01-01

This work is in line with the CoopFlow approach dedicated for workflow advertisement, interconnection, and cooperation in virtual organizations. In order to advertise workflows into a registry, we present in this paper a novel method to abstract behaviors of workflows into symbolic observation

Workflow Management in CLARIN-DK

DEFF Research Database (Denmark)

Jongejan, Bart

2013-01-01

The CLARIN-DK infrastructure is not only a repository of resources, but also a place where users can analyse, annotate, reformat and potentially even translate resources, using tools that are integrated in the infrastructure as web services. In many cases a single tool does not produce the desired...... 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...

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...

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...

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

DEFF Research Database (Denmark)

Mans, Ronny S.; van der Aalst, Willibrordus Martinus Pancratius; Molemann, A.J.

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 Care organizations, such as hospitals, need to support complex and dynamic workflows. Moreover, 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...

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.

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.

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.

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. PMID:25821845

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...

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

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.

Using Mobile Agents to Implement Workflow System

Institute of Scientific and Technical Information of China (English)

LI Jie; LIU Xian-xing; GUO Zheng-wei

2004-01-01

Current workflow management systems usually adopt the existing technologies such as TCP/IP-based Web technologies and CORBA as well to fulfill the bottom communications.Very often it has been considered only from a theoretical point of view, mainly for the lack of concrete possibilities to execute with elasticity.MAT (Mobile Agent Technology) represents a very attractive approach to the distributed control of computer networks and a valid alternative to the implementation of strategies for workflow system.This paper mainly focuses on improving the performance of workflow system by using MAT.Firstly, the performances of workflow systems based on both CORBA and mobile agent are summarized and analyzed; Secondly, the performance contrast is presented by introducing the mathematic model of each kind of data interaction process respectively.Last, a mobile agent-based workflow system named MAWMS is presented and described in detail.

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

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

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

Microseismic event location using global optimization algorithms: An integrated and automated workflow

Science.gov (United States)

Lagos, Soledad R.; Velis, Danilo R.

2018-02-01

We perform the location of microseismic events generated in hydraulic fracturing monitoring scenarios using two global optimization techniques: Very Fast Simulated Annealing (VFSA) and Particle Swarm Optimization (PSO), and compare them against the classical grid search (GS). To this end, we present an integrated and optimized workflow that concatenates into an automated bash script the different steps that lead to the microseismic events location from raw 3C data. First, we carry out the automatic detection, denoising and identification of the P- and S-waves. Secondly, we estimate their corresponding backazimuths using polarization information, and propose a simple energy-based criterion to automatically decide which is the most reliable estimate. Finally, after taking proper care of the size of the search space using the backazimuth information, we perform the location using the aforementioned algorithms for 2D and 3D usual scenarios of hydraulic fracturing processes. We assess the impact of restricting the search space and show the advantages of using either VFSA or PSO over GS to attain significant speed-ups.

Brain-wide mapping of axonal connections: workflow for automated detection and spatial analysis of labeling in microscopic sections

Directory of Open Access Journals (Sweden)

Eszter Agnes ePapp

2016-04-01

Full Text Available Axonal tracing techniques are powerful tools for exploring the structural organization of neuronal connections. Tracers such as biotinylated dextran amine (BDA and Phaseolus vulgaris leucoagglutinin (Pha-L allow brain-wide mapping of connections through analysis of large series of histological section images. We present a workflow for efficient collection and analysis of tract-tracing datasets with a focus on newly developed modules for image processing and assignment of anatomical location to tracing data. New functionality includes automatic detection of neuronal labeling in large image series, alignment of images to a volumetric brain atlas, and analytical tools for measuring the position and extent of labeling. To evaluate the workflow, we used high-resolution microscopic images from axonal tracing experiments in which different parts of the rat primary somatosensory cortex had been injected with BDA or Pha-L. Parameters from a set of representative images were used to automate detection of labeling in image series covering the entire brain, resulting in binary maps of the distribution of labeling. For high to medium labeling densities, automatic detection was found to provide reliable results when compared to manual analysis, whereas weak labeling required manual curation for optimal detection. To identify brain regions corresponding to labeled areas, section images were aligned to the Waxholm Space (WHS atlas of the Sprague Dawley rat brain (v2 by custom-angle slicing of the MRI template to match individual sections. Based on the alignment, WHS coordinates were obtained for labeled elements and transformed to stereotaxic coordinates. The new workflow modules increase the efficiency and reliability of labeling detection in large series of images from histological sections, and enable anchoring to anatomical atlases for further spatial analysis and comparison with other data.

Clinically-inspired automatic classification of ovarian carcinoma subtypes

Directory of Open Access Journals (Sweden)

Aicha BenTaieb

2016-01-01

Full Text Available Context: It has been shown that ovarian carcinoma subtypes are distinct pathologic entities with differing prognostic and therapeutic implications. Histotyping by pathologists has good reproducibility, but occasional cases are challenging and require immunohistochemistry and subspecialty consultation. Motivated by the need for more accurate and reproducible diagnoses and to facilitate pathologists′ workflow, we propose an automatic framework for ovarian carcinoma classification. Materials and Methods: Our method is inspired by pathologists′ workflow. We analyse imaged tissues at two magnification levels and extract clinically-inspired color, texture, and segmentation-based shape descriptors using image-processing methods. We propose a carefully designed machine learning technique composed of four modules: A dissimilarity matrix, dimensionality reduction, feature selection and a support vector machine classifier to separate the five ovarian carcinoma subtypes using the extracted features. Results: This paper presents the details of our implementation and its validation on a clinically derived dataset of eighty high-resolution histopathology images. The proposed system achieved a multiclass classification accuracy of 95.0% when classifying unseen tissues. Assessment of the classifier′s confusion (confusion matrix between the five different ovarian carcinoma subtypes agrees with clinician′s confusion and reflects the difficulty in diagnosing endometrioid and serous carcinomas. Conclusions: Our results from this first study highlight the difficulty of ovarian carcinoma diagnosis which originate from the intrinsic class-imbalance observed among subtypes and suggest that the automatic analysis of ovarian carcinoma subtypes could be valuable to clinician′s diagnostic procedure by providing a second opinion.

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.

A virtual data language and system for scientific workflow management in data grid environments

Science.gov (United States)

Zhao, Yong

With advances in scientific instrumentation and simulation, scientific data is growing fast in both size and analysis complexity. So-called Data Grids aim to provide high performance, distributed data analysis infrastructure for data- intensive sciences, where scientists distributed worldwide need to extract information from large collections of data, and to share both data products and the resources needed to produce and store them. However, the description, composition, and execution of even logically simple scientific workflows are often complicated by the need to deal with "messy" issues like heterogeneous storage formats and ad-hoc file system structures. We show how these difficulties can be overcome via a typed workflow notation called virtual data language, within which issues of physical representation are cleanly separated from logical typing, and by the implementation of this notation within the context of a powerful virtual data system that supports distributed execution. The resulting language and system are capable of expressing complex workflows in a simple compact form, enacting those workflows in distributed environments, monitoring and recording the execution processes, and tracing the derivation history of data products. We describe the motivation, design, implementation, and evaluation of the virtual data language and system, and the application of the virtual data paradigm in various science disciplines, including astronomy, cognitive neuroscience.

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

Contracts for Cross-Organizational Workflow Management

NARCIS (Netherlands)

Koetsier, M.J.; Grefen, P.W.P.J.; Vonk, J.

1999-01-01

Nowadays, many organizations form dynamic partnerships to deal effectively with market requirements. As companies use automated workflow systems to control their processes, a way of linking workflow processes in different organizations is useful in turning the co-operating companies into a seamless

Workflow Patterns for Business Process Modeling

NARCIS (Netherlands)

Thom, Lucineia Heloisa; Lochpe, Cirano; Reichert, M.U.

For its reuse advantages, workflow patterns (e.g., control flow patterns, data patterns, resource patterns) are increasingly attracting the interest of both researchers and vendors. Frequently, business process or workflow models can be assembeled out of a set of recurrent process fragments (or

Body Composition Assessment in Axial CT Images Using FEM-Based Automatic Segmentation of Skeletal Muscle.

Science.gov (United States)

Popuri, Karteek; Cobzas, Dana; Esfandiari, Nina; Baracos, Vickie; Jägersand, Martin

2016-02-01

The proportions of muscle and fat tissues in the human body, referred to as body composition is a vital measurement for cancer patients. Body composition has been recently linked to patient survival and the onset/recurrence of several types of cancers in numerous cancer research studies. This paper introduces a fully automatic framework for the segmentation of muscle and fat tissues from CT images to estimate body composition. We developed a novel finite element method (FEM) deformable model that incorporates a priori shape information via a statistical deformation model (SDM) within the template-based segmentation framework. The proposed method was validated on 1000 abdominal and 530 thoracic CT images and we obtained very good segmentation results with Jaccard scores in excess of 90% for both the muscle and fat regions.

Evaluation of an image-based tracking workflow using a passive marker and resonant micro-coil fiducials for automatic image plane alignment in interventional MRI.

Science.gov (United States)

Neumann, M; Breton, E; Cuvillon, L; Pan, L; Lorenz, C H; de Mathelin, M

2012-01-01

In this paper, an original workflow is presented for MR image plane alignment based on tracking in real-time MR images. A test device consisting of two resonant micro-coils and a passive marker is proposed for detection using image-based algorithms. Micro-coils allow for automated initialization of the object detection in dedicated low flip angle projection images; then the passive marker is tracked in clinical real-time MR images, with alternation between two oblique orthogonal image planes along the test device axis; in case the passive marker is lost in real-time images, the workflow is reinitialized. The proposed workflow was designed to minimize dedicated acquisition time to a single dedicated acquisition in the ideal case (no reinitialization required). First experiments have shown promising results for test-device tracking precision, with a mean position error of 0.79 mm and a mean orientation error of 0.24°.

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.

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)

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.

Optimal resource assignment in workflows for maximizing cooperation

NARCIS (Netherlands)

Kumar, Akhil; Dijkman, R.M.; Song, Minseok; Daniel, Fl.; Wang, J.; Weber, B.

2013-01-01

A workflow is a team process since many actors work on various tasks to complete an instance. Resource management in such workflows deals with assignment of tasks to workers or actors. In team formation, it is necessary to ensure that members of a team are compatible with each other. When a workflow

An Automatic Web Service Composition Framework Using QoS-Based Web Service Ranking Algorithm.

Science.gov (United States)

Mallayya, Deivamani; Ramachandran, Baskaran; Viswanathan, Suganya

2015-01-01

Web service has become the technology of choice for service oriented computing to meet the interoperability demands in web applications. In the Internet era, the exponential addition of web services nominates the "quality of service" as essential parameter in discriminating the web services. In this paper, a user preference based web service ranking (UPWSR) algorithm is proposed to rank web services based on user preferences and QoS aspect of the web service. When the user's request cannot be fulfilled by a single atomic service, several existing services should be composed and delivered as a composition. The proposed framework allows the user to specify the local and global constraints for composite web services which improves flexibility. UPWSR algorithm identifies best fit services for each task in the user request and, by choosing the number of candidate services for each task, reduces the time to generate the composition plans. To tackle the problem of web service composition, QoS aware automatic web service composition (QAWSC) algorithm proposed in this paper is based on the QoS aspects of the web services and user preferences. The proposed framework allows user to provide feedback about the composite service which improves the reputation of the services.

Performing Workflows in Pervasive Environments Based on Context Specifications

OpenAIRE

Xiping Liu; Jianxin Chen

2010-01-01

The workflow performance consists of the performance of activities and transitions between activities. Along with the fast development of varied computing devices, activities in workflows and transitions between activities could be performed in pervasive ways, whichcauses that the workflow performance need to migrate from traditional computing environments to pervasive environments. To perform workflows in pervasive environments needs to take account of the context information which affects b...

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.

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.

Verifying generalized soundness for workflow nets

NARCIS (Netherlands)

Hee, van K.M.; Oanea, O.I.; Sidorova, N.; Voorhoeve, M.; Virbitskaite, I.; Voronkov, A.

2007-01-01

We improve the decision procedure from [10] for the problem of generalized soundness of workflow nets. A workflow net is generalized sound iff every marking reachable from an initial marking with k tokens on the initial place terminates properly, i.e. it can reach a marking with k tokens on the

Automatic extraction of road features in urban environments using dense ALS data

Science.gov (United States)

Soilán, Mario; Truong-Hong, Linh; Riveiro, Belén; Laefer, Debra

2018-02-01

This paper describes a methodology that automatically extracts semantic information from urban ALS data for urban parameterization and road network definition. First, building façades are segmented from the ground surface by combining knowledge-based information with both voxel and raster data. Next, heuristic rules and unsupervised learning are applied to the ground surface data to distinguish sidewalk and pavement points as a means for curb detection. Then radiometric information was employed for road marking extraction. Using high-density ALS data from Dublin, Ireland, this fully automatic workflow was able to generate a F-score close to 95% for pavement and sidewalk identification with a resolution of 20 cm and better than 80% for road marking detection.

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

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 and to ve......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...

Automatic classification of retinal three-dimensional optical coherence tomography images using principal component analysis network with composite kernels.

Science.gov (United States)

Fang, Leyuan; Wang, Chong; Li, Shutao; Yan, Jun; Chen, Xiangdong; Rabbani, Hossein

2017-11-01

We present an automatic method, termed as the principal component analysis network with composite kernel (PCANet-CK), for the classification of three-dimensional (3-D) retinal optical coherence tomography (OCT) images. Specifically, the proposed PCANet-CK method first utilizes the PCANet to automatically learn features from each B-scan of the 3-D retinal OCT images. Then, multiple kernels are separately applied to a set of very important features of the B-scans and these kernels are fused together, which can jointly exploit the correlations among features of the 3-D OCT images. Finally, the fused (composite) kernel is incorporated into an extreme learning machine for the OCT image classification. We tested our proposed algorithm on two real 3-D spectral domain OCT (SD-OCT) datasets (of normal subjects and subjects with the macular edema and age-related macular degeneration), which demonstrated its effectiveness. (2017) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE).

Similarity measures for scientific workflows

OpenAIRE

Starlinger, Johannes

2016-01-01

In Laufe der letzten zehn Jahre haben Scientific Workflows als Werkzeug zur Erstellung von reproduzierbaren, datenverarbeitenden in-silico Experimenten an Aufmerksamkeit gewonnen, in die sowohl lokale Skripte und Anwendungen, als auch Web-Services eingebunden werden können. Über spezialisierte Online-Bibliotheken, sogenannte Repositories, können solche Workflows veröffentlicht und wiederverwendet werden. Mit zunehmender Größe dieser Repositories werden Ähnlichkeitsmaße für Scientific Workfl...

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.

Comparison of Resource Platform Selection Approaches for Scientific Workflows

Energy Technology Data Exchange (ETDEWEB)

Simmhan, Yogesh; Ramakrishnan, Lavanya

2010-03-05

Cloud computing is increasingly considered as an additional computational resource platform for scientific workflows. The cloud offers opportunity to scale-out applications from desktops and local cluster resources. At the same time, it can eliminate the challenges of restricted software environments and queue delays in shared high performance computing environments. Choosing from these diverse resource platforms for a workflow execution poses a challenge for many scientists. Scientists are often faced with deciding resource platform selection trade-offs with limited information on the actual workflows. While many workflow planning methods have explored task scheduling onto different resources, these methods often require fine-scale characterization of the workflow that is onerous for a scientist. In this position paper, we describe our early exploratory work into using blackbox characteristics to do a cost-benefit analysis across of using cloud platforms. We use only very limited high-level information on the workflow length, width, and data sizes. The length and width are indicative of the workflow duration and parallelism. The data size characterizes the IO requirements. We compare the effectiveness of this approach to other resource selection models using two exemplar scientific workflows scheduled on desktops, local clusters, HPC centers, and clouds. Early results suggest that the blackbox model often makes the same resource selections as a more fine-grained whitebox model. We believe the simplicity of the blackbox model can help inform a scientist on the applicability of cloud computing resources even before porting an existing workflow.

SU-E-J-15: Automatically Detect Patient Treatment Position and Orientation in KV Portal Images

International Nuclear Information System (INIS)

Qiu, J; Yang, D

2015-01-01

Purpose: In the course of radiation therapy, the complex information processing workflow will Result in potential errors, such as incorrect or inaccurate patient setups. With automatic image check and patient identification, such errors could be effectively reduced. For this purpose, we developed a simple and rapid image processing method, to automatically detect the patient position and orientation in 2D portal images, so to allow automatic check of positions and orientations for patient daily RT treatments. Methods: Based on the principle of portal image formation, a set of whole body DRR images were reconstructed from multiple whole body CT volume datasets, and fused together to be used as the matching template. To identify the patient setup position and orientation shown in a 2D portal image, the 2D portal image was preprocessed (contrast enhancement, down-sampling and couch table detection), then matched to the template image so to identify the laterality (left or right), position, orientation and treatment site. Results: Five day’s clinical qualified portal images were gathered randomly, then were processed by the automatic detection and matching method without any additional information. The detection results were visually checked by physicists. 182 images were correct detection in a total of 200kV portal images. The correct rate was 91%. Conclusion: The proposed method can detect patient setup and orientation quickly and automatically. It only requires the image intensity information in KV portal images. This method can be useful in the framework of Electronic Chart Check (ECCK) to reduce the potential errors in workflow of radiation therapy and so to improve patient safety. In addition, the auto-detection results, as the patient treatment site position and patient orientation, could be useful to guide the sequential image processing procedures, e.g. verification of patient daily setup accuracy. This work was partially supported by research grant from

SU-E-J-15: Automatically Detect Patient Treatment Position and Orientation in KV Portal Images

Energy Technology Data Exchange (ETDEWEB)

Qiu, J [Washington University in St Louis, Taian, Shandong (China); Yang, D [Washington University School of Medicine, St Louis, MO (United States)

2015-06-15

Purpose: In the course of radiation therapy, the complex information processing workflow will Result in potential errors, such as incorrect or inaccurate patient setups. With automatic image check and patient identification, such errors could be effectively reduced. For this purpose, we developed a simple and rapid image processing method, to automatically detect the patient position and orientation in 2D portal images, so to allow automatic check of positions and orientations for patient daily RT treatments. Methods: Based on the principle of portal image formation, a set of whole body DRR images were reconstructed from multiple whole body CT volume datasets, and fused together to be used as the matching template. To identify the patient setup position and orientation shown in a 2D portal image, the 2D portal image was preprocessed (contrast enhancement, down-sampling and couch table detection), then matched to the template image so to identify the laterality (left or right), position, orientation and treatment site. Results: Five day’s clinical qualified portal images were gathered randomly, then were processed by the automatic detection and matching method without any additional information. The detection results were visually checked by physicists. 182 images were correct detection in a total of 200kV portal images. The correct rate was 91%. Conclusion: The proposed method can detect patient setup and orientation quickly and automatically. It only requires the image intensity information in KV portal images. This method can be useful in the framework of Electronic Chart Check (ECCK) to reduce the potential errors in workflow of radiation therapy and so to improve patient safety. In addition, the auto-detection results, as the patient treatment site position and patient orientation, could be useful to guide the sequential image processing procedures, e.g. verification of patient daily setup accuracy. This work was partially supported by research grant from

LabelFlow Framework for Annotating Workflow Provenance

Directory of Open Access Journals (Sweden)

Pinar Alper

2018-02-01

Full Text Available Scientists routinely analyse and share data for others to use. Successful data (reuse relies on having metadata describing the context of analysis of data. In many disciplines the creation of contextual metadata is referred to as reporting. One method of implementing analyses is with workflows. A stand-out feature of workflows is their ability to record provenance from executions. Provenance is useful when analyses are executed with changing parameters (changing contexts and results need to be traced to respective parameters. In this paper we investigate whether provenance can be exploited to support reporting. Specifically; we outline a case-study based on a real-world workflow and set of reporting queries. We observe that provenance, as collected from workflow executions, is of limited use for reporting, as it supports queries partially. We identify that this is due to the generic nature of provenance, its lack of domain-specific contextual metadata. We observe that the required information is available in implicit form, embedded in data. We describe LabelFlow, a framework comprised of four Labelling Operators for decorating provenance with domain-specific Labels. LabelFlow can be instantiated for a domain by plugging it with domain-specific metadata extractors. We provide a tool that takes as input a workflow, and produces as output a Labelling Pipeline for that workflow, comprised of Labelling Operators. We revisit the case-study and show how Labels provide a more complete implementation of reporting queries.

Provenance-based refresh in data-oriented workflows

KAUST Repository

Ikeda, Robert; Salihoglu, Semih; Widom, Jennifer

2011-01-01

We consider a general workflow setting in which input data sets are processed by a graph of transformations to produce output results. Our goal is to perform efficient selective refresh of elements in the output data, i.e., compute the latest values of specific output elements when the input data may have changed. We explore how data provenance can be used to enable efficient refresh. Our approach is based on capturing one-level data provenance at each transformation when the workflow is run initially. Then at refresh time provenance is used to determine (transitively) which input elements are responsible for given output elements, and the workflow is rerun only on that portion of the data needed for refresh. Our contributions are to formalize the problem setting and the problem itself, to specify properties of transformations and provenance that are required for efficient refresh, and to provide algorithms that apply to a wide class of transformations and workflows. We have built a prototype system supporting the features and algorithms presented in the paper. We report preliminary experimental results on the overhead of provenance capture, and on the crossover point between selective refresh and full workflow recomputation. © 2011 ACM.

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.

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.

WS-VLAM: A GT4 based workflow management system

NARCIS (Netherlands)

Wibisono, A.; Vasyunin, D.; Korkhov, V.; Zhao, Z.; Belloum, A.; de Laat, C.; Adriaans, P.; Hertzberger, B.

2007-01-01

Generic Grid middleware, e.g., Globus Toolkit 4 (GT4), provides basic services for scientific workflow management systems to discover, store and integrate workflow components. Using the state of the art Grid services can advance the functionality of workflow engine in orchestrating distributed Grid

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.

Multi-level meta-workflows: new concept for regularly occurring tasks in quantum chemistry.

Science.gov (United States)

Arshad, Junaid; Hoffmann, Alexander; Gesing, Sandra; Grunzke, Richard; Krüger, Jens; Kiss, Tamas; Herres-Pawlis, Sonja; Terstyanszky, Gabor

2016-01-01

In Quantum Chemistry, many tasks are reoccurring frequently, e.g. geometry optimizations, benchmarking series etc. Here, workflows can help to reduce the time of manual job definition and output extraction. These workflows are executed on computing infrastructures and may require large computing and data resources. Scientific workflows hide these infrastructures and the resources needed to run them. It requires significant efforts and specific expertise to design, implement and test these workflows. Many of these workflows are complex and monolithic entities that can be used for particular scientific experiments. Hence, their modification is not straightforward and it makes almost impossible to share them. To address these issues we propose developing atomic workflows and embedding them in meta-workflows. Atomic workflows deliver a well-defined research domain specific function. Publishing workflows in repositories enables workflow sharing inside and/or among scientific communities. We formally specify atomic and meta-workflows in order to define data structures to be used in repositories for uploading and sharing them. Additionally, we present a formal description focused at orchestration of atomic workflows into meta-workflows. We investigated the operations that represent basic functionalities in Quantum Chemistry, developed the relevant atomic workflows and combined them into meta-workflows. Having these workflows we defined the structure of the Quantum Chemistry workflow library and uploaded these workflows in the SHIWA Workflow Repository.Graphical AbstractMeta-workflows and embedded workflows in the template representation.

Business and scientific workflows a web service-oriented approach

CERN Document Server

Tan, Wei

2013-01-01

Focuses on how to use web service computing and service-based workflow technologies to develop timely, effective workflows for both business and scientific fields Utilizing web computing and Service-Oriented Architecture (SOA), Business and Scientific Workflows: A Web Service-Oriented Approach focuses on how to design, analyze, and deploy web service-based workflows for both business and scientific applications in many areas of healthcare and biomedicine. It also discusses and presents the recent research and development results. This informative reference features app

Improved workflow modelling using role activity diagram-based modelling with application to a radiology service case study.

Science.gov (United States)

Shukla, Nagesh; Keast, John E; Ceglarek, Darek

2014-10-01

The modelling of complex workflows is an important problem-solving technique within healthcare settings. However, currently most of the workflow models use a simplified flow chart of patient flow obtained using on-site observations, group-based debates and brainstorming sessions, together with historic patient data. This paper presents a systematic and semi-automatic methodology for knowledge acquisition with detailed process representation using sequential interviews of people in the key roles involved in the service delivery process. The proposed methodology allows the modelling of roles, interactions, actions, and decisions involved in the service delivery process. This approach is based on protocol generation and analysis techniques such as: (i) initial protocol generation based on qualitative interviews of radiology staff, (ii) extraction of key features of the service delivery process, (iii) discovering the relationships among the key features extracted, and, (iv) a graphical representation of the final structured model of the service delivery process. The methodology is demonstrated through a case study of a magnetic resonance (MR) scanning service-delivery process in the radiology department of a large hospital. A set of guidelines is also presented in this paper to visually analyze the resulting process model for identifying process vulnerabilities. A comparative analysis of different workflow models is also conducted. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

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...

Federated Database Services for Wind Tunnel Experiment Workflows

Directory of Open Access Journals (Sweden)

A. Paventhan

2006-01-01

Full Text Available Enabling the full life cycle of scientific and engineering workflows requires robust middleware and services that support effective data management, near-realtime data movement and custom data processing. Many existing solutions exploit the database as a passive metadata catalog. In this paper, we present an approach that makes use of federation of databases to host data-centric wind tunnel application workflows. The user is able to compose customized application workflows based on database services. We provide a reference implementation that leverages typical business tools and technologies: Microsoft SQL Server for database services and Windows Workflow Foundation for workflow services. The application data and user's code are both hosted in federated databases. With the growing interest in XML Web Services in scientific Grids, and with databases beginning to support native XML types and XML Web services, we can expect the role of databases in scientific computation to grow in importance.

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

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

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...

Workflow-centred evaluation of an automatic lesion tracking software for chemotherapy monitoring by CT

Energy Technology Data Exchange (ETDEWEB)

Moltz, Jan Hendrik; Peitgen, Heinz-Otto [Fraunhofer MEVIS - Institute for Medical Image Computing, Bremen (Germany); D' Anastasi, Melvin [University Hospital Munich-Grosshadern, Department of Clinical Radiology, Muenchen (Germany); Kiessling, Andreas [University Hospital Giessen and Marburg, Department of Diagnostic Radiology, Marburg (Germany); Pinto dos Santos, Daniel [University Hospital Mainz, Department of Diagnostic and Interventional Radiology, Mainz (Germany); Schuelke, Christoph [University Hospital Muenster, Institute of Clinical Radiology, Muenster (Germany)

2012-12-15

In chemotherapy monitoring, an estimation of the change in tumour size is an important criterion for the assessment of treatment success. This requires a comparison between corresponding lesions in the baseline and follow-up computed tomography (CT) examinations. We evaluate the clinical benefits of an automatic lesion tracking tool that identifies the target lesions in the follow-up CT study and pre-computes the lesion volumes. Four radiologists performed volumetric follow-up examinations for 52 patients with and without lesion tracking. In total, 139 lung nodules, liver metastases and lymph nodes were given as target lesions. We measured reading time, inter-reader variability in lesion identification and volume measurements, and the amount of manual adjustments of the segmentation results. With lesion tracking, target lesion assessment time decreased by 38 % or 22 s per lesion. Relative volume difference between readers was reduced from 0.171 to 0.1. Segmentation quality was comparable with and without lesion tracking. Our automatic lesion tracking tool can make interpretation of follow-up CT examinations quicker and provide results that are less reader-dependent. (orig.)

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

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

Workflows for microarray data processing in the Kepler environment.

Science.gov (United States)

Stropp, Thomas; McPhillips, Timothy; Ludäscher, Bertram; Bieda, Mark

2012-05-17

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. 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 R

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

Building and documenting workflows with python-based snakemake

OpenAIRE

Köster, Johannes; Rahmann, Sven

2012-01-01

textabstractSnakemake is a novel workflow engine with a simple Python-derived workflow definition language and an optimizing execution environment. It is the first system that supports multiple named wildcards (or variables) in input and output filenames of each rule definition. It also allows to write human-readable workflows that document themselves. We have found Snakemake especially useful for building high-throughput sequencing data analysis pipelines and present examples from this area....

AUTOMATIC TEXTURE MAPPING OF ARCHITECTURAL AND ARCHAEOLOGICAL 3D MODELS

Directory of Open Access Journals (Sweden)

T. P. Kersten

2012-07-01

Full Text Available Today, detailed, complete and exact 3D models with photo-realistic textures are increasingly demanded for numerous applications in architecture and archaeology. Manual texture mapping of 3D models by digital photographs with software packages, such as Maxon Cinema 4D, Autodesk 3Ds Max or Maya, still requires a complex and time-consuming workflow. So, procedures for automatic texture mapping of 3D models are in demand. In this paper two automatic procedures are presented. The first procedure generates 3D surface models with textures by web services, while the second procedure textures already existing 3D models with the software tmapper. The program tmapper is based on the Multi Layer 3D image (ML3DImage algorithm and developed in the programming language C++. The studies showing that the visibility analysis using the ML3DImage algorithm is not sufficient to obtain acceptable results of automatic texture mapping. To overcome the visibility problem the Point Cloud Painter algorithm in combination with the Z-buffer-procedure will be applied in the future.

Automatic Texture Mapping of Architectural and Archaeological 3d Models

Science.gov (United States)

Kersten, T. P.; Stallmann, D.

2012-07-01

Today, detailed, complete and exact 3D models with photo-realistic textures are increasingly demanded for numerous applications in architecture and archaeology. Manual texture mapping of 3D models by digital photographs with software packages, such as Maxon Cinema 4D, Autodesk 3Ds Max or Maya, still requires a complex and time-consuming workflow. So, procedures for automatic texture mapping of 3D models are in demand. In this paper two automatic procedures are presented. The first procedure generates 3D surface models with textures by web services, while the second procedure textures already existing 3D models with the software tmapper. The program tmapper is based on the Multi Layer 3D image (ML3DImage) algorithm and developed in the programming language C++. The studies showing that the visibility analysis using the ML3DImage algorithm is not sufficient to obtain acceptable results of automatic texture mapping. To overcome the visibility problem the Point Cloud Painter algorithm in combination with the Z-buffer-procedure will be applied in the future.

Concurrency & Asynchrony in Declarative Workflows

DEFF Research Database (Denmark)

Debois, Søren; Hildebrandt, Thomas; Slaats, Tijs

2015-01-01

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....... In this paper, we pro- pose a notion of concurrency for declarative process models, formulated in the context of Dynamic Condition Response (DCR) graphs, and exploiting the so-called “true concurrency” semantics of Labelled Asynchronous Transition Systems. We demonstrate how this semantic underpinning...

Service-oriented workflow to efficiently and automatically fulfill products in a highly individualized web and mobile environment

Science.gov (United States)

Qiao, Mu

2015-03-01

Service Oriented Architecture1 (SOA) is widely used in building flexible and scalable web sites and services. In most of the web or mobile photo book and gifting business space, the products ordered are highly variable without a standard template that one can substitute texts or images from similar to that of commercial variable data printing. In this paper, the author describes a SOA workflow in a multi-sites, multi-product lines fulfillment system where three major challenges are addressed: utilization of hardware and equipment, highly automation with fault recovery, and highly scalable and flexible with order volume fluctuation.

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.

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...

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

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

On the Support of Scientific Workflows over Pub/Sub Brokers

Directory of Open Access Journals (Sweden)

Edwin Cedeño

2013-08-01

Full Text Available The execution of scientific workflows is gaining importance as more computing resources are available in the form of grid environments. The Publish/Subscribe paradigm offers well-proven solutions for sustaining distributed scenarios while maintaining the high level of task decoupling required by scientific workflows. In this paper, we propose a new model for supporting scientific workflows that improves the dissemination of control events. The proposed solution is based on the mapping of workflow tasks to the underlying Pub/Sub event layer, and the definition of interfaces and procedures for execution on brokers. In this paper we also analyze the strengths and weaknesses of current solutions that are based on existing message exchange models for scientific workflows. Finally, we explain how our model improves the information dissemination, event filtering, task decoupling and the monitoring of scientific workflows.

On the support of scientific workflows over Pub/Sub brokers.

Science.gov (United States)

Morales, Augusto; Robles, Tomas; Alcarria, Ramon; Cedeño, Edwin

2013-08-20

The execution of scientific workflows is gaining importance as more computing resources are available in the form of grid environments. The Publish/Subscribe paradigm offers well-proven solutions for sustaining distributed scenarios while maintaining the high level of task decoupling required by scientific workflows. In this paper, we propose a new model for supporting scientific workflows that improves the dissemination of control events. The proposed solution is based on the mapping of workflow tasks to the underlying Pub/Sub event layer, and the definition of interfaces and procedures for execution on brokers. In this paper we also analyze the strengths and weaknesses of current solutions that are based on existing message exchange models for scientific workflows. Finally, we explain how our model improves the information dissemination, event filtering, task decoupling and the monitoring of scientific workflows.

Petri Net-Based R&D Process Modeling and Optimization for Composite Materials

Directory of Open Access Journals (Sweden)

Xiaomei Hu

2013-01-01

Full Text Available Considering the current R&D process for new composite materials involves some complex details, such as formula design, specimen/sample production, materials/sample test, assessment, materials/sample feedback from customers, and mass production, the workflow model of Petri net-based R&D process for new composite materials’ is proposed. By analyzing the time property of the whole Petri net, the optimized model for new composite materials R&D workflow is further proposed. By analyzing the experiment data and application in some materials R&D enterprise, it is demonstrated that the workflow optimization model shortens the period of R&D on new materials for 15%, definitely improving the R&D efficiency. This indicates the feasibility and availability of the model.

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....

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.

Workflow as a Service in the Cloud: Architecture and Scheduling Algorithms

Science.gov (United States)

Wang, Jianwu; Korambath, Prakashan; Altintas, Ilkay; Davis, Jim; Crawl, Daniel

2017-01-01

With more and more workflow systems adopting cloud as their execution environment, it becomes increasingly challenging on how to efficiently manage various workflows, virtual machines (VMs) and workflow execution on VM instances. To make the system scalable and easy-to-extend, we design a Workflow as a Service (WFaaS) architecture with independent services. A core part of the architecture is how to efficiently respond continuous workflow requests from users and schedule their executions in the cloud. Based on different targets, we propose four heuristic workflow scheduling algorithms for the WFaaS architecture, and analyze the differences and best usages of the algorithms in terms of performance, cost and the price/performance ratio via experimental studies. PMID:29399237

Workflow as a Service in the Cloud: Architecture and Scheduling Algorithms.

Science.gov (United States)

Wang, Jianwu; Korambath, Prakashan; Altintas, Ilkay; Davis, Jim; Crawl, Daniel

2014-01-01

With more and more workflow systems adopting cloud as their execution environment, it becomes increasingly challenging on how to efficiently manage various workflows, virtual machines (VMs) and workflow execution on VM instances. To make the system scalable and easy-to-extend, we design a Workflow as a Service (WFaaS) architecture with independent services. A core part of the architecture is how to efficiently respond continuous workflow requests from users and schedule their executions in the cloud. Based on different targets, we propose four heuristic workflow scheduling algorithms for the WFaaS architecture, and analyze the differences and best usages of the algorithms in terms of performance, cost and the price/performance ratio via experimental studies.

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.

The myth of standardized workflow in primary care.

Science.gov (United States)

Holman, G Talley; Beasley, John W; Karsh, Ben-Tzion; Stone, Jamie A; Smith, Paul D; Wetterneck, Tosha B

2016-01-01

Primary care efficiency and quality are essential for the nation's health. The demands on primary care physicians (PCPs) are increasing as healthcare becomes more complex. A more complete understanding of PCP workflow variation is needed to guide future healthcare redesigns. This analysis evaluates workflow variation in terms of the sequence of tasks performed during patient visits. Two patient visits from 10 PCPs from 10 different United States Midwestern primary care clinics were analyzed to determine physician workflow. Tasks and the progressive sequence of those tasks were observed, documented, and coded by task category using a PCP task list. Variations in the sequence and prevalence of tasks at each stage of the primary care visit were assessed considering the physician, the patient, the visit's progression, and the presence of an electronic health record (EHR) at the clinic. PCP workflow during patient visits varies significantly, even for an individual physician, with no single or even common workflow pattern being present. The prevalence of specific tasks shifts significantly as primary care visits progress to their conclusion but, notably, PCPs collect patient information throughout the visit. PCP workflows were unpredictable during face-to-face patient visits. Workflow emerges as the result of a "dance" between physician and patient as their separate agendas are addressed, a side effect of patient-centered practice. Future healthcare redesigns should support a wide variety of task sequences to deliver high-quality primary care. The development of tools such as electronic health records must be based on the realities of primary care visits if they are to successfully support a PCP's mental and physical work, resulting in effective, safe, and efficient primary care. © The Author 2015. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

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.

Scientific workflows as productivity tools for drug discovery.

Science.gov (United States)

Shon, John; Ohkawa, Hitomi; Hammer, Juergen

2008-05-01

Large pharmaceutical companies annually invest tens to hundreds of millions of US dollars in research informatics to support their early drug discovery processes. Traditionally, most of these investments are designed to increase the efficiency of drug discovery. The introduction of do-it-yourself scientific workflow platforms has enabled research informatics organizations to shift their efforts toward scientific innovation, ultimately resulting in a possible increase in return on their investments. Unlike the handling of most scientific data and application integration approaches, researchers apply scientific workflows to in silico experimentation and exploration, leading to scientific discoveries that lie beyond automation and integration. This review highlights some key requirements for scientific workflow environments in the pharmaceutical industry that are necessary for increasing research productivity. Examples of the application of scientific workflows in research and a summary of recent platform advances are also provided.

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.

A three-level atomicity model for decentralized workflow management systems

Science.gov (United States)

Ben-Shaul, Israel Z.; Heineman, George T.

1996-12-01

A workflow management system (WFMS) employs a workflow manager (WM) to execute and automate the various activities within a workflow. To protect the consistency of data, the WM encapsulates each activity with a transaction; a transaction manager (TM) then guarantees the atomicity of activities. Since workflows often group several activities together, the TM is responsible for guaranteeing the atomicity of these units. There are scalability issues, however, with centralized WFMSs. Decentralized WFMSs provide an architecture for multiple autonomous WFMSs to interoperate, thus accommodating multiple workflows and geographically-dispersed teams. When atomic units are composed of activities spread across multiple WFMSs, however, there is a conflict between global atomicity and local autonomy of each WFMS. This paper describes a decentralized atomicity model that enables workflow administrators to specify the scope of multi-site atomicity based upon the desired semantics of multi-site tasks in the decentralized WFMS. We describe an architecture that realizes our model and execution paradigm.

What is needed for effective open access workflows?

CERN Multimedia

CERN. Geneva

2017-01-01

Institutions and funders are pushing forward open access with ever new guidelines and policies. Since institutional repositories are important maintainers of green open access, they should support easy and fast workflows for researchers and libraries to release publications. Based on the requirements specification of researchers, libraries and publishers, possible supporting software extensions are discussed. How does a typical workflow look like? What has to be considered by the researchers and by the editors in the library before releasing a green open access publication? Where and how can software support and improve existing workflows?

Text-mining-assisted biocuration workflows in Argo

Science.gov (United States)

Rak, Rafal; Batista-Navarro, Riza Theresa; Rowley, Andrew; Carter, Jacob; Ananiadou, Sophia

2014-01-01

Biocuration activities have been broadly categorized into the selection of relevant documents, the annotation of biological concepts of interest and identification of interactions between the concepts. Text mining has been shown to have a potential to significantly reduce the effort of biocurators in all the three activities, and various semi-automatic methodologies have been integrated into curation pipelines to support them. We investigate the suitability of Argo, a workbench for building text-mining solutions with the use of a rich graphical user interface, for the process of biocuration. Central to Argo are customizable workflows that users compose by arranging available elementary analytics to form task-specific processing units. A built-in manual annotation editor is the single most used biocuration tool of the workbench, as it allows users to create annotations directly in text, as well as modify or delete annotations created by automatic processing components. Apart from syntactic and semantic analytics, the ever-growing library of components includes several data readers and consumers that support well-established as well as emerging data interchange formats such as XMI, RDF and BioC, which facilitate the interoperability of Argo with other platforms or resources. To validate the suitability of Argo for curation activities, we participated in the BioCreative IV challenge whose purpose was to evaluate Web-based systems addressing user-defined biocuration tasks. Argo proved to have the edge over other systems in terms of flexibility of defining biocuration tasks. As expected, the versatility of the workbench inevitably lengthened the time the curators spent on learning the system before taking on the task, which may have affected the usability of Argo. The participation in the challenge gave us an opportunity to gather valuable feedback and identify areas of improvement, some of which have already been introduced. Database URL: http://argo.nactem.ac.uk PMID

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

First performance evaluation of software for automatic segmentation, labeling and reformation of anatomical aligned axial images of the thoracolumbar spine at CT

Energy Technology Data Exchange (ETDEWEB)

Scholtz, Jan-Erik, E-mail: janerikscholtz@gmail.com; Wichmann, Julian L.; Kaup, Moritz; Fischer, Sebastian; Kerl, J. Matthias; Lehnert, Thomas; Vogl, Thomas J.; Bauer, Ralf W.

2015-03-15

Highlights: •Automatic segmentation and labeling of the thoracolumbar spine. •Automatically generated double-angulated and aligned axial images of spine segments. •High grade of accurateness for the symmetric depiction of anatomical structures. •Time-saving and may improve workflow in daily practice. -- Abstract: Objectives: To evaluate software for automatic segmentation, labeling and reformation of anatomical aligned axial images of the thoracolumbar spine on CT in terms of accuracy, potential for time savings and workflow improvement. Material and methods: 77 patients (28 women, 49 men, mean age 65.3 ± 14.4 years) with known or suspected spinal disorders (degenerative spine disease n = 32; disc herniation n = 36; traumatic vertebral fractures n = 9) underwent 64-slice MDCT with thin-slab reconstruction. Time for automatic labeling of the thoracolumbar spine and reconstruction of double-angulated axial images of the pathological vertebrae was compared with manually performed reconstruction of anatomical aligned axial images. Reformatted images of both reconstruction methods were assessed by two observers regarding accuracy of symmetric depiction of anatomical structures. Results: In 33 cases double-angulated axial images were created in 1 vertebra, in 28 cases in 2 vertebrae and in 16 cases in 3 vertebrae. Correct automatic labeling was achieved in 72 of 77 patients (93.5%). Errors could be manually corrected in 4 cases. Automatic labeling required 1 min in average. In cases where anatomical aligned axial images of 1 vertebra were created, reconstructions made by hand were significantly faster (p < 0.05). Automatic reconstruction was time-saving in cases of 2 and more vertebrae (p < 0.05). Both reconstruction methods revealed good image quality with excellent inter-observer agreement. Conclusion: The evaluated software for automatic labeling and anatomically aligned, double-angulated axial image reconstruction of the thoracolumbar spine on CT is time

VLAM-G: Interactive Data Driven Workflow Engine for Grid-Enabled Resources

Directory of Open Access Journals (Sweden)

Vladimir Korkhov

2007-01-01

Full Text Available Grid brings the power of many computers to scientists. However, the development of Grid-enabled applications requires knowledge about Grid infrastructure and low-level API to Grid services. In turn, workflow management systems provide a high-level environment for rapid prototyping of experimental computing systems. Coupling Grid and workflow paradigms is important for the scientific community: it makes the power of the Grid easily available to the end user. The paradigm of data driven workflow execution is one of the ways to enable distributed workflow on the Grid. The work presented in this paper is carried out in the context of the Virtual Laboratory for e-Science project. We present the VLAM-G workflow management system and its core component: the Run-Time System (RTS. The RTS is a dataflow driven workflow engine which utilizes Grid resources, hiding the complexity of the Grid from a scientist. Special attention is paid to the concept of dataflow and direct data streaming between distributed workflow components. We present the architecture and components of the RTS, describe the features of VLAM-G workflow execution, and evaluate the system by performance measurements and a real life use case.

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.

Reasoning about repairability of workflows at design time

NARCIS (Netherlands)

Tagni, Gaston; Ten Teije, Annette; Van Harmelen, Frank

2009-01-01

This paper describes an approach for reasoning about the repairability of workflows at design time. We propose a heuristic-based analysis of a workflow that aims at evaluating its definition, considering different design aspects and characteristics that affect its repairability (called repairability

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

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.

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.

Building and documenting workflows with python-based snakemake

NARCIS (Netherlands)

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

2012-01-01

textabstractSnakemake is a novel workflow engine with a simple Python-derived workflow definition language and an optimizing execution environment. It is the first system that supports multiple named wildcards (or variables) in input and output filenames of each rule definition. It also allows to

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.

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.

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.

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.

Text mining meets workflow: linking U-Compare with Taverna

Science.gov (United States)

Kano, Yoshinobu; Dobson, Paul; Nakanishi, Mio; Tsujii, Jun'ichi; Ananiadou, Sophia

2010-01-01

Summary: Text mining from the biomedical literature is of increasing importance, yet it is not easy for the bioinformatics community to create and run text mining workflows due to the lack of accessibility and interoperability of the text mining resources. The U-Compare system provides a wide range of bio text mining resources in a highly interoperable workflow environment where workflows can very easily be created, executed, evaluated and visualized without coding. We have linked U-Compare to Taverna, a generic workflow system, to expose text mining functionality to the bioinformatics community. Availability: http://u-compare.org/taverna.html, http://u-compare.org Contact: kano@is.s.u-tokyo.ac.jp Supplementary information: Supplementary data are available at Bioinformatics online. PMID:20709690

Distributed execution of aggregated multi domain workflows using an agent framework

NARCIS (Netherlands)

Zhao, Z.; Belloum, A.; de Laat, C.; Adriaans, P.; Hertzberger, B.; Zhang, L.J.; Watson, T.J.; Yang, J.; Hung, P.C.K.

2007-01-01

In e-Science, meaningful experiment processes and workflow engines emerge as important scientific resources. A complex experiment often involves services and processes developed in different scientific domains. Aggregating different workflows into one meta workflow avoids unnecessary rewriting of

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

Automatic Detection and Positioning of Ground Control Points Using TerraSAR-X Multiaspect Acquisitions

Science.gov (United States)

Montazeri, Sina; Gisinger, Christoph; Eineder, Michael; Zhu, Xiao xiang

2018-05-01

Geodetic stereo Synthetic Aperture Radar (SAR) is capable of absolute three-dimensional localization of natural Persistent Scatterer (PS)s which allows for Ground Control Point (GCP) generation using only SAR data. The prerequisite for the method to achieve high precision results is the correct detection of common scatterers in SAR images acquired from different viewing geometries. In this contribution, we describe three strategies for automatic detection of identical targets in SAR images of urban areas taken from different orbit tracks. Moreover, a complete work-flow for automatic generation of large number of GCPs using SAR data is presented and its applicability is shown by exploiting TerraSAR-X (TS-X) high resolution spotlight images over the city of Oulu, Finland and a test site in Berlin, Germany.

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%.

The P2P approach to interorganizational workflows

NARCIS (Netherlands)

Aalst, van der W.M.P.; Weske, M.H.; Dittrich, K.R.; Geppert, A.; Norrie, M.C.

2001-01-01

This paper describes in an informal way the Public-To-Private (P2P) approach to interorganizational workflows, which is based on a notion of inheritance. The approach consists of three steps: (1) create a common understanding of the interorganizational workflow by specifying a shared public

Open source workflow : a viable direction for BPM?

NARCIS (Netherlands)

Wohed, P.; Russell, N.C.; Hofstede, ter A.H.M.; Andersson, B.; Aalst, van der W.M.P.; Bellahsène, Z.; Léonard, M.

2008-01-01

With the growing interest in open source software in general and business process management and workflow systems in particular, it is worthwhile investigating the state of open source workflow management. The plethora of these offerings (recent surveys such as [4,6], each contain more than 30 such

Privacy-aware workflow management

NARCIS (Netherlands)

Alhaqbani, B.; Adams, M.; Fidge, C.J.; Hofstede, ter A.H.M.; Glykas, M.

2013-01-01

Information security policies play an important role in achieving information security. Confidentiality, Integrity, and Availability are classic information security goals attained by enforcing appropriate security policies. Workflow Management Systems (WfMSs) also benefit from inclusion of these

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...

The BEL information extraction workflow (BELIEF): evaluation in the BioCreative V BEL and IAT track.

Science.gov (United States)

Madan, Sumit; Hodapp, Sven; Senger, Philipp; Ansari, Sam; Szostak, Justyna; Hoeng, Julia; Peitsch, Manuel; Fluck, Juliane

2016-01-01

Network-based approaches have become extremely important in systems biology to achieve a better understanding of biological mechanisms. For network representation, the Biological Expression Language (BEL) is well designed to collate findings from the scientific literature into biological network models. To facilitate encoding and biocuration of such findings in BEL, a BEL Information Extraction Workflow (BELIEF) was developed. BELIEF provides a web-based curation interface, the BELIEF Dashboard, that incorporates text mining techniques to support the biocurator in the generation of BEL networks. The underlying UIMA-based text mining pipeline (BELIEF Pipeline) uses several named entity recognition processes and relationship extraction methods to detect concepts and BEL relationships in literature. The BELIEF Dashboard allows easy curation of the automatically generated BEL statements and their context annotations. Resulting BEL statements and their context annotations can be syntactically and semantically verified to ensure consistency in the BEL network. In summary, the workflow supports experts in different stages of systems biology network building. Based on the BioCreative V BEL track evaluation, we show that the BELIEF Pipeline automatically extracts relationships with an F-score of 36.4% and fully correct statements can be obtained with an F-score of 30.8%. Participation in the BioCreative V Interactive task (IAT) track with BELIEF revealed a systems usability scale (SUS) of 67. Considering the complexity of the task for new users-learning BEL, working with a completely new interface, and performing complex curation-a score so close to the overall SUS average highlights the usability of BELIEF.Database URL: BELIEF is available at http://www.scaiview.com/belief/. © The Author(s) 2016. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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

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.

AUTOMATIC AND GENERIC MOSAICING OF MULTISENSOR IMAGES: AN APPLICATION TO PLEIADES HR

Directory of Open Access Journals (Sweden)

F. Bignalet-Cazalet

2012-07-01

Full Text Available In the early phase of the Pleiades program, the CNES (the French Space Agency specified and developed a fully automatic mosaicing processing unit, in order to generate satellite image mosaics under operational conditions. This tool can automatically put each input image in a common geometry, homogenize the radiometry, and generate orthomosaics using stitching lines. As the image quality commissioning phase of Pleiades1A is on-going, this mosaicing process is being tested for the first time under operational conditions. The French newly launched high resolution satellite can acquire adjacent images for French Civil and Defense User Ground Segments. This paper presents the very firsts results of mosaicing Pleiades1A images. Beyond Pleiades’ use, our mosaicing tool can process a significant variety of images, including other satellites and airborne acquisitions, using automatically-taken or external ground control points, offering time-based image superposition, and more. This paper also presents the design of the mosaicing tool and describes the processing workflow and the additional capabilities and applications.

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.

Autonomic Fuselet Specification and Composition

National Research Council Canada - National Science Library

Mills, Peter H

2006-01-01

... model for its business logic, and to perform workflow composition from a goal and specifications to executable model in a manner that enables feedback mechanisms that can assess and adapt the process...

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...

Contract-Based Transaction Management in Cross-Organizational Workflow Management

NARCIS (Netherlands)

Grefen, P.W.P.J.

Cross-organizational workflow management is an essential ingredient for process integration in virtual enterprises. To obtain cross-organizational workflow processes with robust semantics, these processes should be supported by highlevel cross-organizational transaction management. In this context,

Exploring Dental Providers' Workflow in an Electronic Dental Record Environment.

Science.gov (United States)

Schwei, Kelsey M; Cooper, Ryan; Mahnke, Andrea N; Ye, Zhan; Acharya, Amit

2016-01-01

A workflow is defined as a predefined set of work steps and partial ordering of these steps in any environment to achieve the expected outcome. Few studies have investigated the workflow of providers in a dental office. It is important to understand the interaction of dental providers with the existing technologies at point of care to assess breakdown in the workflow which could contribute to better technology designs. The study objective was to assess electronic dental record (EDR) workflows using time and motion methodology in order to identify breakdowns and opportunities for process improvement. A time and motion methodology was used to study the human-computer interaction and workflow of dental providers with an EDR in four dental centers at a large healthcare organization. A data collection tool was developed to capture the workflow of dental providers and staff while they interacted with an EDR during initial, planned, and emergency patient visits, and at the front desk. Qualitative and quantitative analysis was conducted on the observational data. Breakdowns in workflow were identified while posting charges, viewing radiographs, e-prescribing, and interacting with patient scheduler. EDR interaction time was significantly different between dentists and dental assistants (6:20 min vs. 10:57 min, p = 0.013) and between dentists and dental hygienists (6:20 min vs. 9:36 min, p = 0.003). On average, a dentist spent far less time than dental assistants and dental hygienists in data recording within the EDR.

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.

Time-efficient CT colonography interpretation using an advanced image-gallery-based, computer-aided ''first-reader'' workflow for the detection of colorectal adenomas

International Nuclear Information System (INIS)

Mang, Thomas; Ringl, Helmut; Weber, Michael; Mueller-Mang, Christina; Hermosillo, Gerardo; Wolf, Matthias; Bogoni, Luca; Salganicoff, Marcos; Raykar, Vikas; Graser, Anno

2012-01-01

To assess the performance of an advanced ''first-reader'' workflow for computer-aided detection (CAD) of colorectal adenomas ≥ 6 mm at computed tomographic colonography (CTC) in a low-prevalence cohort. A total of 616 colonoscopy-validated CTC patient-datasets were retrospectively reviewed by a radiologist using a ''first-reader'' CAD workflow. CAD detections were presented as galleries of six automatically generated two-dimensional (2D) and three-dimensional (3D) images together with interactive 3D target views and 2D multiplanar views of the complete dataset. Each patient-dataset was interpreted by initially using CAD image-galleries followed by a fast 2D review to address unprompted colonic areas. Per-patient, per-polyp, and per-adenoma sensitivities were calculated for lesions ≥ 6 mm. Statistical testing employed Fisher's exact and McNemar tests. In 91/616 patients, 131 polyps (92 adenomas, 39 non-adenomas) ≥ 6 mm and two cancers were identified by reference standard. Using the CAD gallery-based first-reader workflow, the radiologist detected all adenomas ≥ 10 mm (34/34) and cancers. Per-patient and polyp sensitivities for lesions ≥ 6 mm were 84.3 % (75/89), and 83.2 % (109/131), respectively, with 89.1 % (57/64) and 85.9 % (79/92) for adenomas. Overall specificity was 95.6 % (504/527). Mean interpretation time was 3.1 min per patient. A CAD algorithm, applied in an image-gallery-based first-reader workflow, can substantially decrease reading times while enabling accurate detection of colorectal adenomas in a low-prevalence population. (orig.)

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.

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.

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

The promise of the electronic medical record (EMR) lies in its ability to reduce the costs of health care delivery and improve the overall quality of care--a promise that is realized through major changes in workflows within the health care organization. Yet little systematic information exists about the workflow effects of EMRs. Moreover, some of the research to-date points to reduced satisfaction among physicians after implementation of the EMR and increased time, i.e., negative workflow effects. A better understanding of the impact of the EMR on workflows is, hence, vital to understanding what the technology really does offer that is new and unique. (i) To empirically develop a physician centric conceptual model of the workflow effects of EMRs; (ii) To use the model to understand the antecedents to the physicians' workflow expectation from the new EMR; (iii) To track physicians' satisfaction overtime, 3 months and 20 months after implementation of the EMR; (iv) To explore the impact of technology learning curves on physicians' reported satisfaction levels. The current research uses the mixed-method technique of concept mapping to empirically develop the conceptual model of an EMR's workflow effects. The model is then used within a controlled study to track physician expectations from a new EMR system as well as their assessments of the EMR's performance 3 months and 20 months after implementation. The research tracks the actual implementation of a new EMR within the outpatient clinics of a large northeastern research hospital. The pre-implementation survey netted 20 physician responses; post-implementation Time 1 survey netted 22 responses, and Time 2 survey netted 26 physician responses. The implementation of the actual EMR served as the intervention. Since the study was conducted within the same setting and tracked a homogenous group of respondents, the overall study design ensured against extraneous influences on the results. Outcome measures were derived

A practical workflow for making anatomical atlases for biological research.

Science.gov (United States)

Wan, Yong; Lewis, A Kelsey; Colasanto, Mary; van Langeveld, Mark; Kardon, Gabrielle; Hansen, Charles

2012-01-01

The anatomical atlas has been at the intersection of science and art for centuries. These atlases are essential to biological research, but high-quality atlases are often scarce. Recent advances in imaging technology have made high-quality 3D atlases possible. However, until now there has been a lack of practical workflows using standard tools to generate atlases from images of biological samples. With certain adaptations, CG artists' workflow and tools, traditionally used in the film industry, are practical for building high-quality biological atlases. Researchers have developed a workflow for generating a 3D anatomical atlas using accessible artists' tools. They used this workflow to build a mouse limb atlas for studying the musculoskeletal system's development. This research aims to raise the awareness of using artists' tools in scientific research and promote interdisciplinary collaborations between artists and scientists. This video (http://youtu.be/g61C-nia9ms) demonstrates a workflow for creating an anatomical atlas.

Modeling, Design, and Implementation of a Cloud Workflow Engine Based on Aneka

OpenAIRE

Zhou, Jiantao; Sun, Chaoxin; Fu, Weina; Liu, Jing; Jia, Lei; Tan, Hongyan

2014-01-01

This paper presents a Petri net-based model for cloud workflow which plays a key role in industry. Three kinds of parallelisms in cloud workflow are characterized and modeled. Based on the analysis of the modeling, a cloud workflow engine is designed and implemented in Aneka cloud environment. The experimental results validate the effectiveness of our approach of modeling, design, and implementation of cloud workflow.

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 alignment was observed in the optimized 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.

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.

Workflow management: an overview

NARCIS (Netherlands)

Ouyang, C.; Adams, M.; Wynn, M.T.; Hofstede, ter A.H.M.; Brocke, vom J.; Rosemann, M.

2010-01-01

Workflow management has its origin in the office automation systems of the seventies, but it is not until fairly recently that conceptual and technological breakthroughs have led to its widespread adoption. In fact, nowadays, processawareness has become an accepted and integral part of various types

A history-tracing XML-based provenance framework for workflows

NARCIS (Netherlands)

Gerhards, M; Belloum, A.; Berretz, F.; Sander, V.; Skorupa, S.

2010-01-01

The importance of validating and reproducing the outcome of computational processes is fundamental to many application domains. Assuring the provenance of workflows will likely become even more important with respect to the incorporation of human tasks to standard workflows by emerging standards

Conceptual framework and architecture for service mediating workflow management

NARCIS (Netherlands)

Hu, Jinmin; Grefen, P.W.P.J.

2003-01-01

This paper proposes a three-layer workflow concept framework to realize workflow enactment flexibility by dynamically binding activities to their implementations at run time. A service mediating layer is added to bridge business process definition and its implementation. Based on this framework, we

Exploring Dental Providers’ Workflow in an Electronic Dental Record Environment

Science.gov (United States)

Schwei, Kelsey M; Cooper, Ryan; Mahnke, Andrea N.; Ye, Zhan

2016-01-01

Summary Background A workflow is defined as a predefined set of work steps and partial ordering of these steps in any environment to achieve the expected outcome. Few studies have investigated the workflow of providers in a dental office. It is important to understand the interaction of dental providers with the existing technologies at point of care to assess breakdown in the workflow which could contribute to better technology designs. Objective The study objective was to assess electronic dental record (EDR) workflows using time and motion methodology in order to identify breakdowns and opportunities for process improvement. Methods A time and motion methodology was used to study the human-computer interaction and workflow of dental providers with an EDR in four dental centers at a large healthcare organization. A data collection tool was developed to capture the workflow of dental providers and staff while they interacted with an EDR during initial, planned, and emergency patient visits, and at the front desk. Qualitative and quantitative analysis was conducted on the observational data. Results Breakdowns in workflow were identified while posting charges, viewing radiographs, e-prescribing, and interacting with patient scheduler. EDR interaction time was significantly different between dentists and dental assistants (6:20 min vs. 10:57 min, p = 0.013) and between dentists and dental hygienists (6:20 min vs. 9:36 min, p = 0.003). Conclusions On average, a dentist spent far less time than dental assistants and dental hygienists in data recording within the EDR. PMID:27437058

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.

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

A Model for Semi-Automatic Composition of Educational Content from Open Repositories of Learning Objects

Directory of Open Access Journals (Sweden)

Paula Andrea Rodríguez Marín

2014-04-01

Full Text Available Learning objects (LOs repositories are important in building educational content and should allow search, retrieval and composition processes to be successfully developed to reach educational goals. However, such processes require so much time-consuming and not always provide the desired results. Thus, the aim of this paper is to propose a model for the semiautomatic composition of LOs, which are automatically recovered from open repositories. For the development of model, various text similarity measures are discussed, while for calibration and validation some comparison experiments were performed using the results obtained by teachers. Experimental results show that when using a value of k (number of LOs selected of at least 3, the percentage of similarities between the model and such made by experts exceeds 75%. To conclude, it can be established that the model proposed allows teachers to save time and effort for LOs selection by performing a pre-filter process.

Workflow automation based on OSI job transfer and manipulation

NARCIS (Netherlands)

van Sinderen, Marten J.; Joosten, Stef M.M.; Guareis de farias, Cléver

1999-01-01

This paper shows that Workflow Management Systems (WFMS) and a data communication standard called Job Transfer and Manipulation (JTM) are built on the same concepts, even though different words are used. The paper analyses the correspondence of workflow concepts and JTM concepts. Besides, the

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.

Dynamic Service Selection in Workflows Using Performance Data

Directory of Open Access Journals (Sweden)

David W. Walker

2007-01-01

Full Text Available An approach to dynamic workflow management and optimisation using near-realtime performance data is presented. Strategies are discussed for choosing an optimal service (based on user-specified criteria from several semantically equivalent Web services. Such an approach may involve finding "similar" services, by first pruning the set of discovered services based on service metadata, and subsequently selecting an optimal service based on performance data. The current implementation of the prototype workflow framework is described, and demonstrated with a simple workflow. Performance results are presented that show the performance benefits of dynamic service selection. A statistical analysis based on the first order statistic is used to investigate the likely improvement in service response time arising from dynamic service selection.

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.

"Intelligent" tools for workflow process redesign : a research agenda

NARCIS (Netherlands)

Netjes, M.; Vanderfeesten, I.T.P.; Reijers, H.A.; Bussler, C.; Haller, A.

2006-01-01

Although much attention is being paid to business processes during the past decades, the design of business processes and particularly workflow processes is still more art than science. In this workshop paper, we present our view on modeling methods for workflow processes and introduce our research

When Workflow Management Systems and Logging Systems Meet: Analyzing Large-Scale Execution Traces

Energy Technology Data Exchange (ETDEWEB)

Gunter, Daniel

2008-07-31

This poster shows the benefits of integrating a workflow management system with logging and log mining capabilities. By combing two existing, mature technologies: Pegasus-WMS and Netlogger, we are able to efficiently process execution logs of earthquake science workflows consisting of hundreds of thousands to one million tasks. In particular we show results of processing logs of CyberShake, a workflow application running on the TeraGrid. Client-side tools allow scientists to quickly gather statistics about a workflow run and find out which tasks executed, where they were executed, what was their runtime, etc. These statistics can be used to understand the performance characteristics of a workflow and help tune the execution parameters of the workflow management system. This poster shows the scalability of the system presenting results of uploading task execution records into the system and by showing results of querying the system for overall workflow performance information.

ExcelAutomat: a tool for systematic processing of files as applied to quantum chemical calculations

Science.gov (United States)

Laloo, Jalal Z. A.; Laloo, Nassirah; Rhyman, Lydia; Ramasami, Ponnadurai

2017-07-01

The processing of the input and output files of quantum chemical calculations often necessitates a spreadsheet as a key component of the workflow. Spreadsheet packages with a built-in programming language editor can automate the steps involved and thus provide a direct link between processing files and the spreadsheet. This helps to reduce user-interventions as well as the need to switch between different programs to carry out each step. The ExcelAutomat tool is the implementation of this method in Microsoft Excel (MS Excel) using the default Visual Basic for Application (VBA) programming language. The code in ExcelAutomat was adapted to work with the platform-independent open-source LibreOffice Calc, which also supports VBA. ExcelAutomat provides an interface through the spreadsheet to automate repetitive tasks such as merging input files, splitting, parsing and compiling data from output files, and generation of unique filenames. Selected extracted parameters can be retrieved as variables which can be included in custom codes for a tailored approach. ExcelAutomat works with Gaussian files and is adapted for use with other computational packages including the non-commercial GAMESS. ExcelAutomat is available as a downloadable MS Excel workbook or as a LibreOffice workbook.

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...

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.

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....

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

Job life cycle management libraries for CMS workflow management projects

International Nuclear Information System (INIS)

Lingen, Frank van; Wilkinson, Rick; Evans, Dave; Foulkes, Stephen; Afaq, Anzar; Vaandering, Eric; Ryu, Seangchan

2010-01-01

Scientific analysis and simulation requires the processing and generation of millions of data samples. These tasks are often comprised of multiple smaller tasks divided over multiple (computing) sites. This paper discusses the Compact Muon Solenoid (CMS) workflow infrastructure, and specifically the Python based workflow library which is used for so called task lifecycle management. The CMS workflow infrastructure consists of three layers: high level specification of the various tasks based on input/output data sets, life cycle management of task instances derived from the high level specification and execution management. The workflow library is the result of a convergence of three CMS sub projects that respectively deal with scientific analysis, simulation and real time data aggregation from the experiment. This will reduce duplication and hence development and maintenance costs.

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...

Incorporating Workflow Interference in Facility Layout Design: The Quartic Assignment Problem

OpenAIRE

Wen-Chyuan Chiang; Panagiotis Kouvelis; Timothy L. Urban

2002-01-01

Although many authors have noted the importance of minimizing workflow interference in facility layout design, traditional layout research tends to focus on minimizing the distance-based transportation cost. This paper formalizes the concept of workflow interference from a facility layout perspective. A model, formulated as a quartic assignment problem, is developed that explicitly considers the interference of workflow. Optimal and heuristic solution methodologies are developed and evaluated.

From the desktop to the grid: scalable bioinformatics via workflow conversion.

Science.gov (United States)

de la Garza, Luis; Veit, Johannes; Szolek, Andras; Röttig, Marc; Aiche, Stephan; Gesing, Sandra; Reinert, Knut; Kohlbacher, Oliver

2016-03-12

Reproducibility is one of the tenets of the scientific method. Scientific experiments often comprise complex data flows, selection of adequate parameters, and analysis and visualization of intermediate and end results. Breaking down the complexity of such experiments into the joint collaboration of small, repeatable, well defined tasks, each with well defined inputs, parameters, and outputs, offers the immediate benefit of identifying bottlenecks, pinpoint sections which could benefit from parallelization, among others. Workflows rest upon the notion of splitting complex work into the joint effort of several manageable tasks. There are several engines that give users the ability to design and execute workflows. Each engine was created to address certain problems of a specific community, therefore each one has its advantages and shortcomings. Furthermore, not all features of all workflow engines are royalty-free -an aspect that could potentially drive away members of the scientific community. We have developed a set of tools that enables the scientific community to benefit from workflow interoperability. We developed a platform-free structured representation of parameters, inputs, outputs of command-line tools in so-called Common Tool Descriptor documents. We have also overcome the shortcomings and combined the features of two royalty-free workflow engines with a substantial user community: the Konstanz Information Miner, an engine which we see as a formidable workflow editor, and the Grid and User Support Environment, a web-based framework able to interact with several high-performance computing resources. We have thus created a free and highly accessible way to design workflows on a desktop computer and execute them on high-performance computing resources. Our work will not only reduce time spent on designing scientific workflows, but also make executing workflows on remote high-performance computing resources more accessible to technically inexperienced users. We

Automatic DNA Diagnosis for 1D Gel Electrophoresis Images using Bio-image Processing Technique.

Science.gov (United States)

Intarapanich, Apichart; Kaewkamnerd, Saowaluck; Shaw, Philip J; Ukosakit, Kittipat; Tragoonrung, Somvong; Tongsima, Sissades

2015-01-01

DNA gel electrophoresis is a molecular biology technique for separating different sizes of DNA fragments. Applications of DNA gel electrophoresis include DNA fingerprinting (genetic diagnosis), size estimation of DNA, and DNA separation for Southern blotting. Accurate interpretation of DNA banding patterns from electrophoretic images can be laborious and error prone when a large number of bands are interrogated manually. Although many bio-imaging techniques have been proposed, none of them can fully automate the typing of DNA owing to the complexities of migration patterns typically obtained. We developed an image-processing tool that automatically calls genotypes from DNA gel electrophoresis images. The image processing workflow comprises three main steps: 1) lane segmentation, 2) extraction of DNA bands and 3) band genotyping classification. The tool was originally intended to facilitate large-scale genotyping analysis of sugarcane cultivars. We tested the proposed tool on 10 gel images (433 cultivars) obtained from polyacrylamide gel electrophoresis (PAGE) of PCR amplicons for detecting intron length polymorphisms (ILP) on one locus of the sugarcanes. These gel images demonstrated many challenges in automated lane/band segmentation in image processing including lane distortion, band deformity, high degree of noise in the background, and bands that are very close together (doublets). Using the proposed bio-imaging workflow, lanes and DNA bands contained within are properly segmented, even for adjacent bands with aberrant migration that cannot be separated by conventional techniques. The software, called GELect, automatically performs genotype calling on each lane by comparing with an all-banding reference, which was created by clustering the existing bands into the non-redundant set of reference bands. The automated genotype calling results were verified by independent manual typing by molecular biologists. This work presents an automated genotyping tool from DNA

Automatic DNA Diagnosis for 1D Gel Electrophoresis Images using Bio-image Processing Technique

Science.gov (United States)

2015-01-01

Background DNA gel electrophoresis is a molecular biology technique for separating different sizes of DNA fragments. Applications of DNA gel electrophoresis include DNA fingerprinting (genetic diagnosis), size estimation of DNA, and DNA separation for Southern blotting. Accurate interpretation of DNA banding patterns from electrophoretic images can be laborious and error prone when a large number of bands are interrogated manually. Although many bio-imaging techniques have been proposed, none of them can fully automate the typing of DNA owing to the complexities of migration patterns typically obtained. Results We developed an image-processing tool that automatically calls genotypes from DNA gel electrophoresis images. The image processing workflow comprises three main steps: 1) lane segmentation, 2) extraction of DNA bands and 3) band genotyping classification. The tool was originally intended to facilitate large-scale genotyping analysis of sugarcane cultivars. We tested the proposed tool on 10 gel images (433 cultivars) obtained from polyacrylamide gel electrophoresis (PAGE) of PCR amplicons for detecting intron length polymorphisms (ILP) on one locus of the sugarcanes. These gel images demonstrated many challenges in automated lane/band segmentation in image processing including lane distortion, band deformity, high degree of noise in the background, and bands that are very close together (doublets). Using the proposed bio-imaging workflow, lanes and DNA bands contained within are properly segmented, even for adjacent bands with aberrant migration that cannot be separated by conventional techniques. The software, called GELect, automatically performs genotype calling on each lane by comparing with an all-banding reference, which was created by clustering the existing bands into the non-redundant set of reference bands. The automated genotype calling results were verified by independent manual typing by molecular biologists. Conclusions This work presents an

Hermes: Seamless delivery of containerized bioinformatics workflows in hybrid cloud (HTC) environments

Science.gov (United States)

Kintsakis, Athanassios M.; Psomopoulos, Fotis E.; Symeonidis, Andreas L.; Mitkas, Pericles A.

Hermes introduces a new "describe once, run anywhere" paradigm for the execution of bioinformatics workflows in hybrid cloud environments. It combines the traditional features of parallelization-enabled workflow management systems and of distributed computing platforms in a container-based approach. It offers seamless deployment, overcoming the burden of setting up and configuring the software and network requirements. Most importantly, Hermes fosters the reproducibility of scientific workflows by supporting standardization of the software execution environment, thus leading to consistent scientific workflow results and accelerating scientific output.

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

High performance workflow implementation for protein surface characterization using grid technology

Directory of Open Access Journals (Sweden)

Clematis Andrea

2005-12-01

Full Text Available Abstract Background This study concerns the development of a high performance workflow that, using grid technology, correlates different kinds of Bioinformatics data, starting from the base pairs of the nucleotide sequence to the exposed residues of the protein surface. The implementation of this workflow is based on the Italian Grid.it project infrastructure, that is a network of several computational resources and storage facilities distributed at different grid sites. Methods Workflows are very common in Bioinformatics because they allow to process large quantities of data by delegating the management of resources to the information streaming. Grid technology optimizes the computational load during the different workflow steps, dividing the more expensive tasks into a set of small jobs. Results Grid technology allows efficient database management, a crucial problem for obtaining good results in Bioinformatics applications. The proposed workflow is implemented to integrate huge amounts of data and the results themselves must be stored into a relational database, which results as the added value to the global knowledge. Conclusion A web interface has been developed to make this technology accessible to grid users. Once the workflow has started, by means of the simplified interface, it is possible to follow all the different steps throughout the data processing. Eventually, when the workflow has been terminated, the different features of the protein, like the amino acids exposed on the protein surface, can be compared with the data present in the output database.

A Collaborative Workflow for the Digitization of Unique Materials

Science.gov (United States)

Gueguen, Gretchen; Hanlon, Ann M.

2009-01-01

This paper examines the experience of one institution, the University of Maryland Libraries, as it made organizational efforts to harness existing workflows and to capture digitization done in the course of responding to patron requests. By examining the way this organization adjusted its existing workflows to put in place more systematic methods…

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.

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

International Nuclear Information System (INIS)

Herbert, L.T.; Hansen, Z.N.L.

2016-01-01

This paper 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 is explored by means of an evolutionary algorithm, where the goals for improvement are defined in terms of optimising quantities, typically employed to model resources, associated with a workflow. The approach is fully automated and only the modelling of the production workflows, potential faults and the expression of the goals require manual input. We present the design of a software tool implementing this framework and explore the practical utility of this approach through an industrial case study in which the risk of production failures and their impact are reduced by restructuring the workflow. - Highlights: • We present a framework which allows for the automated restructuring of workflows. • This framework seeks to minimise the impact of errors on the workflow. • We illustrate a scalable software implementation of this framework. • We explore the practical utility of this approach through an industry case. • The impact of errors can be substantially reduced by restructuring the workflow.

A Prudent Approach to Fair Use Workflow

Directory of Open Access Journals (Sweden)

Karey Patterson

2018-02-01

Full Text Available This poster will outline a new highly efficient workflow for the management of copyright materials that is prudent and accommodates generally and legally accepted Fair Use limits. The workflow allows library or copyright staff an easy means to keep on top of their copyright obligations, manage licenses and review and adjust schedules but is still a highly efficient means to cope with large numbers of requests to use materials. The poster details speed and efficiency gains for professors and library staff while reducing legal exposure.

Hermes: Seamless delivery of containerized bioinformatics workflows in hybrid cloud (HTC environments

Directory of Open Access Journals (Sweden)

Athanassios M. Kintsakis

2017-01-01

Full Text Available Hermes introduces a new “describe once, run anywhere” paradigm for the execution of bioinformatics workflows in hybrid cloud environments. It combines the traditional features of parallelization-enabled workflow management systems and of distributed computing platforms in a container-based approach. It offers seamless deployment, overcoming the burden of setting up and configuring the software and network requirements. Most importantly, Hermes fosters the reproducibility of scientific workflows by supporting standardization of the software execution environment, thus leading to consistent scientific workflow results and accelerating scientific output.

Bio-jETI: a framework for semantics-based service composition

Directory of Open Access Journals (Sweden)

Margaria Tiziana

2009-10-01

Full Text Available Abstract Background The development of bioinformatics databases, algorithms, and tools throughout the last years has lead to a highly distributed world of bioinformatics services. Without adequate management and development support, in silico researchers are hardly able to exploit the potential of building complex, specialized analysis processes from these services. The Semantic Web aims at thoroughly equipping individual data and services with machine-processable meta-information, while workflow systems support the construction of service compositions. However, even in this combination, in silico researchers currently would have to deal manually with the service interfaces, the adequacy of the semantic annotations, type incompatibilities, and the consistency of service compositions. Results In this paper, we demonstrate by means of two examples how Semantic Web technology together with an adequate domain modelling frees in silico researchers from dealing with interfaces, types, and inconsistencies. In Bio-jETI, bioinformatics services can be graphically combined to complex services without worrying about details of their interfaces or about type mismatches of the composition. These issues are taken care of at the semantic level by Bio-jETI's model checking and synthesis features. Whenever possible, they automatically resolve type mismatches in the considered service setting. Otherwise, they graphically indicate impossible/incorrect service combinations. In the latter case, the workflow developer may either modify his service composition using semantically similar services, or ask for help in developing the missing mediator that correctly bridges the detected type gap. Newly developed mediators should then be adequately annotated semantically, and added to the service library for later reuse in similar situations. Conclusion We show the power of semantic annotations in an adequately modelled and semantically enabled domain setting. Using model

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.)

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.)

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.

Handwriting Automaticity: The Search for Performance Thresholds

Science.gov (United States)

Medwell, Jane; Wray, David

2014-01-01

Evidence is accumulating that handwriting has an important role in written composition. In particular, handwriting automaticity appears to relate to success in composition. This relationship has been little explored in British contexts and we currently have little idea of what threshold performance levels might be. In this paper, we report on two…

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.

Styx Grid Services: Lightweight Middleware for Efficient Scientific Workflows

Directory of Open Access Journals (Sweden)

J.D. Blower

2006-01-01

Full Text Available The service-oriented approach to performing distributed scientific research is potentially very powerful but is not yet widely used in many scientific fields. This is partly due to the technical difficulties involved in creating services and workflows and the inefficiency of many workflow systems with regard to handling large datasets. We present the Styx Grid Service, a simple system that wraps command-line programs and allows them to be run over the Internet exactly as if they were local programs. Styx Grid Services are very easy to create and use and can be composed into powerful workflows with simple shell scripts or more sophisticated graphical tools. An important feature of the system is that data can be streamed directly from service to service, significantly increasing the efficiency of workflows that use large data volumes. The status and progress of Styx Grid Services can be monitored asynchronously using a mechanism that places very few demands on firewalls. We show how Styx Grid Services can interoperate with with Web Services and WS-Resources using suitable adapters.

Assessment of the Nurse Medication Administration Workflow Process

Directory of Open Access Journals (Sweden)

Nathan Huynh

2016-01-01

Full Text Available This paper presents findings of an observational study of the Registered Nurse (RN Medication Administration Process (MAP conducted on two comparable medical units in a large urban tertiary care medical center in Columbia, South Carolina. A total of 305 individual MAP observations were recorded over a 6-week period with an average of 5 MAP observations per RN participant for both clinical units. A key MAP variation was identified in terms of unbundled versus bundled MAP performance. In the unbundled workflow, an RN engages in the MAP by performing only MAP tasks during a care episode. In the bundled workflow, an RN completes medication administration along with other patient care responsibilities during the care episode. Using a discrete-event simulation model, this paper addresses the difference between unbundled and bundled workflow and their effects on simulated redesign interventions.

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.

Evaluation of Semi-Automatic Metadata Generation Tools: A Survey of the Current State of the Art

Directory of Open Access Journals (Sweden)

Jung-ran Park

2015-09-01

Full Text Available Assessment of the current landscape of semi-automatic metadata generation tools is particularly important considering the rapid development of digital repositories and the recent explosion of big data. Utilization of (semiautomatic metadata generation is critical in addressing these environmental changes and may be unavoidable in the future considering the costly and complex operation of manual metadata creation. To address such needs, this study examines the range of semi-automatic metadata generation tools (n=39 while providing an analysis of their techniques, features, and functions. The study focuses on open-source tools that can be readily utilized in libraries and other memory institutions.  The challenges and current barriers to implementation of these tools were identified. The greatest area of difficulty lies in the fact that  the piecemeal development of most semi-automatic generation tools only addresses part of the issue of semi-automatic metadata generation, providing solutions to one or a few metadata elements but not the full range elements.  This indicates that significant local efforts will be required to integrate the various tools into a coherent set of a working whole.  Suggestions toward such efforts are presented for future developments that may assist information professionals with incorporation of semi-automatic tools within their daily workflows.

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.

Parametric Room Acoustic workflows with real-time acoustic simulation

DEFF Research Database (Denmark)

Parigi, Dario

2017-01-01

The paper investigates and assesses the opportunities that real-time acoustic simulation offer to engage in parametric acoustics workflow and to influence architectural designs from early design stages......The paper investigates and assesses the opportunities that real-time acoustic simulation offer to engage in parametric acoustics workflow and to influence architectural designs from early design stages...

Exploring the impact of an automated prescription-filling device on community pharmacy technician workflow

Science.gov (United States)

Walsh, Kristin E.; Chui, Michelle Anne; Kieser, Mara A.; Williams, Staci M.; Sutter, Susan L.; Sutter, John G.

2012-01-01

Objective To explore community pharmacy technician workflow change after implementation of an automated robotic prescription-filling device. Methods At an independent community pharmacy in rural Mayville, WI, pharmacy technicians were observed before and 3 months after installation of an automated robotic prescription-filling device. The main outcome measures were sequences and timing of technician workflow steps, workflow interruptions, automation surprises, and workarounds. Results Of the 77 and 80 observations made before and 3 months after robot installation, respectively, 17 different workflow sequences were observed before installation and 38 after installation. Average prescription filling time was reduced by 40 seconds per prescription with use of the robot. Workflow interruptions per observation increased from 1.49 to 1.79 (P = 0.11), and workarounds increased from 10% to 36% after robot use. Conclusion Although automated prescription-filling devices can increase efficiency, workflow interruptions and workarounds may negate that efficiency. Assessing changes in workflow and sequencing of tasks that may result from the use of automation can help uncover opportunities for workflow policy and procedure redesign. PMID:21896459

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....

Workflow interruptions, cognitive failure and near-accidents in health care.

Science.gov (United States)

Elfering, Achim; Grebner, Simone; Ebener, Corinne

2015-01-01

Errors are frequent in health care. A specific model was tested that affirms failure in cognitive action regulation to mediate the influence of nurses' workflow interruptions and safety conscientiousness on near-accidents in health care. One hundred and sixty-five nurses from seven Swiss hospitals participated in a questionnaire survey. Structural equation modelling confirmed the hypothesised mediation model. Cognitive failure in action regulation significantly mediated the influence of workflow interruptions on near-accidents (p accidents via cognitive failure in action regulation was also significant (p accidents; moreover, cognitive failure mediated the association between compliance and near-accidents (p < .05). Contrary to expectations, compliance with safety regulations was not related to workflow interruptions. Workflow interruptions caused by colleagues, patients and organisational constraints are likely to trigger errors in nursing. Work redesign is recommended to reduce cognitive failure and improve safety of nurses and patients.

Distributing Workflows over a Ubiquitous P2P Network

Directory of Open Access Journals (Sweden)

Eddie Al-Shakarchi

2007-01-01

Full Text Available This paper discusses issues in the distribution of bundled workflows across ubiquitous peer-to-peer networks for the application of music information retrieval. The underlying motivation for this work is provided by the DART project, which aims to develop a novel music recommendation system by gathering statistical data using collaborative filtering techniques and the analysis of the audio itsel, in order to create a reliable and comprehensive database of the music that people own and which they listen to. To achieve this, the DART scientists creating the algorithms need the ability to distribute the Triana workflows they create, representing the analysis to be performed, across the network on a regular basis (perhaps even daily in order to update the network as a whole with new workflows to be executed for the analysis. DART uses a similar approach to BOINC but differs in that the workers receive input data in the form of a bundled Triana workflow, which is executed in order to process any MP3 files that they own on their machine. Once analysed, the results are returned to DART's distributed database that collects and aggregates the resulting information. DART employs the use of package repositories to decentralise the distribution of such workflow bundles and this approach is validated in this paper through simulations that show that suitable scalability is maintained through the system as the number of participants increases. The results clearly illustrate the effectiveness of the approach.

MBAT: A scalable informatics system for unifying digital atlasing workflows

Directory of Open Access Journals (Sweden)

Sane Nikhil

2010-12-01

Full Text Available Abstract Background Digital atlases provide a common semantic and spatial coordinate system that can be leveraged to compare, contrast, and correlate data from disparate sources. As the quality and amount of biological data continues to advance and grow, searching, referencing, and comparing this data with a researcher's own data is essential. However, the integration process is cumbersome and time-consuming due to misaligned data, implicitly defined associations, and incompatible data sources. This work addressing these challenges by providing a unified and adaptable environment to accelerate the workflow to gather, align, and analyze the data. Results The MouseBIRN Atlasing Toolkit (MBAT project was developed as a cross-platform, free open-source application that unifies and accelerates the digital atlas workflow. A tiered, plug-in architecture was designed for the neuroinformatics and genomics goals of the project to provide a modular and extensible design. MBAT provides the ability to use a single query to search and retrieve data from multiple data sources, align image data using the user's preferred registration method, composite data from multiple sources in a common space, and link relevant informatics information to the current view of the data or atlas. The workspaces leverage tool plug-ins to extend and allow future extensions of the basic workspace functionality. A wide variety of tool plug-ins were developed that integrate pre-existing as well as newly created technology into each workspace. Novel atlasing features were also developed, such as supporting multiple label sets, dynamic selection and grouping of labels, and synchronized, context-driven display of ontological data. Conclusions MBAT empowers researchers to discover correlations among disparate data by providing a unified environment for bringing together distributed reference resources, a user's image data, and biological atlases into the same spatial or semantic context

Considering Time in Orthophotography Production: from a General Workflow to a Shortened Workflow for a Faster Disaster Response

Science.gov (United States)

Lucas, G.

2015-08-01

This article overall deals with production time with orthophoto imagery with medium size digital frame camera. The workflow examination follows two main parts: data acquisition and post-processing. The objectives of the research are fourfold: 1/ gathering time references for the most important steps of orthophoto production (it turned out that literature is missing on this topic); these figures are used later for total production time estimation; 2/ identifying levers for reducing orthophoto production time; 3/ building a simplified production workflow for emergency response: less exigent with accuracy and faster; and compare it to a classical workflow; 4/ providing methodical elements for the estimation of production time with a custom project. In the data acquisition part a comprehensive review lists and describes all the factors that may affect the acquisition efficiency. Using a simulation with different variables (average line length, time of the turns, flight speed) their effect on acquisition efficiency is quantitatively examined. Regarding post-processing, the time references figures were collected from the processing of a 1000 frames case study with 15 cm GSD covering a rectangular area of 447 km2; the time required to achieve each step during the production is written down. When several technical options are possible, each one is tested and time documented so as all alternatives are available. Based on a technical choice with the workflow and using the compiled time reference of the elementary steps, a total time is calculated for the post-processing of the 1000 frames. Two scenarios are compared as regards to time and accuracy. The first one follows the "normal" practices, comprising triangulation, orthorectification and advanced mosaicking methods (feature detection, seam line editing and seam applicator); the second is simplified and make compromise over positional accuracy (using direct geo-referencing) and seamlines preparation in order to achieve

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

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

Directory of Open Access Journals (Sweden)

Elspeth Haston

2012-07-01

Full Text Available 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.

Data mining workflow templates for intelligent discovery assistance in RapidMiner

OpenAIRE

Kietz, J U; Serban, F; Bernstein, A; Fischer, S

2010-01-01

Knowledge Discovery in Databases (KDD) has evolved during the last years and reached a mature stage offering plenty of operators to solve complex tasks. User support for building workflows, in contrast, has not increased proportionally. The large number of operators available in current KDD systems make it difficult for users to successfully analyze data. Moreover, workflows easily contain a large number of operators and parts of the workflows are applied several times, thus it is hard for us...

Requirements for Secure Logging of Decentralized Cross-Organizational Workflow Executions

NARCIS (Netherlands)

Wombacher, Andreas; Wieringa, Roelf J.; Jonker, Willem; Knezevic, P.; Pokraev, S.; meersman, R; Tari, Z; herrero, p; Méndez, G.; Cavedon, L.; Martin, D.; Hinze, A.; Buchanan, G.

2005-01-01

The control of actions performed by parties involved in a decentralized cross-organizational workflow is done by several independent workflow engines. Due to the lack of a centralized coordination control, an auditing is required which supports a reliable and secure detection of malicious actions

CrossFlow: Cross-Organizational Workflow Management in Dynamic Virtual Enterprises

NARCIS (Netherlands)

Grefen, P.W.P.J.; Aberer, Karl; Hoffner, Yigal; Ludwig, Heiko

In this report, we present the approach to cross-organizational workflow management of the CrossFlow project. CrossFlow is a European research project aiming at the support of cross-organizational workflows in dynamic virtual enterprises. The cooperation in these virtual enterprises is based on

CrossFlow : cross-organizational workflow management in dynamic virtual enterprises

NARCIS (Netherlands)

Grefen, P.W.P.J.; Aberer, K.; Hoffner, Y.

2000-01-01

This paper gives a detailed overview of the approach to cross-organizational workflow management developed in the CrossFlow project. CrossFlow is a European research project aiming at the support of cross-organizational workflows in dynamic virtual enterprises. The cooperation in these virtual

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

Research and Implementation of Key Technologies in Multi-Agent System to Support Distributed Workflow

Science.gov (United States)

Pan, Tianheng

2018-01-01

In recent years, the combination of workflow management system and Multi-agent technology is a hot research field. The problem of lack of flexibility in workflow management system can be improved by introducing multi-agent collaborative management. The workflow management system adopts distributed structure. It solves the problem that the traditional centralized workflow structure is fragile. In this paper, the agent of Distributed workflow management system is divided according to its function. The execution process of each type of agent is analyzed. The key technologies such as process execution and resource management are analyzed.

Integration of the radiotherapy irradiation planning in the digital workflow

International Nuclear Information System (INIS)

Roehner, F.; Schmucker, M.; Henne, K.; Bruggmoser, G.; Grosu, A.L.; Frommhold, H.; Heinemann, F.E.; Momm, F.

2013-01-01

Background and purpose: At the Clinic of Radiotherapy at the University Hospital Freiburg, all relevant workflow is paperless. After implementing the Operating Schedule System (OSS) as a framework, all processes are being implemented into the departmental system MOSAIQ. Designing a digital workflow for radiotherapy irradiation planning is a large challenge, it requires interdisciplinary expertise and therefore the interfaces between the professions also have to be interdisciplinary. For every single step of radiotherapy irradiation planning, distinct responsibilities have to be defined and documented. All aspects of digital storage, backup and long-term availability of data were considered and have already been realized during the OSS project. Method: After an analysis of the complete workflow and the statutory requirements, a detailed project plan was designed. In an interdisciplinary workgroup, problems were discussed and a detailed flowchart was developed. The new functionalities were implemented in a testing environment by the Clinical and Administrative IT Department (CAI). After extensive tests they were integrated into the new modular department system. Results and conclusion: The Clinic of Radiotherapy succeeded in realizing a completely digital workflow for radiotherapy irradiation planning. During the testing phase, our digital workflow was examined and afterwards was approved by the responsible authority. (orig.)

A deep convolutional neural network-based automatic delineation strategy for multiple brain metastases stereotactic radiosurgery.

Directory of Open Access Journals (Sweden)

Yan Liu

Full Text Available Accurate and automatic brain metastases target delineation is a key step for efficient and effective stereotactic radiosurgery (SRS treatment planning. In this work, we developed a deep learning convolutional neural network (CNN algorithm for segmenting brain metastases on contrast-enhanced T1-weighted magnetic resonance imaging (MRI datasets. We integrated the CNN-based algorithm into an automatic brain metastases segmentation workflow and validated on both Multimodal Brain Tumor Image Segmentation challenge (BRATS data and clinical patients' data. Validation on BRATS data yielded average DICE coefficients (DCs of 0.75±0.07 in the tumor core and 0.81±0.04 in the enhancing tumor, which outperformed most techniques in the 2015 BRATS challenge. Segmentation results of patient cases showed an average of DCs 0.67±0.03 and achieved an area under the receiver operating characteristic curve of 0.98±0.01. The developed automatic segmentation strategy surpasses current benchmark levels and offers a promising tool for SRS treatment planning for multiple brain metastases.

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.

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...

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.

Design and implementation of a secure workflow system based on PKI/PMI

Science.gov (United States)

Yan, Kai; Jiang, Chao-hui

2013-03-01

As the traditional workflow system in privilege management has the following weaknesses: low privilege management efficiency, overburdened for administrator, lack of trust authority etc. A secure workflow model based on PKI/PMI is proposed after studying security requirements of the workflow systems in-depth. This model can achieve static and dynamic authorization after verifying user's ID through PKC and validating user's privilege information by using AC in workflow system. Practice shows that this system can meet the security requirements of WfMS. Moreover, it can not only improve system security, but also ensures integrity, confidentiality, availability and non-repudiation of the data in the system.

Characterizing workflow for pediatric asthma patients in emergency departments using electronic health records.

Science.gov (United States)

Ozkaynak, Mustafa; Dziadkowiec, Oliwier; Mistry, Rakesh; Callahan, Tiffany; He, Ze; Deakyne, Sara; Tham, Eric

2015-10-01

The purpose of this study was to describe a workflow analysis approach and apply it in emergency departments (EDs) using data extracted from the electronic health record (EHR) system. We used data that were obtained during 2013 from the ED of a children's hospital and its four satellite EDs. Workflow-related data were extracted for all patient visits with either a primary or secondary diagnosis on discharge of asthma (ICD-9 code=493). For each patient visit, eight different a priori time-stamped events were identified. Data were also collected on mode of arrival, patient demographics, triage score (i.e. acuity level), and primary/secondary diagnosis. Comparison groups were by acuity levels 2 and 3 with 2 being more acute than 3, arrival mode (ambulance versus walk-in), and site. Data were analyzed using a visualization method and Markov Chains. To demonstrate the viability and benefit of the approach, patient care workflows were visually and quantitatively compared. The analysis of the EHR data allowed for exploration of workflow patterns and variation across groups. Results suggest that workflow was different for different arrival modes, settings and acuity levels. EHRs can be used to explore workflow with statistical and visual analytics techniques novel to the health care setting. The results generated by the proposed approach could be utilized to help institutions identify workflow issues, plan for varied workflows and ultimately improve efficiency in caring for diverse patient groups. EHR data and novel analytic techniques in health care can expand our understanding of workflow in both large and small ED units. Copyright © 2015 Elsevier Inc. All rights reserved.

Automatic atlas based electron density and structure contouring for MRI-based prostate radiation therapy on the cloud

International Nuclear Information System (INIS)

Dowling, J A; Burdett, N; Chandra, S; Rivest-Hénault, D; Ghose, S; Salvado, O; Fripp, J; Greer, P B; Sun, J; Parker, J; Pichler, P; Stanwell, P

2014-01-01

Our group have been developing methods for MRI-alone prostate cancer radiation therapy treatment planning. To assist with clinical validation of the workflow we are investigating a cloud platform solution for research purposes. Benefits of cloud computing can include increased scalability, performance and extensibility while reducing total cost of ownership. In this paper we demonstrate the generation of DICOM-RT directories containing an automatic average atlas based electron density image and fast pelvic organ contouring from whole pelvis MR scans.

Automatic Atlas Based Electron Density and Structure Contouring for MRI-based Prostate Radiation Therapy on the Cloud

Science.gov (United States)

Dowling, J. A.; Burdett, N.; Greer, P. B.; Sun, J.; Parker, J.; Pichler, P.; Stanwell, P.; Chandra, S.; Rivest-Hénault, D.; Ghose, S.; Salvado, O.; Fripp, J.

2014-03-01

Our group have been developing methods for MRI-alone prostate cancer radiation therapy treatment planning. To assist with clinical validation of the workflow we are investigating a cloud platform solution for research purposes. Benefits of cloud computing can include increased scalability, performance and extensibility while reducing total cost of ownership. In this paper we demonstrate the generation of DICOM-RT directories containing an automatic average atlas based electron density image and fast pelvic organ contouring from whole pelvis MR scans.

A Workflow-Oriented Approach To Propagation Models In Heliophysics

Directory of Open Access Journals (Sweden)

Gabriele Pierantoni

2014-01-01

Full Text Available The Sun is responsible for the eruption of billions of tons of plasma andthe generation of near light-speed particles that propagate throughout the solarsystem and beyond. If directed towards Earth, these events can be damaging toour tecnological infrastructure. Hence there is an effort to understand the causeof the eruptive events and how they propagate from Sun to Earth. However, thephysics governing their propagation is not well understood, so there is a need todevelop a theoretical description of their propagation, known as a PropagationModel, in order to predict when they may impact Earth. It is often difficultto define a single propagation model that correctly describes the physics ofsolar eruptive events, and even more difficult to implement models capable ofcatering for all these complexities and to validate them using real observational data.In this paper, we envisage that workflows offer both a theoretical andpractical framerwork for a novel approach to propagation models. We definea mathematical framework that aims at encompassing the different modalitieswith which workflows can be used, and provide a set of generic building blockswritten in the TAVERNA workflow language that users can use to build theirown propagation models. Finally we test both the theoretical model and thecomposite building blocks of the workflow with a real Science Use Case that wasdiscussed during the 4th CDAW (Coordinated Data Analysis Workshop eventheld by the HELIO project. We show that generic workflow building blocks canbe used to construct a propagation model that succesfully describes the transitof solar eruptive events toward Earth and predict a correct Earth-impact time

Analog to digital workflow improvement: a quantitative study.

Science.gov (United States)

Wideman, Catherine; Gallet, Jacqueline

2006-01-01

This study tracked a radiology department's conversion from utilization of a Kodak Amber analog system to a Kodak DirectView DR 5100 digital system. Through the use of ProModel Optimization Suite, a workflow simulation software package, significant quantitative information was derived from workflow process data measured before and after the change to a digital system. Once the digital room was fully operational and the radiology staff comfortable with the new system, average patient examination time was reduced from 9.24 to 5.28 min, indicating that a higher patient throughput could be achieved. Compared to the analog system, chest examination time for modality specific activities was reduced by 43%. The percentage of repeat examinations experienced with the digital system also decreased to 8% vs. the level of 9.5% experienced with the analog system. The study indicated that it is possible to quantitatively study clinical workflow and productivity by using commercially available software.

AnalyzeThis: An Analysis Workflow-Aware Storage System

Energy Technology Data Exchange (ETDEWEB)

Sim, Hyogi [ORNL; Kim, Youngjae [ORNL; Vazhkudai, Sudharshan S [ORNL; Tiwari, Devesh [ORNL; Anwar, Ali [Virginia Tech, Blacksburg, VA; Butt, Ali R [Virginia Tech, Blacksburg, VA; Ramakrishnan, Lavanya [Lawrence Berkeley National Laboratory (LBNL)

2015-01-01

The need for novel data analysis is urgent in the face of a data deluge from modern applications. Traditional approaches to data analysis incur significant data movement costs, moving data back and forth between the storage system and the processor. Emerging Active Flash devices enable processing on the flash, where the data already resides. An array of such Active Flash devices allows us to revisit how analysis workflows interact with storage systems. By seamlessly blending together the flash storage and data analysis, we create an analysis workflow-aware storage system, AnalyzeThis. Our guiding principle is that analysis-awareness be deeply ingrained in each and every layer of the storage, elevating data analyses as first-class citizens, and transforming AnalyzeThis into a potent analytics-aware appliance. We implement the AnalyzeThis storage system atop an emulation platform of the Active Flash array. Our results indicate that AnalyzeThis is viable, expediting workflow execution and minimizing data movement.

An integrated billing application to streamline clinician workflow.

Science.gov (United States)

Vawdrey, David K; Walsh, Colin; Stetson, Peter D

2014-01-01

Between 2008 and 2010, our academic medical center transitioned to electronic provider documentation using a commercial electronic health record system. For attending physicians, one of the most frustrating aspects of this experience was the system's failure to support their existing electronic billing workflow. Because of poor system integration, it was difficult to verify the supporting documentation for each bill and impractical to track whether billable notes had corresponding charges. We developed and deployed in 2011 an integrated billing application called "iCharge" that streamlines clinicians' documentation and billing workflow, and simultaneously populates the inpatient problem list using billing diagnosis codes. Each month, over 550 physicians use iCharge to submit approximately 23,000 professional service charges for over 4,200 patients. On average, about 2.5 new problems are added to each patient's problem list. This paper describes the challenges and benefits of workflow integration across disparate applications and presents an example of innovative software development within a commercial EHR framework.

CMS Alignement and Calibration workflows: lesson learned and future plans

CERN Document Server

AUTHOR|(CDS)2069172

2014-01-01

We review the online and offline workflows designed to align and calibrate the CMS detector. Starting from the gained experience during the first LHC run, we discuss the expected developments for Run II. In particular, we describe the envisioned different stages, from the alignment using cosmic rays data to the detector alignment and calibration using the first proton-proton collisions data ( O(100 pb-1) ) and a larger dataset ( O(1 fb-1) ) to reach the target precision. The automatisation of the workflow and the integration in the online and offline activity (dedicated triggers and datasets, data skims, workflows to compute the calibration and alignment constants) are discussed.

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

Logical provenance in data-oriented workflows?

KAUST Repository

Ikeda, R.; Das Sarma, Akash; Widom, J.

2013-01-01

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

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

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

the concept of scientific workflows. Second, we implemented an interface in the G-EX Portal Learn Module to demonstrate the workflow learning model. The workflow interface allows users to drag learning artifacts uploaded to the G-EX Portal onto a central whiteboard and then annotate the workflow using text and drawing tools. Once completed, users can visit the assembled workflow to get an idea of the kind, number, and scale of analysis steps, view individual learning artifacts associated with each node in the workflow, and ask questions about the overall workflow or individual learning artifacts through the associated forums. An example learning workflow in the domain of epidemiology is provided to demonstrate the effectiveness of the approach. RESULTS/CONCLUSIONS: In the context of geovisual analytics, GIScientists are not only responsible for developing software to facilitate visually-mediated reasoning about large and complex spatiotemporal information, but also for ensuring that this software works. The workflow learning model discussed in this paper and demonstrated in the G-EX Portal Learn Module is one approach to improving the utility of geovisual analytics software. While development of the G-EX Portal Learn Module is ongoing, we expect to release the G-EX Portal Learn Module by Summer 2009.

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

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.

The CMS tracker calibration workflow: Experience with cosmic ray data

International Nuclear Information System (INIS)

Frosali, Simone

2010-01-01

During the second part of 2008 a CMS commissioning was performed with the acquisition of cosmic events in global runs. Cosmic rays detected in the muon chambers were used to trigger the readout of all CMS subdetectors in the general data acquisition system. A total of about 300M of tracks were collected by the CMS Muon Chambers with a 3.8T magnetic field produced by the CMS superconducting solenoid, 6M of which pointing to the tracker region and reconstructed by the Si-Strip Tracker (SST) detectors. Other 1M of cosmic tracks were collected with the magnetic field off. Using the cosmic data available it was possible to validate the performances of the CMS tracker calibration workflows. In this paper the adopted calibration workflow is described. In particular, the three main calibration workflows requested for the low level reconstruction of the SST, i.e. gain calibration, Lorentz angle calibration and bad components identification, are described. The results obtained using cosmic tracks for these three calibration workflows are also presented.

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

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 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...

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.

A-Posteriori Detection of Sensor Infrastructure Errors in Correlated Sensor Data and Business Workflows

NARCIS (Netherlands)

Wombacher, Andreas; Rinderle-Ma, Stefanie; Toumani, Farouk; Wolf, Karsten

Some physical objects are influenced by business workflows and are observed by sensors. Since both sensor infrastructures and business workflows must deal with imprecise information, the correlation of sensor data and business workflow data related to physical objects might be used a-posteriori to

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...

Machine learning for the automatic detection of anomalous events

Science.gov (United States)

Fisher, Wendy D.

In this dissertation, we describe our research contributions for a novel approach to the application of machine learning for the automatic detection of anomalous events. We work in two different domains to ensure a robust data-driven workflow that could be generalized for monitoring other systems. Specifically, in our first domain, we begin with the identification of internal erosion events in earth dams and levees (EDLs) using geophysical data collected from sensors located on the surface of the levee. As EDLs across the globe reach the end of their design lives, effectively monitoring their structural integrity is of critical importance. The second domain of interest is related to mobile telecommunications, where we investigate a system for automatically detecting non-commercial base station routers (BSRs) operating in protected frequency space. The presence of non-commercial BSRs can disrupt the connectivity of end users, cause service issues for the commercial providers, and introduce significant security concerns. We provide our motivation, experimentation, and results from investigating a generalized novel data-driven workflow using several machine learning techniques. In Chapter 2, we present results from our performance study that uses popular unsupervised clustering algorithms to gain insights to our real-world problems, and evaluate our results using internal and external validation techniques. Using EDL passive seismic data from an experimental laboratory earth embankment, results consistently show a clear separation of events from non-events in four of the five clustering algorithms applied. Chapter 3 uses a multivariate Gaussian machine learning model to identify anomalies in our experimental data sets. For the EDL work, we used experimental data from two different laboratory earth embankments. Additionally, we explore five wavelet transform methods for signal denoising. The best performance is achieved with the Haar wavelets. We achieve up to 97

Deadline-constrained workflow scheduling algorithms for Infrastructure as a Service Clouds

NARCIS (Netherlands)

Abrishami, S.; Naghibzadeh, M.; Epema, D.H.J.

2013-01-01

The advent of Cloud computing as a new model of service provisioning in distributed systems encourages researchers to investigate its benefits and drawbacks on executing scientific applications such as workflows. One of the most challenging problems in Clouds is workflow scheduling, i.e., the

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.

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.

Managing and Communicating Operational Workflow: Designing and Implementing an Electronic Outpatient Whiteboard.

Science.gov (United States)

Steitz, Bryan D; Weinberg, Stuart T; Danciu, Ioana; Unertl, Kim M

2016-01-01

Healthcare team members in emergency department contexts have used electronic whiteboard solutions to help manage operational workflow for many years. Ambulatory clinic settings have highly complex operational workflow, but are still limited in electronic assistance to communicate and coordinate work activities. To describe and discuss the design, implementation, use, and ongoing evolution of a coordination and collaboration tool supporting ambulatory clinic operational workflow at Vanderbilt University Medical Center (VUMC). The outpatient whiteboard tool was initially designed to support healthcare work related to an electronic chemotherapy order-entry application. After a highly successful initial implementation in an oncology context, a high demand emerged across the organization for the outpatient whiteboard implementation. Over the past 10 years, developers have followed an iterative user-centered design process to evolve the tool. The electronic outpatient whiteboard system supports 194 separate whiteboards and is accessed by over 2800 distinct users on a typical day. Clinics can configure their whiteboards to support unique workflow elements. Since initial release, features such as immunization clinical decision support have been integrated into the system, based on requests from end users. The success of the electronic outpatient whiteboard demonstrates the usefulness of an operational workflow tool within the ambulatory clinic setting. Operational workflow tools can play a significant role in supporting coordination, collaboration, and teamwork in ambulatory healthcare settings.

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.

Thermal Remote Sensing with Uav-Based Workflows

Science.gov (United States)

Boesch, R.

2017-08-01

Climate change will have a significant influence on vegetation health and growth. Predictions of higher mean summer temperatures and prolonged summer draughts may pose a threat to agriculture areas and forest canopies. Rising canopy temperatures can be an indicator of plant stress because of the closure of stomata and a decrease in the transpiration rate. Thermal cameras are available for decades, but still often used for single image analysis, only in oblique view manner or with visual evaluations of video sequences. Therefore remote sensing using a thermal camera can be an important data source to understand transpiration processes. Photogrammetric workflows allow to process thermal images similar to RGB data. But low spatial resolution of thermal cameras, significant optical distortion and typically low contrast require an adapted workflow. Temperature distribution in forest canopies is typically completely unknown and less distinct than for urban or industrial areas, where metal constructions and surfaces yield high contrast and sharp edge information. The aim of this paper is to investigate the influence of interior camera orientation, tie point matching and ground control points on the resulting accuracy of bundle adjustment and dense cloud generation with a typically used photogrammetric workflow for UAVbased thermal imagery in natural environments.

Design scheme of automatic feeding equipment of domestic uranium chemical concentrate

International Nuclear Information System (INIS)

Hu Jinming; Wang Chao; Peng Jinhui; Zhang Libo

2014-01-01

In order to solve problems by artificial feeding mode with low work efficiency, large intensity manual labor and environmental pollution in domestic uranium concentrate purification process, the design scheme of automatic feeding device was set up, including work flow sheet, composition of automatic equipment and operation. By application of automatic feeding equipment, the feeding speed can be greatly increased, labor force can be reduced, and harm to workman health can be decreased. (authors)

Parallel workflow tools to facilitate human brain MRI post-processing

Directory of Open Access Journals (Sweden)

Zaixu eCui

2015-05-01

Full Text Available Multi-modal magnetic resonance imaging (MRI techniques are widely applied in human brain studies. To obtain specific brain measures of interest from MRI datasets, a number of complex image post-processing steps are typically required. Parallel workflow tools have recently been developed, concatenating individual processing steps and enabling fully automated processing of raw MRI data to obtain the final results. These workflow tools are also designed to make optimal use of available computational resources and to support the parallel processing of different subjects or of independent processing steps for a single subject. Automated, parallel MRI post-processing tools can greatly facilitate relevant brain investigations and are being increasingly applied. In this review, we briefly summarize these parallel workflow tools and discuss relevant issues.

Barriers to critical thinking: workflow interruptions and task switching among nurses.

Science.gov (United States)

Cornell, Paul; Riordan, Monica; Townsend-Gervis, Mary; Mobley, Robin

2011-10-01

Nurses are increasingly called upon to engage in critical thinking. However, current workflow inhibits this goal with frequent task switching and unpredictable demands. To assess workflow's cognitive impact, nurses were observed at 2 hospitals with different patient loads and acuity levels. Workflow on a medical/surgical and pediatric oncology unit was observed, recording tasks, tools, collaborators, and locations. Nineteen nurses were observed for a total of 85.2 hours. Tasks were short with a mean duration of 62.4 and 81.6 seconds on the 2 units. More than 50% of the recorded tasks were less than 30 seconds in length. An analysis of task sequence revealed few patterns and little pairwise repetition. Performance on specific tasks differed between the 2 units, but the character of the workflow was highly similar. The nonrepetitive flow and high amount of switching indicate nurses experience a heavy cognitive load with little uninterrupted time. This implies that nurses rarely have the conditions necessary for critical thinking.

Task Delegation Based Access Control Models for Workflow Systems

Science.gov (United States)

Gaaloul, Khaled; Charoy, François

e-Government organisations are facilitated and conducted using workflow management systems. Role-based access control (RBAC) is recognised as an efficient access control model for large organisations. The application of RBAC in workflow systems cannot, however, grant permissions to users dynamically while business processes are being executed. We currently observe a move away from predefined strict workflow modelling towards approaches supporting flexibility on the organisational level. One specific approach is that of task delegation. Task delegation is a mechanism that supports organisational flexibility, and ensures delegation of authority in access control systems. In this paper, we propose a Task-oriented Access Control (TAC) model based on RBAC to address these requirements. We aim to reason about task from organisational perspectives and resources perspectives to analyse and specify authorisation constraints. Moreover, we present a fine grained access control protocol to support delegation based on the TAC model.

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

Towards better digital pathology workflows: programming libraries for high-speed sharpness assessment of Whole Slide Images.

Science.gov (United States)

Ameisen, David; Deroulers, Christophe; Perrier, Valérie; Bouhidel, Fatiha; Battistella, Maxime; Legrès, Luc; Janin, Anne; Bertheau, Philippe; Yunès, Jean-Baptiste

2014-01-01

Since microscopic slides can now be automatically digitized and integrated in the clinical workflow, quality assessment of Whole Slide Images (WSI) has become a crucial issue. We present a no-reference quality assessment method that has been thoroughly tested since 2010 and is under implementation in multiple sites, both public university-hospitals and private entities. It is part of the FlexMIm R&D project which aims to improve the global workflow of digital pathology. For these uses, we have developed two programming libraries, in Java and Python, which can be integrated in various types of WSI acquisition systems, viewers and image analysis tools. Development and testing have been carried out on a MacBook Pro i7 and on a bi-Xeon 2.7GHz server. Libraries implementing the blur assessment method have been developed in Java, Python, PHP5 and MySQL5. For web applications, JavaScript, Ajax, JSON and Sockets were also used, as well as the Google Maps API. Aperio SVS files were converted into the Google Maps format using VIPS and Openslide libraries. We designed the Java library as a Service Provider Interface (SPI), extendable by third parties. Analysis is computed in real-time (3 billion pixels per minute). Tests were made on 5000 single images, 200 NDPI WSI, 100 Aperio SVS WSI converted to the Google Maps format. Applications based on our method and libraries can be used upstream, as calibration and quality control tool for the WSI acquisition systems, or as tools to reacquire tiles while the WSI is being scanned. They can also be used downstream to reacquire the complete slides that are below the quality threshold for surgical pathology analysis. WSI may also be displayed in a smarter way by sending and displaying the regions of highest quality before other regions. Such quality assessment scores could be integrated as WSI's metadata shared in clinical, research or teaching contexts, for a more efficient medical informatics workflow.

Towards better digital pathology workflows: programming libraries for high-speed sharpness assessment of Whole Slide Images

Science.gov (United States)

2014-01-01

Background Since microscopic slides can now be automatically digitized and integrated in the clinical workflow, quality assessment of Whole Slide Images (WSI) has become a crucial issue. We present a no-reference quality assessment method that has been thoroughly tested since 2010 and is under implementation in multiple sites, both public university-hospitals and private entities. It is part of the FlexMIm R&D project which aims to improve the global workflow of digital pathology. For these uses, we have developed two programming libraries, in Java and Python, which can be integrated in various types of WSI acquisition systems, viewers and image analysis tools. Methods Development and testing have been carried out on a MacBook Pro i7 and on a bi-Xeon 2.7GHz server. Libraries implementing the blur assessment method have been developed in Java, Python, PHP5 and MySQL5. For web applications, JavaScript, Ajax, JSON and Sockets were also used, as well as the Google Maps API. Aperio SVS files were converted into the Google Maps format using VIPS and Openslide libraries. Results We designed the Java library as a Service Provider Interface (SPI), extendable by third parties. Analysis is computed in real-time (3 billion pixels per minute). Tests were made on 5000 single images, 200 NDPI WSI, 100 Aperio SVS WSI converted to the Google Maps format. Conclusions Applications based on our method and libraries can be used upstream, as calibration and quality control tool for the WSI acquisition systems, or as tools to reacquire tiles while the WSI is being scanned. They can also be used downstream to reacquire the complete slides that are below the quality threshold for surgical pathology analysis. WSI may also be displayed in a smarter way by sending and displaying the regions of highest quality before other regions. Such quality assessment scores could be integrated as WSI's metadata shared in clinical, research or teaching contexts, for a more efficient medical informatics

e-BioFlow: improving practical use of workflow systems in bioinformatics

NARCIS (Netherlands)

Wassink, I.; Ooms, M.; Neerincx, P.; Rauwerda, H.; Leunissen, J.A.M.; Breit, T.M.; Nijholt, A.; Vet, van der P.

2010-01-01

Workflow management systems (WfMSs) are useful tools for bioinformaticians. As experiences with using WfMSs accumulate, shortcomings of current systems become apparent. In this paper, we focus on practical issues that hinder WfMS users and that arise in the design and execution of workflows, and in

VisTrails is an open-source scientific workflow and provenance management system

CSIR Research Space (South Africa)

Mthombeni, Thabo DM

2011-12-01

Full Text Available VisTrails is an open-source scientific workflow and provenance management system that provides support for simulations, data exploration and visualization. Whereas workflows have been traditionally used to automate repetitive tasks, for applications...

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.

Translating Unstructured Workflow Processes to Readable BPEL: Theory and Implementation

DEFF Research Database (Denmark)

van der Aalst, Willibrordus Martinus Pancratius; Lassen, Kristian Bisgaard

2008-01-01

and not easy to use by end-users. Therefore, we provide a mapping from Workflow Nets (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. In addition to this we have implemented the algorithm in a tool called...... WorkflowNet2BPEL4WS....

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...

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...

BIFI: a Taverna plugin for a simplified and user-friendly workflow platform.

Science.gov (United States)

Yildiz, Ahmet; Dilaveroglu, Erkan; Visne, Ilhami; Günay, Bilal; Sefer, Emrah; Weinhausel, Andreas; Rattay, Frank; Goble, Carole A; Pandey, Ram Vinay; Kriegner, Albert

2014-10-20

Heterogeneity in the features, input-output behaviour and user interface for available bioinformatics tools and services is still a bottleneck for both expert and non-expert users. Advancement in providing common interfaces over such tools and services are gaining interest among researchers. However, the lack of (meta-) information about input-output data and parameter prevents to provide automated and standardized solutions, which can assist users in setting the appropriate parameters. These limitations must be resolved especially in the workflow-based solution in order to ease the integration of software. We report a Taverna Workbench plugin: the XworX BIFI (Beautiful Interfaces for Inputs) implemented as a solution for the aforementioned issues. BIFI provides a Graphical User Interface (GUI) definition language used to layout the user interface and to define parameter options for Taverna workflows. BIFI is also able to submit GUI Definition Files (GDF) directly or discover appropriate instances from a configured repository. In the absence of a GDF, BIFI generates a default interface. The Taverna Workbench is an open source software providing the ability to combine various services within a workflow. Nevertheless, users can supply input data to the workflow via a simple user interface providing only a text area to enter the input in text form. The workflow may contain meta-information in human readable form such as description text for the port and an example value. However, not all workflow ports are documented so well or have all the required information.BIFI uses custom user interface components for ports which give users feedback on the parameter data type or structure to be used for service execution and enables client-side data validations. Moreover, BIFI offers user interfaces that allow users to interactively construct workflow views and share them with the community, thus significantly increasing usability of heterogeneous, distributed service

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

Exploring Two Approaches for an End-to-End Scientific Analysis Workflow

Science.gov (United States)

Dodelson, Scott; Kent, Steve; Kowalkowski, Jim; Paterno, Marc; Sehrish, Saba

2015-12-01

The scientific discovery process can be advanced by the integration of independently-developed programs run on disparate computing facilities into coherent workflows usable by scientists who are not experts in computing. For such advancement, we need a system which scientists can use to formulate analysis workflows, to integrate new components to these workflows, and to execute different components on resources that are best suited to run those components. In addition, we need to monitor the status of the workflow as components get scheduled and executed, and to access the intermediate and final output for visual exploration and analysis. Finally, it is important for scientists to be able to share their workflows with collaborators. We have explored two approaches for such an analysis framework for the Large Synoptic Survey Telescope (LSST) Dark Energy Science Collaboration (DESC); the first one is based on the use and extension of Galaxy, a web-based portal for biomedical research, and the second one is based on a programming language, Python. In this paper, we present a brief description of the two approaches, describe the kinds of extensions to the Galaxy system we have found necessary in order to support the wide variety of scientific analysis in the cosmology community, and discuss how similar efforts might be of benefit to the HEP community.

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.

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

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…

Create, run, share, publish, and reference your LC-MS, FIA-MS, GC-MS, and NMR data analysis workflows with the Workflow4Metabolomics 3.0 Galaxy online infrastructure for metabolomics.

Science.gov (United States)

Guitton, Yann; Tremblay-Franco, Marie; Le Corguillé, Gildas; Martin, Jean-François; Pétéra, Mélanie; Roger-Mele, Pierrick; Delabrière, Alexis; Goulitquer, Sophie; Monsoor, Misharl; Duperier, Christophe; Canlet, Cécile; Servien, Rémi; Tardivel, Patrick; Caron, Christophe; Giacomoni, Franck; Thévenot, Etienne A

2017-12-01

Metabolomics is a key approach in modern functional genomics and systems biology. Due to the complexity of metabolomics data, the variety of experimental designs, and the multiplicity of bioinformatics tools, providing experimenters with a simple and efficient resource to conduct comprehensive and rigorous analysis of their data is of utmost importance. In 2014, we launched the Workflow4Metabolomics (W4M; http://workflow4metabolomics.org) online infrastructure for metabolomics built on the Galaxy environment, which offers user-friendly features to build and run data analysis workflows including preprocessing, statistical analysis, and annotation steps. Here we present the new W4M 3.0 release, which contains twice as many tools as the first version, and provides two features which are, to our knowledge, unique among online resources. First, data from the four major metabolomics technologies (i.e., LC-MS, FIA-MS, GC-MS, and NMR) can be analyzed on a single platform. By using three studies in human physiology, alga evolution, and animal toxicology, we demonstrate how the 40 available tools can be easily combined to address biological issues. Second, the full analysis (including the workflow, the parameter values, the input data and output results) can be referenced with a permanent digital object identifier (DOI). Publication of data analyses is of major importance for robust and reproducible science. Furthermore, the publicly shared workflows are of high-value for e-learning and training. The Workflow4Metabolomics 3.0 e-infrastructure thus not only offers a unique online environment for analysis of data from the main metabolomics technologies, but it is also the first reference repository for metabolomics workflows. Copyright © 2017 Elsevier Ltd. All rights reserved.

Formalizing an integrative, multidisciplinary cancer therapy discovery workflow

Science.gov (United States)

McGuire, Mary F.; Enderling, Heiko; Wallace, Dorothy I.; Batra, Jaspreet; Jordan, Marie; Kumar, Sushil; Panetta, John C.; Pasquier, Eddy

2014-01-01

Although many clinicians and researchers work to understand cancer, there has been limited success to effectively combine forces and collaborate over time, distance, data and budget constraints. Here we present a workflow template for multidisciplinary cancer therapy that was developed during the 2nd Annual Workshop on Cancer Systems Biology sponsored by Tufts University, Boston, MA in July 2012. The template was applied to the development of a metronomic therapy backbone for neuroblastoma. Three primary groups were identified: clinicians, biologists, and scientists (mathematicians, computer scientists, physicists and engineers). The workflow described their integrative interactions; parallel or sequential processes; data sources and computational tools at different stages as well as the iterative nature of therapeutic development from clinical observations to in vitro, in vivo, and clinical trials. We found that theoreticians in dialog with experimentalists could develop calibrated and parameterized predictive models that inform and formalize sets of testable hypotheses, thus speeding up discovery and validation while reducing laboratory resources and costs. The developed template outlines an interdisciplinary collaboration workflow designed to systematically investigate the mechanistic underpinnings of a new therapy and validate that therapy to advance development and clinical acceptance. PMID:23955390

Improved compliance by BPM-driven workflow automation.

Science.gov (United States)

Holzmüller-Laue, Silke; Göde, Bernd; Fleischer, Heidi; Thurow, Kerstin

2014-12-01

Using methods and technologies of business process management (BPM) for the laboratory automation has important benefits (i.e., the agility of high-level automation processes, rapid interdisciplinary prototyping and implementation of laboratory tasks and procedures, and efficient real-time process documentation). A principal goal of the model-driven development is the improved transparency of processes and the alignment of process diagrams and technical code. First experiences of using the business process model and notation (BPMN) show that easy-to-read graphical process models can achieve and provide standardization of laboratory workflows. The model-based development allows one to change processes quickly and an easy adaption to changing requirements. The process models are able to host work procedures and their scheduling in compliance with predefined guidelines and policies. Finally, the process-controlled documentation of complex workflow results addresses modern laboratory needs of quality assurance. BPMN 2.0 as an automation language to control every kind of activity or subprocess is directed to complete workflows in end-to-end relationships. BPMN is applicable as a system-independent and cross-disciplinary graphical language to document all methods in laboratories (i.e., screening procedures or analytical processes). That means, with the BPM standard, a communication method of sharing process knowledge of laboratories is also available. © 2014 Society for Laboratory Automation and Screening.

PGen: large-scale genomic variations analysis workflow and browser in SoyKB.

Science.gov (United States)

Liu, Yang; Khan, Saad M; Wang, Juexin; Rynge, Mats; Zhang, Yuanxun; Zeng, Shuai; Chen, Shiyuan; Maldonado Dos Santos, Joao V; Valliyodan, Babu; Calyam, Prasad P; Merchant, Nirav; Nguyen, Henry T; Xu, Dong; Joshi, Trupti

2016-10-06

With the advances in next-generation sequencing (NGS) technology and significant reductions in sequencing costs, it is now possible to sequence large collections of germplasm in crops for detecting genome-scale genetic variations and to apply the knowledge towards improvements in traits. To efficiently facilitate large-scale NGS resequencing data analysis of genomic variations, we have developed "PGen", an integrated and optimized workflow using the Extreme Science and Engineering Discovery Environment (XSEDE) high-performance computing (HPC) virtual system, iPlant cloud data storage resources and Pegasus workflow management system (Pegasus-WMS). The workflow allows users to identify single nucleotide polymorphisms (SNPs) and insertion-deletions (indels), perform SNP annotations and conduct copy number variation analyses on multiple resequencing datasets in a user-friendly and seamless way. We have developed both a Linux version in GitHub ( https://github.com/pegasus-isi/PGen-GenomicVariations-Workflow ) and a web-based implementation of the PGen workflow integrated within the Soybean Knowledge Base (SoyKB), ( http://soykb.org/Pegasus/index.php ). Using PGen, we identified 10,218,140 single-nucleotide polymorphisms (SNPs) and 1,398,982 indels from analysis of 106 soybean lines sequenced at 15X coverage. 297,245 non-synonymous SNPs and 3330 copy number variation (CNV) regions were identified from this analysis. SNPs identified using PGen from additional soybean resequencing projects adding to 500+ soybean germplasm lines in total have been integrated. These SNPs are being utilized for trait improvement using genotype to phenotype prediction approaches developed in-house. In order to browse and access NGS data easily, we have also developed an NGS resequencing data browser ( http://soykb.org/NGS_Resequence/NGS_index.php ) within SoyKB to provide easy access to SNP and downstream analysis results for soybean researchers. PGen workflow has been optimized for the most

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.

Inter-observer reliability assessments in time motion studies: the foundation for meaningful clinical workflow analysis.

Science.gov (United States)

Lopetegui, Marcelo A; Bai, Shasha; Yen, Po-Yin; Lai, Albert; Embi, Peter; Payne, Philip R O

2013-01-01

Understanding clinical workflow is critical for researchers and healthcare decision makers. Current workflow studies tend to oversimplify and underrepresent the complexity of clinical workflow. Continuous observation time motion studies (TMS) could enhance clinical workflow studies by providing rich quantitative data required for in-depth workflow analyses. However, methodological inconsistencies have been reported in continuous observation TMS, potentially reducing the validity of TMS' data and limiting their contribution to the general state of knowledge. We believe that a cornerstone in standardizing TMS is to ensure the reliability of the human observers. In this manuscript we review the approaches for inter-observer reliability assessment (IORA) in a representative sample of TMS focusing on clinical workflow. We found that IORA is an uncommon practice, inconsistently reported, and often uses methods that provide partial and overestimated measures of agreement. Since a comprehensive approach to IORA is yet to be proposed and validated, we provide initial recommendations for IORA reporting in continuous observation TMS.

BIM Workflow for Mechanical Ventilation Design : Object-Based Modeling with Autodesk Revit®

OpenAIRE

Bonduel, Mathias

2016-01-01

This study is conducted for the Belgian engineering firm CENERGIE, whose main business activities are within the fields of building systems and sustainable buildings. The company wants to change their current design workflows to adapt the use of Building Information Modeling (BIM) with Autodesk Revit The research focused on the development of a BIM workflow where no models are exchanged between building partners. The aim of this study was to develop such a Revit BIM workflow for the desig...

Soundness of Timed-Arc Workflow Nets

DEFF Research Database (Denmark)

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

2014-01-01

, 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....

Workflow for high-content, individual cell quantification of fluorescent markers from universal microscope data, supported by open source software.

Science.gov (United States)

Stockwell, Simon R; Mittnacht, Sibylle

2014-12-16

Advances in understanding the control mechanisms governing the behavior of cells in adherent mammalian tissue culture models are becoming increasingly dependent on modes of single-cell analysis. Methods which deliver composite data reflecting the mean values of biomarkers from cell populations risk losing subpopulation dynamics that reflect the heterogeneity of the studied biological system. In keeping with this, traditional approaches are being replaced by, or supported with, more sophisticated forms of cellular assay developed to allow assessment by high-content microscopy. These assays potentially generate large numbers of images of fluorescent biomarkers, which enabled by accompanying proprietary software packages, allows for multi-parametric measurements per cell. However, the relatively high capital costs and overspecialization of many of these devices have prevented their accessibility to many investigators. Described here is a universally applicable workflow for the quantification of multiple fluorescent marker intensities from specific subcellular regions of individual cells suitable for use with images from most fluorescent microscopes. Key to this workflow is the implementation of the freely available Cell Profiler software(1) to distinguish individual cells in these images, segment them into defined subcellular regions and deliver fluorescence marker intensity values specific to these regions. The extraction of individual cell intensity values from image data is the central purpose of this workflow and will be illustrated with the analysis of control data from a siRNA screen for G1 checkpoint regulators in adherent human cells. However, the workflow presented here can be applied to analysis of data from other means of cell perturbation (e.g., compound screens) and other forms of fluorescence based cellular markers and thus should be useful for a wide range of laboratories.

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.

Improving Radiology Workflow with Automated Examination Tracking and Alerts.

Science.gov (United States)

Pianykh, Oleg S; Jaworsky, Christina; Shore, M T; Rosenthal, Daniel I

2017-07-01

The modern radiology workflow is a production line where imaging examinations pass in sequence through many steps. In busy clinical environments, even a minor delay in any step can propagate through the system and significantly lengthen the examination process. This is particularly true for the tasks delegated to the human operators, who may be distracted or stressed. We have developed an application to track examinations through a critical part of the workflow, from the image-acquisition scanners to the PACS archive. Our application identifies outliers and actively alerts radiology managers about the need to resolve these problems as soon as they happen. In this study, we investigate how this real-time tracking and alerting affected the speed of examination delivery to the radiologist. We demonstrate that active alerting produced a 3-fold reduction of examination-to-PACS delays. Additionally, we discover an overall improvement in examination-to-PACS delivery, evidence that the tracking and alerts instill a culture where timely processing is essential. By providing supervisors with information about exactly where delays emerge in their workflow and alerting the correct staff to take action, applications like ours create more robust radiology workflow with predictable, timely outcomes. Copyright © 2017 American College of Radiology. Published by Elsevier Inc. All rights reserved.

A reliable computational workflow for the selection of optimal screening libraries.

Science.gov (United States)

Gilad, Yocheved; Nadassy, Katalin; Senderowitz, Hanoch

2015-01-01

The experimental screening of compound collections is a common starting point in many drug discovery projects. Successes of such screening campaigns critically depend on the quality of the screened library. Many libraries are currently available from different vendors yet the selection of the optimal screening library for a specific project is challenging. We have devised a novel workflow for the rational selection of project-specific screening libraries. The workflow accepts as input a set of virtual candidate libraries and applies the following steps to each library: (1) data curation; (2) assessment of ADME/T profile; (3) assessment of the number of promiscuous binders/frequent HTS hitters; (4) assessment of internal diversity; (5) assessment of similarity to known active compound(s) (optional); (6) assessment of similarity to in-house or otherwise accessible compound collections (optional). For ADME/T profiling, Lipinski's and Veber's rule-based filters were implemented and a new blood brain barrier permeation model was developed and validated (85 and 74 % success rate for training set and test set, respectively). Diversity and similarity descriptors which demonstrated best performances in terms of their ability to select either diverse or focused sets of compounds from three databases (Drug Bank, CMC and CHEMBL) were identified and used for diversity and similarity assessments. The workflow was used to analyze nine common screening libraries available from six vendors. The results of this analysis are reported for each library providing an assessment of its quality. Furthermore, a consensus approach was developed to combine the results of these analyses into a single score for selecting the optimal library under different scenarios. We have devised and tested a new workflow for the rational selection of screening libraries under different scenarios. The current workflow was implemented using the Pipeline Pilot software yet due to the usage of generic

An observation tool for studying patient-oriented workflow in hospital emergency departments.

Science.gov (United States)

Ozkaynak, M; Brennan, P

2013-01-01

Studying workflow is a critical step in designing, implementing and evaluating informatics interventions in complex sociotechnical settings, such as hospital emergency departments (EDs). Known approaches to studying workflow in clinical settings attend to the activities of individual clinicians, thus being inadequate to characterize patient care as a cooperative work. The purpose of this paper is twofold. First, we introduce a novel, theory-driven patient-oriented workflow methodology, which better addresses the complex, multiple-provider nature of patient care. Second, we report the development of an observational tool and protocol for use in studies of this type, and the results of an evaluation study. We created a tablet computer implementation of an instrument to efficiently capture patient-oriented workflow, and evaluated it through a field study in three EDs. We focused on activities occurring over time during a single patient care episode as well as the roles of the ED staff members who conducted the activities. The evidence generated supports the validity, viability, and reliability of the tool. The coverage of the tool in terms of activities and roles was satisfactory. The tool was able to capture the sequence of activity-role pairs for 108 patient care episodes. The inter-rater reliability assessment yielded a high kappa value (0.79). The patient-oriented workflow methodology has the potential to facilitate modeling patient care in EDs by characterizing both roles and activities in sequence. The methodology also provides researchers and practitioners a more realistic and comprehensive workflow perspective that can inform the design, implementation and evaluation of health information technology interventions.

A data model for analyzing user collaborations in workflow-driven e-Science

NARCIS (Netherlands)

Altintas, I.; Anand, M.K.; Vuong, T.N.; Bowers, S.; Ludäscher, B.; Sloot, P.M.A.

2011-01-01

Scientific discoveries are often the result of methodical execution of many interrelated scientific workflows, where workflows and datasets published by one set of users can be used by other users to perform subsequent analyses, leading to implicit or explicit collaboration. In this paper, we

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-t...

Optimization of business processes in banks through flexible workflow

Science.gov (United States)

Postolache, V.

2017-08-01

This article describes an integrated business model of a commercial bank. There are examples of components that go into its composition: wooden models and business processes, strategic goals, organizational structure, system architecture, operational and marketing risk models, etc. The practice has shown that the development and implementation of the integrated business model of the bank significantly increase operating efficiency and its management, ensures organizational and technology stable development. Considering the evolution of business processes in the banking sector, should be analysed their common characteristics. From the author’s point of view, a business process is a set of various activities of a commercial bank in which “Input” is one or more financial and material resources, as a result of this activity and “output” is created by banking product, which is some value to consumer. Using workflow technology, management business process efficiency issue is a matter of managing the integration of resources and sequence of actions aimed at achieving this goal. In turn, it implies management of jobs or functions’ interaction, synchronizing of the assignments periods, reducing delays in the transmission of the results etc. Workflow technology is very important for managers at all levels, as they can use it to easily strengthen the control over what is happening in a particular unit, and in the bank as a whole. The manager is able to plan, to implement rules, to interact within the framework of the company’s procedures and tasks entrusted to the system of the distribution function and execution control, alert on the implementation and issuance of the statistical data on the effectiveness of operating procedures. Development and active use of the integrated bank business model is one of the key success factors that contribute to long-term and stable development of the bank, increase employee efficiency and business processes, implement the

Automatic Integration Testbeds validation on Open Science Grid

International Nuclear Information System (INIS)

Caballero, J; Potekhin, M; Thapa, S; Gardner, R

2011-01-01

A recurring challenge in deploying high quality production middleware is the extent to which realistic testing occurs before release of the software into the production environment. We describe here an automated system for validating releases of the Open Science Grid software stack that leverages the (pilot-based) PanDA job management system developed and used by the ATLAS experiment. The system was motivated by a desire to subject the OSG Integration Testbed to more realistic validation tests. In particular those which resemble to every extent possible actual job workflows used by the experiments thus utilizing job scheduling at the compute element (CE), use of the worker node execution environment, transfer of data to/from the local storage element (SE), etc. The context is that candidate releases of OSG compute and storage elements can be tested by injecting large numbers of synthetic jobs varying in complexity and coverage of services tested. The native capabilities of the PanDA system can thus be used to define jobs, monitor their execution, and archive the resulting run statistics including success and failure modes. A repository of generic workflows and job types to measure various metrics of interest has been created. A command-line toolset has been developed so that testbed managers can quickly submit 'VO-like' jobs into the system when newly deployed services are ready for testing. A system for automatic submission has been crafted to send jobs to integration testbed sites, collecting the results in a central service and generating regular reports for performance and reliability.

Automatic Integration Testbeds validation on Open Science Grid

Science.gov (United States)

Caballero, J.; Thapa, S.; Gardner, R.; Potekhin, M.

2011-12-01

A recurring challenge in deploying high quality production middleware is the extent to which realistic testing occurs before release of the software into the production environment. We describe here an automated system for validating releases of the Open Science Grid software stack that leverages the (pilot-based) PanDA job management system developed and used by the ATLAS experiment. The system was motivated by a desire to subject the OSG Integration Testbed to more realistic validation tests. In particular those which resemble to every extent possible actual job workflows used by the experiments thus utilizing job scheduling at the compute element (CE), use of the worker node execution environment, transfer of data to/from the local storage element (SE), etc. The context is that candidate releases of OSG compute and storage elements can be tested by injecting large numbers of synthetic jobs varying in complexity and coverage of services tested. The native capabilities of the PanDA system can thus be used to define jobs, monitor their execution, and archive the resulting run statistics including success and failure modes. A repository of generic workflows and job types to measure various metrics of interest has been created. A command-line toolset has been developed so that testbed managers can quickly submit "VO-like" jobs into the system when newly deployed services are ready for testing. A system for automatic submission has been crafted to send jobs to integration testbed sites, collecting the results in a central service and generating regular reports for performance and reliability.

A standard-enabled workflow for synthetic biology

KAUST Repository

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

2017-01-01

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

Multi-Objective Approach for Energy-Aware Workflow Scheduling in Cloud Computing Environments

Directory of Open Access Journals (Sweden)

Sonia Yassa

2013-01-01

Full Text Available We address the problem of scheduling workflow applications on heterogeneous computing systems like cloud computing infrastructures. In general, the cloud workflow scheduling is a complex optimization problem which requires considering different criteria so as to meet a large number of QoS (Quality of Service requirements. Traditional research in workflow scheduling mainly focuses on the optimization constrained by time or cost without paying attention to energy consumption. The main contribution of this study is to propose a new approach for multi-objective workflow scheduling in clouds, and present the hybrid PSO algorithm to optimize the scheduling performance. Our method is based on the Dynamic Voltage and Frequency Scaling (DVFS technique to minimize energy consumption. This technique allows processors to operate in different voltage supply levels by sacrificing clock frequencies. This multiple voltage involves a compromise between the quality of schedules and energy. Simulation results on synthetic and real-world scientific applications highlight the robust performance of the proposed approach.

Multi-Objective Approach for Energy-Aware Workflow Scheduling in Cloud Computing Environments

Science.gov (United States)

Kadima, Hubert; Granado, Bertrand

2013-01-01

We address the problem of scheduling workflow applications on heterogeneous computing systems like cloud computing infrastructures. In general, the cloud workflow scheduling is a complex optimization problem which requires considering different criteria so as to meet a large number of QoS (Quality of Service) requirements. Traditional research in workflow scheduling mainly focuses on the optimization constrained by time or cost without paying attention to energy consumption. The main contribution of this study is to propose a new approach for multi-objective workflow scheduling in clouds, and present the hybrid PSO algorithm to optimize the scheduling performance. Our method is based on the Dynamic Voltage and Frequency Scaling (DVFS) technique to minimize energy consumption. This technique allows processors to operate in different voltage supply levels by sacrificing clock frequencies. This multiple voltage involves a compromise between the quality of schedules and energy. Simulation results on synthetic and real-world scientific applications highlight the robust performance of the proposed approach. PMID:24319361

AutoDrug: fully automated macromolecular crystallography workflows for fragment-based drug discovery

International Nuclear Information System (INIS)

Tsai, Yingssu; McPhillips, Scott E.; González, Ana; McPhillips, Timothy M.; Zinn, Daniel; Cohen, Aina E.; Feese, Michael D.; Bushnell, David; Tiefenbrunn, Theresa; Stout, C. David; Ludaescher, Bertram; Hedman, Britt; Hodgson, Keith O.; Soltis, S. Michael

2013-01-01

New software has been developed for automating the experimental and data-processing stages of fragment-based drug discovery at a macromolecular crystallography beamline. A new workflow-automation framework orchestrates beamline-control and data-analysis software while organizing results from multiple samples. AutoDrug is software based upon the scientific workflow paradigm that integrates the Stanford Synchrotron Radiation Lightsource macromolecular crystallography beamlines and third-party processing software to automate the crystallography steps of the fragment-based drug-discovery process. AutoDrug screens a cassette of fragment-soaked crystals, selects crystals for data collection based on screening results and user-specified criteria and determines optimal data-collection strategies. It then collects and processes diffraction data, performs molecular replacement using provided models and detects electron density that is likely to arise from bound fragments. All processes are fully automated, i.e. are performed without user interaction or supervision. Samples can be screened in groups corresponding to particular proteins, crystal forms and/or soaking conditions. A single AutoDrug run is only limited by the capacity of the sample-storage dewar at the beamline: currently 288 samples. AutoDrug was developed in conjunction with RestFlow, a new scientific workflow-automation framework. RestFlow simplifies the design of AutoDrug by managing the flow of data and the organization of results and by orchestrating the execution of computational pipeline steps. It also simplifies the execution and interaction of third-party programs and the beamline-control system. Modeling AutoDrug as a scientific workflow enables multiple variants that meet the requirements of different user groups to be developed and supported. A workflow tailored to mimic the crystallography stages comprising the drug-discovery pipeline of CoCrystal Discovery Inc. has been deployed and successfully

Differentiated protection services with failure probability guarantee for workflow-based applications

Science.gov (United States)

Zhong, Yaoquan; Guo, Wei; Jin, Yaohui; Sun, Weiqiang; Hu, Weisheng

2010-12-01

A cost-effective and service-differentiated provisioning strategy is very desirable to service providers so that they can offer users satisfactory services, while optimizing network resource allocation. Providing differentiated protection services to connections for surviving link failure has been extensively studied in recent years. However, the differentiated protection services for workflow-based applications, which consist of many interdependent tasks, have scarcely been studied. This paper investigates the problem of providing differentiated services for workflow-based applications in optical grid. In this paper, we develop three differentiated protection services provisioning strategies which can provide security level guarantee and network-resource optimization for workflow-based applications. The simulation demonstrates that these heuristic algorithms provide protection cost-effectively while satisfying the applications' failure probability requirements.

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

IT-benchmarking of clinical workflows: concept, implementation, and evaluation.

Science.gov (United States)

Thye, Johannes; Straede, Matthias-Christopher; Liebe, Jan-David; Hübner, Ursula

2014-01-01

Due to the emerging evidence of health IT as opportunity and risk for clinical workflows, health IT must undergo a continuous measurement of its efficacy and efficiency. IT-benchmarks are a proven means for providing this information. The aim of this study was to enhance the methodology of an existing benchmarking procedure by including, in particular, new indicators of clinical workflows and by proposing new types of visualisation. Drawing on the concept of information logistics, we propose four workflow descriptors that were applied to four clinical processes. General and specific indicators were derived from these descriptors and processes. 199 chief information officers (CIOs) took part in the benchmarking. These hospitals were assigned to reference groups of a similar size and ownership from a total of 259 hospitals. Stepwise and comprehensive feedback was given to the CIOs. Most participants who evaluated the benchmark rated the procedure as very good, good, or rather good (98.4%). Benchmark information was used by CIOs for getting a general overview, advancing IT, preparing negotiations with board members, and arguing for a new IT project.

Automated quality control in a file-based broadcasting workflow

Science.gov (United States)

Zhang, Lina

2014-04-01

Benefit from the development of information and internet technologies, television broadcasting is transforming from inefficient tape-based production and distribution to integrated file-based workflows. However, no matter how many changes have took place, successful broadcasting still depends on the ability to deliver a consistent high quality signal to the audiences. After the transition from tape to file, traditional methods of manual quality control (QC) become inadequate, subjective, and inefficient. Based on China Central Television's full file-based workflow in the new site, this paper introduces an automated quality control test system for accurate detection of hidden troubles in media contents. It discusses the system framework and workflow control when the automated QC is added. It puts forward a QC criterion and brings forth a QC software followed this criterion. It also does some experiments on QC speed by adopting parallel processing and distributed computing. The performance of the test system shows that the adoption of automated QC can make the production effective and efficient, and help the station to achieve a competitive advantage in the media market.

Implementation of a Workflow Management System for Non-Expert Users

DEFF Research Database (Denmark)

Jongejan, Bart

2016-01-01

tools, the CLARIN-DK workflow management system (WMS) computes combinations of tools that will give the desired result. This advanced functionality was originally not envisaged, but came within reach by writing the WMS partly in Java and partly in a programming language for symbolic computation, Bracmat....... Handling LT tool profiles, including the computation of workflows, is easier with Bracmat's language constructs for tree pattern matching and tree construction than with the language constructs offered by mainstream programming languages....

Routine digital pathology workflow: The Catania experience

Directory of Open Access Journals (Sweden)

Filippo Fraggetta

2017-01-01

Full Text Available Introduction: Successful implementation of whole slide imaging (WSI for routine clinical practice has been accomplished in only a few pathology laboratories worldwide. We report the transition to an effective and complete digital surgical pathology workflow in the pathology laboratory at Cannizzaro Hospital in Catania, Italy. Methods: All (100% permanent histopathology glass slides were digitized at ×20 using Aperio AT2 scanners. Compatible stain and scanning slide racks were employed to streamline operations. eSlide Manager software was bidirectionally interfaced with the anatomic pathology laboratory information system. Virtual slide trays connected to the two-dimensional (2D barcode tracking system allowed pathologists to confirm that they were correctly assigned slides and that all tissues on these glass slides were scanned. Results: Over 115,000 glass slides were digitized with a scan fail rate of around 1%. Drying glass slides before scanning minimized them sticking to scanner racks. Implementation required introduction of a 2D barcode tracking system and modification of histology workflow processes. Conclusion: Our experience indicates that effective adoption of WSI for primary diagnostic use was more dependent on optimizing preimaging variables and integration with the laboratory information system than on information technology infrastructure and ensuring pathologist buy-in. Implementation of digital pathology for routine practice not only leveraged the benefits of digital imaging but also creates an opportunity for establishing standardization of workflow processes in the pathology laboratory.

Collaborative e-Science Experiments and Scientific Workflows

NARCIS (Netherlands)

Belloum, A.; Inda, M.A.; Vasunin, D.; Korkhov, V.; Zhao, Z.; Rauwerda, H.; Breit, T.M.; Bubak, M.; Hertzberger, L.O.

2011-01-01

Recent advances in Internet and grid technologies have greatly enhanced scientific experiments' life cycle. In addition to compute- and data-intensive tasks, large-scale collaborations involving geographically distributed scientists and e-infrastructure are now possible. Scientific workflows, which

A Strategy for an MLS Workflow Management System

National Research Council Canada - National Science Library

Kang, Myong H; Froscher, Judith N; Eppinger, Brian J; Moskowitz, Ira S

1999-01-01

.... Therefore, DoD needs MLS workflow management systems (WFMS) to enable globally distributed users and existing applications to cooperate across classification domains to achieve mission critical goals...

Widening the adoption of workflows to include human and human-machine scientific processes

Science.gov (United States)

Salayandia, L.; Pinheiro da Silva, P.; Gates, A. Q.

2010-12-01

Scientific workflows capture knowledge in the form of technical recipes to access and manipulate data that help scientists manage and reuse established expertise to conduct their work. Libraries of scientific workflows are being created in particular fields, e.g., Bioinformatics, where combined with cyber-infrastructure environments that provide on-demand access to data and tools, result in powerful workbenches for scientists of those communities. The focus in these particular fields, however, has been more on automating rather than documenting scientific processes. As a result, technical barriers have impeded a wider adoption of scientific workflows by scientific communities that do not rely as heavily on cyber-infrastructure and computing environments. Semantic Abstract Workflows (SAWs) are introduced to widen the applicability of workflows as a tool to document scientific recipes or processes. SAWs intend to capture a scientists’ perspective about the process of how she or he would collect, filter, curate, and manipulate data to create the artifacts that are relevant to her/his work. In contrast, scientific workflows describe the process from the point of view of how technical methods and tools are used to conduct the work. By focusing on a higher level of abstraction that is closer to a scientist’s understanding, SAWs effectively capture the controlled vocabularies that reflect a particular scientific community, as well as the types of datasets and methods used in a particular domain. From there on, SAWs provide the flexibility to adapt to different environments to carry out the recipes or processes. These environments range from manual fieldwork to highly technical cyber-infrastructure environments, i.e., such as those already supported by scientific workflows. Two cases, one from Environmental Science and another from Geophysics, are presented as illustrative examples.

Flexible Data-Aware Scheduling for Workflows over an In-Memory Object Store

Energy Technology Data Exchange (ETDEWEB)

Duro, Francisco Rodrigo; Garcia Blas, Javier; Isaila, Florin; Wozniak, Justin M.; Carretero, Jesus; Ross, Rob

2016-01-01

This paper explores novel techniques for improving the performance of many-task workflows based on the Swift scripting language. We propose novel programmer options for automated distributed data placement and task scheduling. These options trigger a data placement mechanism used for distributing intermediate workflow data over the servers of Hercules, a distributed key-value store that can be used to cache file system data. We demonstrate that these new mechanisms can significantly improve the aggregated throughput of many-task workflows with up to 86x, reduce the contention on the shared file system, exploit the data locality, and trade off locality and load balance.

Implementation of workflow engine technology to deliver basic clinical decision support functionality.

Science.gov (United States)

Huser, Vojtech; Rasmussen, Luke V; Oberg, Ryan; Starren, Justin B

2011-04-10

Workflow engine technology represents a new class of software with the ability to graphically model step-based knowledge. We present application of this novel technology to the domain of clinical decision support. Successful implementation of decision support within an electronic health record (EHR) remains an unsolved research challenge. Previous research efforts were mostly based on healthcare-specific representation standards and execution engines and did not reach wide adoption. We focus on two challenges in decision support systems: the ability to test decision logic on retrospective data prior prospective deployment and the challenge of user-friendly representation of clinical logic. We present our implementation of a workflow engine technology that addresses the two above-described challenges in delivering clinical decision support. Our system is based on a cross-industry standard of XML (extensible markup language) process definition language (XPDL). The core components of the system are a workflow editor for modeling clinical scenarios and a workflow engine for execution of those scenarios. We demonstrate, with an open-source and publicly available workflow suite, that clinical decision support logic can be executed on retrospective data. The same flowchart-based representation can also function in a prospective mode where the system can be integrated with an EHR system and respond to real-time clinical events. We limit the scope of our implementation to decision support content generation (which can be EHR system vendor independent). We do not focus on supporting complex decision support content delivery mechanisms due to lack of standardization of EHR systems in this area. We present results of our evaluation of the flowchart-based graphical notation as well as architectural evaluation of our implementation using an established evaluation framework for clinical decision support architecture. We describe an implementation of a free workflow technology

Implementation of workflow engine technology to deliver basic clinical decision support functionality

Science.gov (United States)

2011-01-01

Background Workflow engine technology represents a new class of software with the ability to graphically model step-based knowledge. We present application of this novel technology to the domain of clinical decision support. Successful implementation of decision support within an electronic health record (EHR) remains an unsolved research challenge. Previous research efforts were mostly based on healthcare-specific representation standards and execution engines and did not reach wide adoption. We focus on two challenges in decision support systems: the ability to test decision logic on retrospective data prior prospective deployment and the challenge of user-friendly representation of clinical logic. Results We present our implementation of a workflow engine technology that addresses the two above-described challenges in delivering clinical decision support. Our system is based on a cross-industry standard of XML (extensible markup language) process definition language (XPDL). The core components of the system are a workflow editor for modeling clinical scenarios and a workflow engine for execution of those scenarios. We demonstrate, with an open-source and publicly available workflow suite, that clinical decision support logic can be executed on retrospective data. The same flowchart-based representation can also function in a prospective mode where the system can be integrated with an EHR system and respond to real-time clinical events. We limit the scope of our implementation to decision support content generation (which can be EHR system vendor independent). We do not focus on supporting complex decision support content delivery mechanisms due to lack of standardization of EHR systems in this area. We present results of our evaluation of the flowchart-based graphical notation as well as architectural evaluation of our implementation using an established evaluation framework for clinical decision support architecture. Conclusions We describe an implementation of

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.

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.

modeling workflow management in a distributed computing system

African Journals Online (AJOL)

Dr Obe

communication system, which allows for computerized support. ... Keywords: Distributed computing system; Petri nets;Workflow management. 1. ... A distributed operating system usually .... the questionnaire is returned with invalid data,.

Addressing informatics challenges in Translational Research with workflow technology.

Science.gov (United States)

Beaulah, Simon A; Correll, Mick A; Munro, Robin E J; Sheldon, Jonathan G

2008-09-01

Interest in Translational Research has been growing rapidly in recent years. In this collision of different data, technologies and cultures lie tremendous opportunities for the advancement of science and business for organisations that are able to integrate, analyse and deliver this information effectively to users. Workflow-based integration and analysis systems are becoming recognised as a fast and flexible way to build applications that are tailored to scientific areas, yet are built on a common platform. Workflow systems are allowing organisations to meet the key informatics challenges in Translational Research and improve disease understanding and patient care.

An automated analysis workflow for optimization of force-field parameters using neutron scattering data

Energy Technology Data Exchange (ETDEWEB)

Lynch, Vickie E.; Borreguero, Jose M. [Neutron Data Analysis & Visualization Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831 (United States); Bhowmik, Debsindhu [Computational Sciences & Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831 (United States); Ganesh, Panchapakesan; Sumpter, Bobby G. [Center for Nanophase Material Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37831 (United States); Computational Sciences & Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831 (United States); Proffen, Thomas E. [Neutron Data Analysis & Visualization Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831 (United States); Goswami, Monojoy, E-mail: goswamim@ornl.gov [Center for Nanophase Material Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37831 (United States); Computational Sciences & Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831 (United States)

2017-07-01

Graphical abstract: - Highlights: • An automated workflow to optimize force-field parameters. • Used the workflow to optimize force-field parameter for a system containing nanodiamond and tRNA. • The mechanism relies on molecular dynamics simulation and neutron scattering experimental data. • The workflow can be generalized to any other experimental and simulation techniques. - Abstract: Large-scale simulations and data analysis are often required to explain neutron scattering experiments to establish a connection between the fundamental physics at the nanoscale and data probed by neutrons. However, to perform simulations at experimental conditions it is critical to use correct force-field (FF) parameters which are unfortunately not available for most complex experimental systems. In this work, we have developed a workflow optimization technique to provide optimized FF parameters by comparing molecular dynamics (MD) to neutron scattering data. We describe the workflow in detail by using an example system consisting of tRNA and hydrophilic nanodiamonds in a deuterated water (D{sub 2}O) environment. Quasi-elastic neutron scattering (QENS) data show a faster motion of the tRNA in the presence of nanodiamond than without the ND. To compare the QENS and MD results quantitatively, a proper choice of FF parameters is necessary. We use an efficient workflow to optimize the FF parameters between the hydrophilic nanodiamond and water by comparing to the QENS data. Our results show that we can obtain accurate FF parameters by using this technique. The workflow can be generalized to other types of neutron data for FF optimization, such as vibrational spectroscopy and spin echo.

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

Automatic generation of 2D micromechanical finite element model of silicon–carbide/aluminum metal matrix composites: Effects of the boundary conditions

DEFF Research Database (Denmark)

Qing, Hai

2013-01-01

Two-dimensional finite element (FE) simulations of the deformation and damage evolution of Silicon–Carbide (SiC) particle reinforced aluminum alloy composite including interphase are carried out for different microstructures and particle volume fractions of the composites. A program is developed...... for the automatic generation of 2D micromechanical FE-models with randomly distributed SiC particles. In order to simulate the damage process in aluminum alloy matrix and SiC particles, a damage parameter based on the stress triaxial indicator and the maximum principal stress criterion based elastic brittle damage...... model are developed within Abaqus/Standard Subroutine USDFLD, respectively. An Abaqus/Standard Subroutine MPC, which allows defining multi-point constraints, is developed to realize the symmetric boundary condition (SBC) and periodic boundary condition (PBC). A series of computational experiments...

Distributed interoperable workflow support for electronic commerce

NARCIS (Netherlands)

Papazoglou, M.; Jeusfeld, M.A.; Weigand, H.; Jarke, M.

1998-01-01

Abstract. This paper describes a flexible distributed transactional workflow environment based on an extensible object-oriented framework built around class libraries, application programming interfaces, and shared services. The purpose of this environment is to support a range of EC-like business

SU-F-T-252: An Investigation of Gamma Knife Frame Definition Error When Using a Pre-Planning Workflow

International Nuclear Information System (INIS)

Johnson, P

2016-01-01

Purpose: To determine causal factors related to high frame definition error when treating GK patients using a pre-planning workflow. Methods: 160 cases were retrospectively reviewed. All patients received treatment using a pre-planning workflow whereby stereotactic coordinates are determined from a CT scan acquired after framing using a fiducial box. The planning software automatically detects the fiducials and compares their location to expected values based on the rigid design of the fiducial system. Any difference is reported as mean and maximum frame definition error. The manufacturer recommends these values be less than 1.0 mm and 1.5 mm. In this study, frame definition error was analyzed in comparison with a variety of factors including which neurosurgeon/oncologist/physicist was involved with the procedure, number of post used during framing (3 or 4), type of lesion, and which CT scanner was utilized for acquisition. An analysis of variance (ANOVA) approach was used to statistically evaluate the data and determine causal factors related to instances of high frame definition error. Results: Two factors were identified as significant: number of post (p=0.0003) and CT scanner (p=0.0001). Further analysis showed that one of the four scanners was significantly different than the others. This diagnostic scanner was identified as an older model with localization lasers not tightly calibrated. The average value for maximum frame definition error using this scanner was 1.48 mm (4 posts) and 1.75 mm (3 posts). For the other scanners this value was 1.13 mm (4 posts) and 1.40 mm (3 posts). Conclusion: In utilizing a pre-planning workflow the choice of CT scanner matters. Any scanner utilized for GK should undergo routine QA at a level appropriate for radiation oncology. In terms of 3 vs 4 post, it is hypothesized that three posts provide less stability during CT acquisition. This will be tested in future work.

SU-F-T-252: An Investigation of Gamma Knife Frame Definition Error When Using a Pre-Planning Workflow

Energy Technology Data Exchange (ETDEWEB)

Johnson, P [University of Miami, Miami, FL (United States)

2016-06-15

Purpose: To determine causal factors related to high frame definition error when treating GK patients using a pre-planning workflow. Methods: 160 cases were retrospectively reviewed. All patients received treatment using a pre-planning workflow whereby stereotactic coordinates are determined from a CT scan acquired after framing using a fiducial box. The planning software automatically detects the fiducials and compares their location to expected values based on the rigid design of the fiducial system. Any difference is reported as mean and maximum frame definition error. The manufacturer recommends these values be less than 1.0 mm and 1.5 mm. In this study, frame definition error was analyzed in comparison with a variety of factors including which neurosurgeon/oncologist/physicist was involved with the procedure, number of post used during framing (3 or 4), type of lesion, and which CT scanner was utilized for acquisition. An analysis of variance (ANOVA) approach was used to statistically evaluate the data and determine causal factors related to instances of high frame definition error. Results: Two factors were identified as significant: number of post (p=0.0003) and CT scanner (p=0.0001). Further analysis showed that one of the four scanners was significantly different than the others. This diagnostic scanner was identified as an older model with localization lasers not tightly calibrated. The average value for maximum frame definition error using this scanner was 1.48 mm (4 posts) and 1.75 mm (3 posts). For the other scanners this value was 1.13 mm (4 posts) and 1.40 mm (3 posts). Conclusion: In utilizing a pre-planning workflow the choice of CT scanner matters. Any scanner utilized for GK should undergo routine QA at a level appropriate for radiation oncology. In terms of 3 vs 4 post, it is hypothesized that three posts provide less stability during CT acquisition. This will be tested in future work.

Workflow Scheduling Using Hybrid GA-PSO Algorithm in Cloud Computing

Directory of Open Access Journals (Sweden)

Ahmad M. Manasrah

2018-01-01

Full Text Available Cloud computing environment provides several on-demand services and resource sharing for clients. Business processes are managed using the workflow technology over the cloud, which represents one of the challenges in using the resources in an efficient manner due to the dependencies between the tasks. In this paper, a Hybrid GA-PSO algorithm is proposed to allocate tasks to the resources efficiently. The Hybrid GA-PSO algorithm aims to reduce the makespan and the cost and balance the load of the dependent tasks over the heterogonous resources in cloud computing environments. The experiment results show that the GA-PSO algorithm decreases the total execution time of the workflow tasks, in comparison with GA, PSO, HSGA, WSGA, and MTCT algorithms. Furthermore, it reduces the execution cost. In addition, it improves the load balancing of the workflow application over the available resources. Finally, the obtained results also proved that the proposed algorithm converges to optimal solutions faster and with higher quality compared to other algorithms.

Implementation of the electronic DDA workflow for NSSS system design

International Nuclear Information System (INIS)

Eom, Young Sam; Kim, Yeon Sung; Lee, Suk Hee; Kim, Mi Kyung

1996-06-01

For improving NSSS design quality, and productivity several cases of the nuclear developed nation's integrated management system, such as Mitsubishi's NUWINGS (Japan), AECL's CANDID (Canada) and Duke Powes's (USA) were investigated, and it was studied in this report that the system implementation of NSSS design document computerization and the major workflow process of the DDA (Document Distribution for Agreement). On the basis of the requirements of design document computerization which covered preparation, review, approval and distribution of the engineering documents, KAERI Engineering Information Management System (KEIMS) was implemented. Major effects of this report are to implement GUI panel for input and retrieval of the document index information, to setup electronic document workflow, and to provide quality assurance verification by tracing the workflow history. Major effects of NSSS design document computerization are the improvement of efficiency and reliability and the engineering cost reduction by means of the fast documents verification capability and electronic document transferring system. 2 tabs., 16 figs., 9 refs. (Author)

Integrating Process Mining and Cognitive Analysis to Study EHR Workflow.

Science.gov (United States)

Furniss, Stephanie K; Burton, Matthew M; Grando, Adela; Larson, David W; Kaufman, David R

2016-01-01

There are numerous methods to study workflow. However, few produce the kinds of in-depth analyses needed to understand EHR-mediated workflow. Here we investigated variations in clinicians' EHR workflow by integrating quantitative analysis of patterns of users' EHR-interactions with in-depth qualitative analysis of user performance. We characterized 6 clinicians' patterns of information-gathering using a sequential process-mining approach. The analysis revealed 519 different screen transition patterns performed across 1569 patient cases. No one pattern was followed for more than 10% of patient cases, the 15 most frequent patterns accounted for over half ofpatient cases (53%), and 27% of cases exhibited unique patterns. By triangulating quantitative and qualitative analyses, we found that participants' EHR-interactive behavior was associated with their routine processes, patient case complexity, and EHR default settings. The proposed approach has significant potential to inform resource allocation for observation and training. In-depth observations helped us to explain variation across users.

The medical simulation markup language - simplifying the biomechanical modeling workflow.

Science.gov (United States)

Suwelack, Stefan; Stoll, Markus; Schalck, Sebastian; Schoch, Nicolai; Dillmann, Rüdiger; Bendl, Rolf; Heuveline, Vincent; Speidel, Stefanie

2014-01-01

Modeling and simulation of the human body by means of continuum mechanics has become an important tool in diagnostics, computer-assisted interventions and training. This modeling approach seeks to construct patient-specific biomechanical models from tomographic data. Usually many different tools such as segmentation and meshing algorithms are involved in this workflow. In this paper we present a generalized and flexible description for biomechanical models. The unique feature of the new modeling language is that it not only describes the final biomechanical simulation, but also the workflow how the biomechanical model is constructed from tomographic data. In this way, the MSML can act as a middleware between all tools used in the modeling pipeline. The MSML thus greatly facilitates the prototyping of medical simulation workflows for clinical and research purposes. In this paper, we not only detail the XML-based modeling scheme, but also present a concrete implementation. Different examples highlight the flexibility, robustness and ease-of-use of the approach.

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

Realizing parameterless automatic classification of remote sensing imagery using ontology engineering and cyberinfrastructure techniques

Science.gov (United States)

Sun, Ziheng; Fang, Hui; Di, Liping; Yue, Peng

2016-09-01

It was an untouchable dream for remote sensing experts to realize total automatic image classification without inputting any parameter values. Experts usually spend hours and hours on tuning the input parameters of classification algorithms in order to obtain the best results. With the rapid development of knowledge engineering and cyberinfrastructure, a lot of data processing and knowledge reasoning capabilities become online accessible, shareable and interoperable. Based on these recent improvements, this paper presents an idea of parameterless automatic classification which only requires an image and automatically outputs a labeled vector. No parameters and operations are needed from endpoint consumers. An approach is proposed to realize the idea. It adopts an ontology database to store the experiences of tuning values for classifiers. A sample database is used to record training samples of image segments. Geoprocessing Web services are used as functionality blocks to finish basic classification steps. Workflow technology is involved to turn the overall image classification into a total automatic process. A Web-based prototypical system named PACS (Parameterless Automatic Classification System) is implemented. A number of images are fed into the system for evaluation purposes. The results show that the approach could automatically classify remote sensing images and have a fairly good average accuracy. It is indicated that the classified results will be more accurate if the two databases have higher quality. Once the experiences and samples in the databases are accumulated as many as an expert has, the approach should be able to get the results with similar quality to that a human expert can get. Since the approach is total automatic and parameterless, it can not only relieve remote sensing workers from the heavy and time-consuming parameter tuning work, but also significantly shorten the waiting time for consumers and facilitate them to engage in image

Extending a Petri-net based workflow description language for e-business atomicity support

NARCIS (Netherlands)

Norta, A.H.; Artishchev, S.

2004-01-01

In this paper an extension of XRL is presented for supporting Webbased and inter-organizational e-business atomicity spheres in workflow applications. XRL (eXchangable Routing Language), is an extensible, instance-based language that is intended for inter-organizational workflow processes having an

Dynamic work distribution in workflow management systems : how to balance quality and performance

NARCIS (Netherlands)

Kumar, Akhil; Aalst, van der W.M.P.; Verbeek, H.M.W.

2002-01-01

Today's workflow management systems offer work items to workers using rather primitive mechanisms.Although most workflow systems support a role-based distribution of work, they have problems dealing with unavailability of workers as a result of vacation or illness, overloading, context-dependent

A method to build and analyze scientific workflows from provenance through process mining

NARCIS (Netherlands)

Zeng, R.; He, X.; Li, Jiafei; Liu, Zheng; Aalst, van der W.M.P.

2011-01-01

Scientific workflows have recently emerged as a new paradigm for representing and managing complex distributed scientific computations and are used to accelerate the pace of scientific discovery. In many disciplines, individual workflows are large due to the large quantities of data used. As

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

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

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...

Sufficient and Necessary Condition to Decide Compatibility for a Class of Interorganizational Workflow Nets

Directory of Open Access Journals (Sweden)

Guanjun Liu

2015-01-01

Full Text Available Interorganizational Workflow nets (IWF-nets can well model many concurrent systems such as web service composition, in which multiple processes interact via sending/receiving messages. Compatibility of IWF-nets is a crucial criterion for the correctness of these systems. It guarantees that a system has no deadlock, livelock, or dead tasks. In our previous work we proved that the compatibility problem is PSPACE-complete for safe IWF-nets. This paper defines a subclass of IWF-nets that can model many cases about interactions. Necessary and sufficient condition is presented to decide their compatibility, and it depends on the net structures only. Finally, an algorithm is developed based on the condition.

Composite Classifiers for Automatic Target Recognition

National Research Council Canada - National Science Library

Wang, Lin-Cheng

1998-01-01

...) using forward-looking infrared (FLIR) imagery. Two existing classifiers, one based on learning vector quantization and the other on modular neural networks, are used as the building blocks for our composite classifiers...

Workflow-Based Software Development Environment

Science.gov (United States)

Izygon, Michel E.

2013-01-01

The Software Developer's Assistant (SDA) helps software teams more efficiently and accurately conduct or execute software processes associated with NASA mission-critical software. SDA is a process enactment platform that guides software teams through project-specific standards, processes, and procedures. Software projects are decomposed into all of their required process steps or tasks, and each task is assigned to project personnel. SDA orchestrates the performance of work required to complete all process tasks in the correct sequence. The software then notifies team members when they may begin work on their assigned tasks and provides the tools, instructions, reference materials, and supportive artifacts that allow users to compliantly perform the work. A combination of technology components captures and enacts any software process use to support the software lifecycle. It creates an adaptive workflow environment that can be modified as needed. SDA achieves software process automation through a Business Process Management (BPM) approach to managing the software lifecycle for mission-critical projects. It contains five main parts: TieFlow (workflow engine), Business Rules (rules to alter process flow), Common Repository (storage for project artifacts, versions, history, schedules, etc.), SOA (interface to allow internal, GFE, or COTS tools integration), and the Web Portal Interface (collaborative web environment

Facilitating Stewardship of scientific data through standards based workflows

Science.gov (United States)

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

2013-12-01

scientific data acquisition and analysis requirements and effective interoperable data management and delivery. This includes participating in national and international dialogue on development of standards, embedding data management activities in business processes, and developing scientific staff as effective data stewards. Similar approach is applied to the geophysical data. By ensuring the geophysical datasets at GA strictly follow metadata and industry standards we are able to implement a provenance based workflow where the data is easily discoverable, geophysical processing can be applied to it and results can be stored. The provenance based workflow enables metadata records for the results to be produced automatically from the input dataset metadata.

A Community-Driven Workflow Recommendation and Reuse Infrastructure

Data.gov (United States)

National Aeronautics and Space Administration — Promote and encourage process and workflow reuse  within NASA Earth eXchange (NEX) by developing a proactive recommendation technology based on collective NEX user...

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.

Ultrasonic examination of ceramics and composites for porosities in an automatic scanning system

Energy Technology Data Exchange (ETDEWEB)

Gundtoft, H.E.

1988-05-01

Using a very precise scanning system and computer evaluation, we can get quantitative results from automatic ultrasonic examination. In this paper two examples dealing with nonmetallic materials are presented. In a ceramic plate (>1 inch thick) small spherical prorosities (down to 0.1 mm) would harm the final product. Several artificial defects made in the plate were used for calibration and optimisation of the technique. Areas with with a microscope. Good agreement with the predicted values from the ultrasonic examination was found. From the NDT-examination the exact position of a porosity is known in all 3 coordinates (x, y and z). The size of the defect can also be measured. A single porosity with a diameter of 0.1 mm can be detected. Carbon-reinforced composites were examined. 8 prepregs were stacked and hardened in an autoclave to form a sheet (1 mm thick). Air trapped in the material resulted in porosities in the final product. A double trough transmission-scanning technique was used for the examination. The porosity percentages were determined by the NDT-technique, and agreement with destructivly determined values on samples from the same sheet was found.

Using location tracking data to assess efficiency in established clinical workflows.

Science.gov (United States)

Meyer, Mark; Fairbrother, Pamela; Egan, Marie; Chueh, Henry; Sandberg, Warren S

2006-01-01

Location tracking systems are becoming more prevalent in clinical settings yet applications still are not common. We have designed a system to aid in the assessment of clinical workflow efficiency. Location data is captured from active RFID tags and processed into usable data. These data are stored and presented visually with trending capability over time. The system allows quick assessments of the impact of process changes on workflow, and isolates areas for improvement.

Workflow interruptions, social stressors from supervisor(s) and attention failure in surgery personnel.

Science.gov (United States)

Pereira, Diana; Müller, Patrick; Elfering, Achim

2015-01-01

Workflow interruptions and social stressors among surgery personnel may cause attention failure at work that may increase rumination about work issues during leisure time. The test of these assumptions should contribute to the understanding of exhaustion in surgery personnel and patient safety. Workflow interruptions and supervisor-related social stressors were tested to predict attention failure that predicts work-related rumination during leisure time. One hundred ninety-four theatre nurses, anaesthetists and surgeons from a Swiss University hospital participated in a cross-sectional survey. The participation rate was 58%. Structural equation modelling confirmed both indirect paths from workflow interruptions and social stressors via attention failure on rumination (both pworkflow interruptions and social stressors on rumination-could not be empirically supported. Workflow interruptions and social stressors at work are likely to trigger attention failure in surgery personnel. Work redesign and team intervention could help surgery personnel to maintain a high level of quality and patient safety and detach from work related issues to recover during leisure time.

Health information technology: integration of clinical workflow into meaningful use of electronic health records.

Science.gov (United States)

Bowens, Felicia M; Frye, Patricia A; Jones, Warren A

2010-10-01

This article examines the role that clinical workflow plays in successful implementation and meaningful use of electronic health record (EHR) technology in ambulatory care. The benefits and barriers of implementing EHRs in ambulatory care settings are discussed. The researchers conclude that widespread adoption and meaningful use of EHR technology rely on the successful integration of health information technology (HIT) into clinical workflow. Without successful integration of HIT into clinical workflow, clinicians in today's ambulatory care settings will continue to resist adoption and implementation of EHR technology.

Nanocuration workflows: Establishing best practices for identifying, inputting, and sharing data to inform decisions on nanomaterials

Directory of Open Access Journals (Sweden)

Christina M. Powers

2015-09-01

Full Text Available There is a critical opportunity in the field of nanoscience to compare and integrate information across diverse fields of study through informatics (i.e., nanoinformatics. This paper is one in a series of articles on the data curation process in nanoinformatics (nanocuration. Other articles in this series discuss key aspects of nanocuration (temporal metadata, data completeness, database integration, while the focus of this article is on the nanocuration workflow, or the process of identifying, inputting, and reviewing nanomaterial data in a data repository. In particular, the article discusses: 1 the rationale and importance of a defined workflow in nanocuration, 2 the influence of organizational goals or purpose on the workflow, 3 established workflow practices in other fields, 4 current workflow practices in nanocuration, 5 key challenges for workflows in emerging fields like nanomaterials, 6 examples to make these challenges more tangible, and 7 recommendations to address the identified challenges. Throughout the article, there is an emphasis on illustrating key concepts and current practices in the field. Data on current practices in the field are from a group of stakeholders active in nanocuration. In general, the development of workflows for nanocuration is nascent, with few individuals formally trained in data curation or utilizing available nanocuration resources (e.g., ISA-TAB-Nano. Additional emphasis on the potential benefits of cultivating nanomaterial data via nanocuration processes (e.g., capability to analyze data from across research groups and providing nanocuration resources (e.g., training will likely prove crucial for the wider application of nanocuration workflows in the scientific community.

The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud

NARCIS (Netherlands)

Wolstencroft, K.; Haines, R.; Fellows, D.; Williams, A.; Withers, D.; Owen, S.; Soiland-Reyes, S.; Dunlop, I.; Nenadic, A.; Fisher, P.; Bhagat, J.; Belhajjame, K.; Bacall, F.; Hardisty, A.; Nieva de la Hidalga, A.; Balcazar Vargas, M.P.; Sufi, S.; Goble, C.

2013-01-01

The Taverna workflow tool suite (http://www.taverna.org.uk) is designed to combine distributed Web Services and/or local tools into complex analysis pipelines. These pipelines can be executed on local desktop machines or through larger infrastructure (such as supercomputers, Grids or cloud

An Integrated Workflow For Secondary Use of Patient Data for Clinical Research.

Science.gov (United States)

Bouzillé, Guillaume; Sylvestre, Emmanuelle; Campillo-Gimenez, Boris; Renault, Eric; Ledieu, Thibault; Delamarre, Denis; Cuggia, Marc

2015-01-01

This work proposes an integrated workflow for secondary use of medical data to serve feasibility studies, and the prescreening and monitoring of research studies. All research issues are initially addressed by the Clinical Research Office through a research portal and subsequently redirected to relevant experts in the determined field of concentration. For secondary use of data, the workflow is then based on the clinical data warehouse of the hospital. A datamart with potentially eligible research candidates is constructed. Datamarts can either produce aggregated data, de-identified data, or identified data, according to the kind of study being treated. In conclusion, integrating the secondary use of data process into a general research workflow allows visibility of information technologies and improves the accessability of clinical data.

From remote sensing data about information extraction for 3D geovisualization - Development of a workflow

International Nuclear Information System (INIS)

Tiede, D.

2010-01-01

With an increased availability of high (spatial) resolution remote sensing imagery since the late nineties, the need to develop operative workflows for the automated extraction, provision and communication of information from such data has grown. Monitoring requirements, aimed at the implementation of environmental or conservation targets, management of (environmental-) resources, and regional planning as well as international initiatives, especially the joint initiative of the European Commission and ESA (European Space Agency) for Global Monitoring for Environment and Security (GMES) play also a major part. This thesis addresses the development of an integrated workflow for the automated provision of information derived from remote sensing data. Considering applied data and fields of application, this work aims to design the workflow as generic as possible. Following research questions are discussed: What are the requirements of a workflow architecture that seamlessly links the individual workflow elements in a timely manner and secures accuracy of the extracted information effectively? How can the workflow retain its efficiency if mounds of data are processed? How can the workflow be improved with regards to automated object-based image analysis (OBIA)? Which recent developments could be of use? What are the limitations or which workarounds could be applied in order to generate relevant results? How can relevant information be prepared target-oriented and communicated effectively? How can the more recently developed freely available virtual globes be used for the delivery of conditioned information under consideration of the third dimension as an additional, explicit carrier of information? Based on case studies comprising different data sets and fields of application it is demonstrated how methods to extract and process information as well as to effectively communicate results can be improved and successfully combined within one workflow. It is shown that (1

Development and validation of automatic tools for interactive recurrence analysis in radiation therapy: optimization of treatment algorithms for locally advanced pancreatic cancer.

Science.gov (United States)

Kessel, Kerstin A; Habermehl, Daniel; Jäger, Andreas; Floca, Ralf O; Zhang, Lanlan; Bendl, Rolf; Debus, Jürgen; Combs, Stephanie E

2013-06-07

In radiation oncology recurrence analysis is an important part in the evaluation process and clinical quality assurance of treatment concepts. With the example of 9 patients with locally advanced pancreatic cancer we developed and validated interactive analysis tools to support the evaluation workflow. After an automatic registration of the radiation planning CTs with the follow-up images, the recurrence volumes are segmented manually. Based on these volumes the DVH (dose volume histogram) statistic is calculated, followed by the determination of the dose applied to the region of recurrence and the distance between the boost and recurrence volume. We calculated the percentage of the recurrence volume within the 80%-isodose volume and compared it to the location of the recurrence within the boost volume, boost + 1 cm, boost + 1.5 cm and boost + 2 cm volumes. Recurrence analysis of 9 patients demonstrated that all recurrences except one occurred within the defined GTV/boost volume; one recurrence developed beyond the field border/outfield. With the defined distance volumes in relation to the recurrences, we could show that 7 recurrent lesions were within the 2 cm radius of the primary tumor. Two large recurrences extended beyond the 2 cm, however, this might be due to very rapid growth and/or late detection of the tumor progression. The main goal of using automatic analysis tools is to reduce time and effort conducting clinical analyses. We showed a first approach and use of a semi-automated workflow for recurrence analysis, which will be continuously optimized. In conclusion, despite the limitations of the automatic calculations we contributed to in-house optimization of subsequent study concepts based on an improved and validated target volume definition.

Automatic localization of the da Vinci surgical instrument tips in 3-D transrectal ultrasound.

Science.gov (United States)

Mohareri, Omid; Ramezani, Mahdi; Adebar, Troy K; Abolmaesumi, Purang; Salcudean, Septimiu E

2013-09-01

Robot-assisted laparoscopic radical prostatectomy (RALRP) using the da Vinci surgical system is the current state-of-the-art treatment option for clinically confined prostate cancer. Given the limited field of view of the surgical site in RALRP, several groups have proposed the integration of transrectal ultrasound (TRUS) imaging in the surgical workflow to assist with accurate resection of the prostate and the sparing of the neurovascular bundles (NVBs). We previously introduced a robotic TRUS manipulator and a method for automatically tracking da Vinci surgical instruments with the TRUS imaging plane, in order to facilitate the integration of intraoperative TRUS in RALRP. Rapid and automatic registration of the kinematic frames of the da Vinci surgical system and the robotic TRUS probe manipulator is a critical component of the instrument tracking system. In this paper, we propose a fully automatic registration technique based on automatic 3-D TRUS localization of robot instrument tips pressed against the air-tissue boundary anterior to the prostate. The detection approach uses a multiscale filtering technique to identify and localize surgical instrument tips in the TRUS volume, and could also be used to detect other surface fiducials in 3-D ultrasound. Experiments have been performed using a tissue phantom and two ex vivo tissue samples to show the feasibility of the proposed methods. Also, an initial in vivo evaluation of the system has been carried out on a live anaesthetized dog with a da Vinci Si surgical system and a target registration error (defined as the root mean square distance of corresponding points after registration) of 2.68 mm has been achieved. Results show this method's accuracy and consistency for automatic registration of TRUS images to the da Vinci surgical system.

EPUB as publication format in Open Access journals: Tools and workflow

Directory of Open Access Journals (Sweden)

Trude Eikebrokk

2014-04-01

Full Text Available In this article, we present a case study of how the main publishing format of an Open Access journal was changed from PDF to EPUB by designing a new workflow using JATS as the basic XML source format. We state the reasons and discuss advantages for doing this, how we did it, and the costs of changing an established Microsoft Word workflow. As an example, we use one typical sociology article with tables, illustrations and references. We then follow the article from JATS markup through different transformations resulting in XHTML, EPUB and MOBI versions. In the end, we put everything together in an automated XProc pipeline. The process has been developed on free and open source tools, and we describe and evaluate these tools in the article. The workflow is suitable for non-professional publishers, and all code is attached and free for reuse by others.

Image data compression in diagnostic imaging. International literature review and workflow recommendation

International Nuclear Information System (INIS)

Braunschweig, R.; Kaden, Ingmar; Schwarzer, J.; Sprengel, C.; Klose, K.

2009-01-01

Purpose: Today healthcare policy is based on effectiveness. Diagnostic imaging became a ''pace-setter'' due to amazing technical developments (e.g. multislice CT), extensive data volumes, and especially the well defined workflow-orientated scenarios on a local and (inter)national level. To make centralized networks sufficient, image data compression has been regarded as the key to a simple and secure solution. In February 2008 specialized working groups of the DRG held a consensus conference. They designed recommended data compression techniques and ratios. Material und methoden: The purpose of our paper is an international review of the literature of compression technologies, different imaging procedures (e.g. DR, CT etc.), and targets (abdomen, etc.) and to combine recommendations for compression ratios and techniques with different workflows. The studies were assigned to 4 different levels (0-3) according to the evidence. 51 studies were assigned to the highest level 3. Results: We recommend a compression factor of 1: 8 (excluding cranial scans 1:5). For workflow reasons data compression should be based on the modalities (CT, etc.). PACS-based compression is currently possible but fails to maximize workflow benefits. Only the modality-based scenarios achieve all benefits. (orig.)

Image data compression in diagnostic imaging. International literature review and workflow recommendation

Energy Technology Data Exchange (ETDEWEB)

Braunschweig, R.; Kaden, Ingmar [Klinik fuer Bildgebende Diagnostik und Interventionsradiologie, BG-Kliniken Bergmannstrost Halle (Germany); Schwarzer, J.; Sprengel, C. [Dept. of Management Information System and Operations Research, Martin-Luther-Univ. Halle Wittenberg (Germany); Klose, K. [Medizinisches Zentrum fuer Radiologie, Philips-Univ. Marburg (Germany)

2009-07-15

Purpose: Today healthcare policy is based on effectiveness. Diagnostic imaging became a ''pace-setter'' due to amazing technical developments (e.g. multislice CT), extensive data volumes, and especially the well defined workflow-orientated scenarios on a local and (inter)national level. To make centralized networks sufficient, image data compression has been regarded as the key to a simple and secure solution. In February 2008 specialized working groups of the DRG held a consensus conference. They designed recommended data compression techniques and ratios. Material und methoden: The purpose of our paper is an international review of the literature of compression technologies, different imaging procedures (e.g. DR, CT etc.), and targets (abdomen, etc.) and to combine recommendations for compression ratios and techniques with different workflows. The studies were assigned to 4 different levels (0-3) according to the evidence. 51 studies were assigned to the highest level 3. Results: We recommend a compression factor of 1: 8 (excluding cranial scans 1:5). For workflow reasons data compression should be based on the modalities (CT, etc.). PACS-based compression is currently possible but fails to maximize workflow benefits. Only the modality-based scenarios achieve all benefits. (orig.)

Reproducible Research Data Analyses using the Common Workflow Language standards

CERN Multimedia

CERN. Geneva

2017-01-01

This talk will introduce the Common Workflow Language project. In July 2016 they released standards that enable the portable, interoperable, and executable description of command line data analysis tools and workflow made from those tools. These descriptions are enhanced by CWL's first class (but optional) support for Docker containers. CWL originated from the world of bioinformatics but is not discipline specific and is gaining interest and use in other fields. Attendees who want to play with CWL prior to attending the presentation are invited to go through the "Gentle Introduction to the Common Workflow Language" tutorial on any OS X or Linux machine on their own time. About the speaker Michael R. Crusoe is one of the co-founders of the CWL project and is the CWL Community Engineer. His facilitation, technical contributions, and training on behalf of the project draw from his time as the former lead developer of C. Titus Brown's k-h-mer project, his previous career as a sysadmin and programmer, and his ex...

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.

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

A workflow for improving estimates of microplastic contamination in marine waters: A case study from North-Western Australia.

Science.gov (United States)

Kroon, Frederieke; Motti, Cherie; Talbot, Sam; Sobral, Paula; Puotinen, Marji

2018-07-01

Plastic pollution is ubiquitous throughout the marine environment, with microplastic (i.e. contamination a global issue of emerging concern. The lack of universally accepted methods for quantifying microplastic contamination, including consistent application of microscopy, photography, an spectroscopy and photography, may result in unrealistic contamination estimates. Here, we present and apply an analysis workflow tailored to quantifying microplastic contamination in marine waters, incorporating stereomicroscopic visual sorting, microscopic photography and attenuated total reflectance (ATR) Fourier transform infrared (FTIR) spectroscopy. The workflow outlines step-by-step processing and associated decision making, thereby reducing bias in plastic identification and improving confidence in contamination estimates. Specific processing steps include (i) the use of a commercial algorithm-based comparison of particle spectra against an extensive commercially curated spectral library, followed by spectral interpretation to establish the chemical composition, (ii) a comparison against a customised contaminant spectral library to eliminate procedural contaminants, and (iii) final assignment of particles as either natural- or anthropogenic-derived materials, based on chemical type, a compare analysis of each particle against other particle spectra, and physical characteristics of particles. Applying this workflow to 54 tow samples collected in marine waters of North-Western Australia visually identified 248 potential anthropogenic particles. Subsequent ATR-FTIR spectroscopy, chemical assignment and visual re-inspection of photographs established 144 (58%) particles to be of anthropogenic origin. Of the original 248 particles, 97 (39%) were ultimately confirmed to be plastics, with 85 of these (34%) classified as microplastics, demonstrating that over 60% of particles may be misidentified as plastics if visual identification is not complemented by spectroscopy. Combined

A web service for service composition to aid geospatial modelers

Science.gov (United States)

Bigagli, L.; Santoro, M.; Roncella, R.; Mazzetti, P.

2012-04-01

The identification of appropriate mechanisms for process reuse, chaining and composition is considered a key enabler for the effective uptake of a global Earth Observation infrastructure, currently pursued by the international geospatial research community. In the Earth and Space Sciences, such a facility could primarily enable integrated and interoperable modeling, for what several approaches have been proposed and developed, over the last years. In fact, GEOSS is specifically tasked with the development of the so-called "Model Web". At increasing levels of abstraction and generalization, the initial stove-pipe software tools have evolved to community-wide modeling frameworks, to Component-Based Architecture solution, and, more recently, started to embrace Service-Oriented Architectures technologies, such as the OGC WPS specification and the WS-* stack of W3C standards for service composition. However, so far, the level of abstraction seems too low for implementing the Model Web vision, and far too complex technological aspects must still be addressed by both providers and users, resulting in limited usability and, eventually, difficult uptake. As by the recent ICT trend of resource virtualization, it has been suggested that users in need of a particular processing capability, required by a given modeling workflow, may benefit from outsourcing the composition activities into an external first-class service, according to the Composition as a Service (CaaS) approach. A CaaS system provides the necessary interoperability service framework for adaptation, reuse and complementation of existing processing resources (including models and geospatial services in general) in the form of executable workflows. This work introduces the architecture of a CaaS system, as a distributed information system for creating, validating, editing, storing, publishing, and executing geospatial workflows. This way, the users can be freed from the need of a composition infrastructure and

Modeling Complex Workflow in Molecular Diagnostics

Science.gov (United States)

Gomah, Mohamed E.; Turley, James P.; Lu, Huimin; Jones, Dan

2010-01-01

One of the hurdles to achieving personalized medicine has been implementing the laboratory processes for performing and reporting complex molecular tests. The rapidly changing test rosters and complex analysis platforms in molecular diagnostics have meant that many clinical laboratories still use labor-intensive manual processing and testing without the level of automation seen in high-volume chemistry and hematology testing. We provide here a discussion of design requirements and the results of implementation of a suite of lab management tools that incorporate the many elements required for use of molecular diagnostics in personalized medicine, particularly in cancer. These applications provide the functionality required for sample accessioning and tracking, material generation, and testing that are particular to the evolving needs of individualized molecular diagnostics. On implementation, the applications described here resulted in improvements in the turn-around time for reporting of more complex molecular test sets, and significant changes in the workflow. Therefore, careful mapping of workflow can permit design of software applications that simplify even the complex demands of specialized molecular testing. By incorporating design features for order review, software tools can permit a more personalized approach to sample handling and test selection without compromising efficiency. PMID:20007844

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

Computational workflow for the fine-grained analysis of metagenomic samples.

Science.gov (United States)

Pérez-Wohlfeil, Esteban; Arjona-Medina, Jose A; Torreno, Oscar; Ulzurrun, Eugenia; Trelles, Oswaldo

2016-10-25

The field of metagenomics, defined as the direct genetic analysis of uncultured samples of genomes contained within an environmental sample, is gaining increasing popularity. The aim of studies of metagenomics is to determine the species present in an environmental community and identify changes in the abundance of species under different conditions. Current metagenomic analysis software faces bottlenecks due to the high computational load required to analyze complex samples. A computational open-source workflow has been developed for the detailed analysis of metagenomes. This workflow provides new tools and datafile specifications that facilitate the identification of differences in abundance of reads assigned to taxa (mapping), enables the detection of reads of low-abundance bacteria (producing evidence of their presence), provides new concepts for filtering spurious matches, etc. Innovative visualization ideas for improved display of metagenomic diversity are also proposed to better understand how reads are mapped to taxa. Illustrative examples are provided based on the study of two collections of metagenomes from faecal microbial communities of adult female monozygotic and dizygotic twin pairs concordant for leanness or obesity and their mothers. The proposed workflow provides an open environment that offers the opportunity to perform the mapping process using different reference databases. Additionally, this workflow shows the specifications of the mapping process and datafile formats to facilitate the development of new plugins for further post-processing. This open and extensible platform has been designed with the aim of enabling in-depth analysis of metagenomic samples and better understanding of the underlying biological processes.

Computational workflow for the fine-grained analysis of metagenomic samples

Directory of Open Access Journals (Sweden)

Esteban Pérez-Wohlfeil

2016-10-01

Full Text Available Abstract Background The field of metagenomics, defined as the direct genetic analysis of uncultured samples of genomes contained within an environmental sample, is gaining increasing popularity. The aim of studies of metagenomics is to determine the species present in an environmental community and identify changes in the abundance of species under different conditions. Current metagenomic analysis software faces bottlenecks due to the high computational load required to analyze complex samples. Results A computational open-source workflow has been developed for the detailed analysis of metagenomes. This workflow provides new tools and datafile specifications that facilitate the identification of differences in abundance of reads assigned to taxa (mapping, enables the detection of reads of low-abundance bacteria (producing evidence of their presence, provides new concepts for filtering spurious matches, etc. Innovative visualization ideas for improved display of metagenomic diversity are also proposed to better understand how reads are mapped to taxa. Illustrative examples are provided based on the study of two collections of metagenomes from faecal microbial communities of adult female monozygotic and dizygotic twin pairs concordant for leanness or obesity and their mothers. Conclusions The proposed workflow provides an open environment that offers the opportunity to perform the mapping process using different reference databases. Additionally, this workflow shows the specifications of the mapping process and datafile formats to facilitate the development of new plugins for further post-processing. This open and extensible platform has been designed with the aim of enabling in-depth analysis of metagenomic samples and better understanding of the underlying biological processes.

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.

Formal Model of Web Service Composition: An Actor-Based Approach to Unifying Orchestration and Choreography

OpenAIRE

Wang, Yong

2013-01-01

Web Service Composition creates new composite Web Services from the collection of existing ones to be composed further and embodies the added values and potential usages of Web Services. Web Service Composition includes two aspects: Web Service orchestration denoting a workflow-like composition pattern and Web Service choreography which represents an aggregate composition pattern. There were only a few works which give orchestration and choreography a relationship. In this paper, we introduce...

Grid workflow validation using ontology-based tacit knowledge: A case study for quantitative remote sensing applications

Science.gov (United States)

Liu, Jia; Liu, Longli; Xue, Yong; Dong, Jing; Hu, Yingcui; Hill, Richard; Guang, Jie; Li, Chi

2017-01-01

Workflow for remote sensing quantitative retrieval is the ;bridge; between Grid services and Grid-enabled application of remote sensing quantitative retrieval. Workflow averts low-level implementation details of the Grid and hence enables users to focus on higher levels of application. The workflow for remote sensing quantitative retrieval plays an important role in remote sensing Grid and Cloud computing services, which can support the modelling, construction and implementation of large-scale complicated applications of remote sensing science. The validation of workflow is important in order to support the large-scale sophisticated scientific computation processes with enhanced performance and to minimize potential waste of time and resources. To research the semantic correctness of user-defined workflows, in this paper, we propose a workflow validation method based on tacit knowledge research in the remote sensing domain. We first discuss the remote sensing model and metadata. Through detailed analysis, we then discuss the method of extracting the domain tacit knowledge and expressing the knowledge with ontology. Additionally, we construct the domain ontology with Protégé. Through our experimental study, we verify the validity of this method in two ways, namely data source consistency error validation and parameters matching error validation.

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

MRI-alone radiation therapy planning for prostate cancer: Automatic fiducial marker detection

International Nuclear Information System (INIS)

Ghose, Soumya; Mitra, Jhimli; Rivest-Hénault, David; Fazlollahi, Amir; Fripp, Jurgen; Dowling, Jason A.; Stanwell, Peter; Pichler, Peter; Sun, Jidi; Greer, Peter B.

2016-01-01

Purpose: The feasibility of radiation therapy treatment planning using substitute computed tomography (sCT) generated from magnetic resonance images (MRIs) has been demonstrated by a number of research groups. One challenge with an MRI-alone workflow is the accurate identification of intraprostatic gold fiducial markers, which are frequently used for prostate localization prior to each dose delivery fraction. This paper investigates a template-matching approach for the detection of these seeds in MRI. Methods: Two different gradient echo T1 and T2* weighted MRI sequences were acquired from fifteen prostate cancer patients and evaluated for seed detection. For training, seed templates from manual contours were selected in a spectral clustering manifold learning framework. This aids in clustering “similar” gold fiducial markers together. The marker with the minimum distance to a cluster centroid was selected as the representative template of that cluster during training. During testing, Gaussian mixture modeling followed by a Markovian model was used in automatic detection of the probable candidates. The probable candidates were rigidly registered to the templates identified from spectral clustering, and a similarity metric is computed for ranking and detection. Results: A fiducial detection accuracy of 95% was obtained compared to manual observations. Expert radiation therapist observers were able to correctly identify all three implanted seeds on 11 of the 15 scans (the proposed method correctly identified all seeds on 10 of the 15). Conclusions: An novel automatic framework for gold fiducial marker detection in MRI is proposed and evaluated with detection accuracies comparable to manual detection. When radiation therapists are unable to determine the seed location in MRI, they refer back to the planning CT (only available in the existing clinical framework); similarly, an automatic quality control is built into the automatic software to ensure that all gold

MRI-alone radiation therapy planning for prostate cancer: Automatic fiducial marker detection

Energy Technology Data Exchange (ETDEWEB)

Ghose, Soumya, E-mail: soumya.ghose@case.edu; Mitra, Jhimli [Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio 44106 and CSIRO Health and Biosecurity, The Australian e-Health & Research Centre, Herston, QLD 4029 (Australia); Rivest-Hénault, David; Fazlollahi, Amir; Fripp, Jurgen; Dowling, Jason A. [CSIRO Health and Biosecurity, The Australian e-Health & Research Centre, Herston, QLD 4029 (Australia); Stanwell, Peter [School of health sciences, The University of Newcastle, Newcastle, NSW 2308 (Australia); Pichler, Peter [Department of Radiation Oncology, Cavalry Mater Newcastle Hospital, Newcastle, NSW 2298 (Australia); Sun, Jidi; Greer, Peter B. [School of Mathematical and Physical Sciences, The University of Newcastle, Newcastle, NSW 2308, Australia and Department of Radiation Oncology, Cavalry Mater Newcastle Hospital, Newcastle, NSW 2298 (Australia)

2016-05-15

Purpose: The feasibility of radiation therapy treatment planning using substitute computed tomography (sCT) generated from magnetic resonance images (MRIs) has been demonstrated by a number of research groups. One challenge with an MRI-alone workflow is the accurate identification of intraprostatic gold fiducial markers, which are frequently used for prostate localization prior to each dose delivery fraction. This paper investigates a template-matching approach for the detection of these seeds in MRI. Methods: Two different gradient echo T1 and T2* weighted MRI sequences were acquired from fifteen prostate cancer patients and evaluated for seed detection. For training, seed templates from manual contours were selected in a spectral clustering manifold learning framework. This aids in clustering “similar” gold fiducial markers together. The marker with the minimum distance to a cluster centroid was selected as the representative template of that cluster during training. During testing, Gaussian mixture modeling followed by a Markovian model was used in automatic detection of the probable candidates. The probable candidates were rigidly registered to the templates identified from spectral clustering, and a similarity metric is computed for ranking and detection. Results: A fiducial detection accuracy of 95% was obtained compared to manual observations. Expert radiation therapist observers were able to correctly identify all three implanted seeds on 11 of the 15 scans (the proposed method correctly identified all seeds on 10 of the 15). Conclusions: An novel automatic framework for gold fiducial marker detection in MRI is proposed and evaluated with detection accuracies comparable to manual detection. When radiation therapists are unable to determine the seed location in MRI, they refer back to the planning CT (only available in the existing clinical framework); similarly, an automatic quality control is built into the automatic software to ensure that all gold

Beyond GIS with EO4V is Trails: a geospatio-temporal scientific workflow environment

CSIR Research Space (South Africa)

Van Zyl, T

2012-10-01

Full Text Available be accommodated at once. The scientific workflows approach has other advantages to such as provenance, repeatability and collaboration. The paper presents EO4VisTrails as an example of such a scientific workflows approach to integration and discusses the benefit...

ATLAS job transforms: a data driven workflow engine

International Nuclear Information System (INIS)

Stewart, G A; Breaden-Madden, W B; Maddocks, H J; Harenberg, T; Sandhoff, M; Sarrazin, B

2014-01-01

The need to run complex workflows for a high energy physics experiment such as ATLAS has always been present. However, as computing resources have become even more constrained, compared to the wealth of data generated by the LHC, the need to use resources efficiently and manage complex workflows within a single grid job have increased. In ATLAS, a new Job Transform framework has been developed that we describe in this paper. This framework manages the multiple execution steps needed to 'transform' one data type into another (e.g., RAW data to ESD to AOD to final ntuple) and also provides a consistent interface for the ATLAS production system. The new framework uses a data driven workflow definition which is both easy to manage and powerful. After a transform is defined, jobs are expressed simply by specifying the input data and the desired output data. The transform infrastructure then executes only the necessary substeps to produce the final data products. The global execution cost of running the job is minimised and the transform can adapt to scenarios where data can be produced along different execution paths. Transforms for specific physics tasks which support up to 60 individual substeps have been successfully run. As the new transforms infrastructure has been deployed in production many features have been added to the framework which improve reliability, quality of error reporting and also provide support for multi-process jobs.

Sources of variation in primary care clinical workflow: implications for the design of cognitive support.

Science.gov (United States)

Militello, Laura G; Arbuckle, Nicole B; Saleem, Jason J; Patterson, Emily; Flanagan, Mindy; Haggstrom, David; Doebbeling, Bradley N

2014-03-01

This article identifies sources of variation in clinical workflow and implications for the design and implementation of electronic clinical decision support. Sources of variation in workflow were identified via rapid ethnographic observation, focus groups, and interviews across a total of eight medical centers in both the Veterans Health Administration and academic medical centers nationally regarded as leaders in developing and using clinical decision support. Data were reviewed for types of variability within the social and technical subsystems and the external environment as described in the sociotechnical systems theory. Two researchers independently identified examples of variation and their sources, and then met with each other to discuss them until consensus was reached. Sources of variation were categorized as environmental (clinic staffing and clinic pace), social (perception of health information technology and real-time use with patients), or technical (computer access and information access). Examples of sources of variation within each of the categories are described and discussed in terms of impact on clinical workflow. As technologies are implemented, barriers to use become visible over time as users struggle to adapt workflow and work practices to accommodate new technologies. Each source of variability identified has implications for the effective design and implementation of useful health information technology. Accommodating moderate variability in workflow is anticipated to avoid brittle and inflexible workflow designs, while also avoiding unnecessary complexity for implementers and users.

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.

Changes of workflow in a radiolocigal department with RIS, PACS and flatpanel detectors implementation

International Nuclear Information System (INIS)

Imhof, H.; Dirisamer, A.; Fischer, H.; Grampp, S.; Heiner, L.; Kaderk, M.; Krestan, C.; Kainberger, F.

2002-01-01

Implementation of radiological information systems (RIS) and picture archiving and communicating systems (PACS) results in significant changes of workflow in a radiological department. Additional connection with flatpanel detectors leads to a shortening of the work process. RIS and PACS implementation alone reduces the complete workflow by 21-80%. With flatpanel technology the image production process is further shortened by 25-30%. The workflow-steps are changed from original 17-12 with the implementation of RIS and PACS and to 5 with the integrated use of flatpanels.This clearly recognizable advantages in the workflow need an according financial investment. Several studies could show that the capitalisationfactor calculated over eight years is positive, with a gain range between 5-25%. Whether the additional implementation of flatpanel detectors results also in a positive capitalisation over the years, cannot be estimated exactly, at the moment, because the experiences are too short. Particuarly critical are the interfaces, which needs a constant quality control. Our flatpanel detector-system is fixed, special images - as we have them in about 3-5% of all cases - need still conventional filmscreen or phosphorplate-systems. Full-spine and long-leg examinations cannot be performed with sufficient exactness. Without any questions implementation of integrated RIS, PACS and flatpanel detector-system needs excellent training of the employees, because of the changes in workflow etc. The main profits of such an integrated implementation are an increase in quality in image and report datas, easier handling - there are almost no more cassettes necessary - and excessive shortening of workflow. (orig.) [de

Eleven quick tips for architecting biomedical informatics workflows with cloud computing

Science.gov (United States)

Moore, Jason H.

2018-01-01

Cloud computing has revolutionized the development and operations of hardware and software across diverse technological arenas, yet academic biomedical research has lagged behind despite the numerous and weighty advantages that cloud computing offers. Biomedical researchers who embrace cloud computing can reap rewards in cost reduction, decreased development and maintenance workload, increased reproducibility, ease of sharing data and software, enhanced security, horizontal and vertical scalability, high availability, a thriving technology partner ecosystem, and much more. Despite these advantages that cloud-based workflows offer, the majority of scientific software developed in academia does not utilize cloud computing and must be migrated to the cloud by the user. In this article, we present 11 quick tips for architecting biomedical informatics workflows on compute clouds, distilling knowledge gained from experience developing, operating, maintaining, and distributing software and virtualized appliances on the world’s largest cloud. Researchers who follow these tips stand to benefit immediately by migrating their workflows to cloud computing and embracing the paradigm of abstraction. PMID:29596416

Eleven quick tips for architecting biomedical informatics workflows with cloud computing.

Science.gov (United States)

Cole, Brian S; Moore, Jason H

2018-03-01

Cloud computing has revolutionized the development and operations of hardware and software across diverse technological arenas, yet academic biomedical research has lagged behind despite the numerous and weighty advantages that cloud computing offers. Biomedical researchers who embrace cloud computing can reap rewards in cost reduction, decreased development and maintenance workload, increased reproducibility, ease of sharing data and software, enhanced security, horizontal and vertical scalability, high availability, a thriving technology partner ecosystem, and much more. Despite these advantages that cloud-based workflows offer, the majority of scientific software developed in academia does not utilize cloud computing and must be migrated to the cloud by the user. In this article, we present 11 quick tips for architecting biomedical informatics workflows on compute clouds, distilling knowledge gained from experience developing, operating, maintaining, and distributing software and virtualized appliances on the world's largest cloud. Researchers who follow these tips stand to benefit immediately by migrating their workflows to cloud computing and embracing the paradigm of abstraction.

Eleven quick tips for architecting biomedical informatics workflows with cloud computing.

Directory of Open Access Journals (Sweden)

Brian S Cole

2018-03-01

Full Text Available Cloud computing has revolutionized the development and operations of hardware and software across diverse technological arenas, yet academic biomedical research has lagged behind despite the numerous and weighty advantages that cloud computing offers. Biomedical researchers who embrace cloud computing can reap rewards in cost reduction, decreased development and maintenance workload, increased reproducibility, ease of sharing data and software, enhanced security, horizontal and vertical scalability, high availability, a thriving technology partner ecosystem, and much more. Despite these advantages that cloud-based workflows offer, the majority of scientific software developed in academia does not utilize cloud computing and must be migrated to the cloud by the user. In this article, we present 11 quick tips for architecting biomedical informatics workflows on compute clouds, distilling knowledge gained from experience developing, operating, maintaining, and distributing software and virtualized appliances on the world's largest cloud. Researchers who follow these tips stand to benefit immediately by migrating their workflows to cloud computing and embracing the paradigm of abstraction.

Accelerometer-based automatic voice onset detection in speech mapping with navigated repetitive transcranial magnetic stimulation.

Science.gov (United States)

Vitikainen, Anne-Mari; Mäkelä, Elina; Lioumis, Pantelis; Jousmäki, Veikko; Mäkelä, Jyrki P

2015-09-30

The use of navigated repetitive transcranial magnetic stimulation (rTMS) in mapping of speech-related brain areas has recently shown to be useful in preoperative workflow of epilepsy and tumor patients. However, substantial inter- and intraobserver variability and non-optimal replicability of the rTMS results have been reported, and a need for additional development of the methodology is recognized. In TMS motor cortex mappings the evoked responses can be quantitatively monitored by electromyographic recordings; however, no such easily available setup exists for speech mappings. We present an accelerometer-based setup for detection of vocalization-related larynx vibrations combined with an automatic routine for voice onset detection for rTMS speech mapping applying naming. The results produced by the automatic routine were compared with the manually reviewed video-recordings. The new method was applied in the routine navigated rTMS speech mapping for 12 consecutive patients during preoperative workup for epilepsy or tumor surgery. The automatic routine correctly detected 96% of the voice onsets, resulting in 96% sensitivity and 71% specificity. Majority (63%) of the misdetections were related to visible throat movements, extra voices before the response, or delayed naming of the previous stimuli. The no-response errors were correctly detected in 88% of events. The proposed setup for automatic detection of voice onsets provides quantitative additional data for analysis of the rTMS-induced speech response modifications. The objectively defined speech response latencies increase the repeatability, reliability and stratification of the rTMS results. Copyright © 2015 Elsevier B.V. All rights reserved.

User Interaction in Semi-Automatic Segmentation of Organs at Risk: a Case Study in Radiotherapy.

Science.gov (United States)

Ramkumar, Anjana; Dolz, Jose; Kirisli, Hortense A; Adebahr, Sonja; Schimek-Jasch, Tanja; Nestle, Ursula; Massoptier, Laurent; Varga, Edit; Stappers, Pieter Jan; Niessen, Wiro J; Song, Yu

2016-04-01

Accurate segmentation of organs at risk is an important step in radiotherapy planning. Manual segmentation being a tedious procedure and prone to inter- and intra-observer variability, there is a growing interest in automated segmentation methods. However, automatic methods frequently fail to provide satisfactory result, and post-processing corrections are often needed. Semi-automatic segmentation methods are designed to overcome these problems by combining physicians' expertise and computers' potential. This study evaluates two semi-automatic segmentation methods with different types of user interactions, named the "strokes" and the "contour", to provide insights into the role and impact of human-computer interaction. Two physicians participated in the experiment. In total, 42 case studies were carried out on five different types of organs at risk. For each case study, both the human-computer interaction process and quality of the segmentation results were measured subjectively and objectively. Furthermore, different measures of the process and the results were correlated. A total of 36 quantifiable and ten non-quantifiable correlations were identified for each type of interaction. Among those pairs of measures, 20 of the contour method and 22 of the strokes method were strongly or moderately correlated, either directly or inversely. Based on those correlated measures, it is concluded that: (1) in the design of semi-automatic segmentation methods, user interactions need to be less cognitively challenging; (2) based on the observed workflows and preferences of physicians, there is a need for flexibility in the interface design; (3) the correlated measures provide insights that can be used in improving user interaction design.

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.

A workflow for the automatic segmentation of organelles in electron microscopy image stacks

Science.gov (United States)

Perez, Alex J.; Seyedhosseini, Mojtaba; Deerinck, Thomas J.; Bushong, Eric A.; Panda, Satchidananda; Tasdizen, Tolga; Ellisman, Mark H.

2014-01-01

Electron microscopy (EM) facilitates analysis of the form, distribution, and functional status of key organelle systems in various pathological processes, including those associated with neurodegenerative disease. Such EM data often provide important new insights into the underlying disease mechanisms. The development of more accurate and efficient methods to quantify changes in subcellular microanatomy has already proven key to understanding the pathogenesis of Parkinson's and Alzheimer's diseases, as well as glaucoma. While our ability to acquire large volumes of 3D EM data is progressing rapidly, more advanced analysis tools are needed to assist in measuring precise three-dimensional morphologies of organelles within data sets that can include hundreds to thousands of whole cells. Although new imaging instrument throughputs can exceed teravoxels of data per day, image segmentation and analysis remain significant bottlenecks to achieving quantitative descriptions of whole cell structural organellomes. Here, we present a novel method for the automatic segmentation of organelles in 3D EM image stacks. Segmentations are generated using only 2D image information, making the method suitable for anisotropic imaging techniques such as serial block-face scanning electron microscopy (SBEM). Additionally, no assumptions about 3D organelle morphology are made, ensuring the method can be easily expanded to any number of structurally and functionally diverse organelles. Following the presentation of our algorithm, we validate its performance by assessing the segmentation accuracy of different organelle targets in an example SBEM dataset and demonstrate that it can be efficiently parallelized on supercomputing resources, resulting in a dramatic reduction in runtime. PMID:25426032

Automatic detection of clinical mastitis is improved by in-line monitoring of somatic cell count

NARCIS (Netherlands)

Kamphuis, C.; Sherlock, R.; Jago, J.; Mein, G.; Hogeveen, H.

2008-01-01

This study explored the potential value of in-line composite somatic cell count (ISCC) sensing as a sole criterion or in combination with quarter-based electrical conductivity (EC) of milk, for automatic detection of clinical mastitis (CM) during automatic milking. Data generated from a New Zealand

Database supported electronic retrospective analyses in radiation oncology. Establishing a workflow using the example of pancreatic cancer; Datenbankbasierte digitale retrospektive Auswertung von Patientenkollektiven in der Radioonkologie. Etablierung eines Workflows am Beispiel des Pankreaskarzinoms

Energy Technology Data Exchange (ETDEWEB)

Kessel, K.A.; Habermehl, D.; Bougatf, N.; Debus, J.; Combs, S.E. [Universitatesklinikum Heidelberg (Germany). Abt. fuer Radioonkologie und Strahlentherapie; Bohn, C. [CHILI GmbH, Dossenheim (Germany); Jaeger, A.; Floca, R.O.; Zhang, L. [Deutsches Krebsforschungszentrum (DKFZ), Heidelberg (Germany); Bendl, R. [Hochschule Heilbronn (Germany). Fakultaet fuer Medizinische Informatik

2012-12-15

Purpose: Especially in the field of radiation oncology, handling a large variety of voluminous datasets from various information systems in different documentation styles efficiently is crucial for patient care and research. To date, conducting retrospective clinical analyses is rather difficult and time consuming. With the example of patients with pancreatic cancer treated with radio-chemotherapy, we performed a therapy evaluation by using an analysis system connected with a documentation system. Materials and methods: A total number of 783 patients have been documented into a professional, database-based documentation system. Information about radiation therapy, diagnostic images and dose distributions have been imported into the web-based system. Results: For 36 patients with disease progression after neoadjuvant chemoradiation, we designed and established an analysis workflow. After an automatic registration of the radiation plans with the follow-up images, the recurrence volumes are segmented manually. Based on these volumes the DVH (dose volume histogram) statistic is calculated, followed by the determination of the dose applied to the region of recurrence. All results are saved in the database and included in statistical calculations. Conclusion: The main goal of using an automatic analysis tool is to reduce time and effort conducting clinical analyses, especially with large patient groups. We showed a first approach and use of some existing tools, however manual interaction is still necessary. Further steps need to be taken to enhance automation. Already, it has become apparent that the benefits of digital data management and analysis lie in the central storage of data and reusability of the results. Therefore, we intend to adapt the analysis system to other types of tumors in radiation oncology. (orig.)

Web service composition languages: old wine in new bottles?

NARCIS (Netherlands)

Aalst, van der W.M.P.; Dumas, M.; Hofstede, ter A.H.M.; Chroust, G.; Hofer, C.

2003-01-01

Recently, several languages for Web service composition have emerged (e.g., BPEL4WS and WSCI). The goal of these languages is to glue Web services together in a process-oriented way. For this purpose, these languages typically borrow concepts from workflow management systems and embed these concepts

A Generalized Email Classification System for Workflow Analysis

NARCIS (Netherlands)

P. Chaipornkaew (Piyanuch); T. Prexawanprasut (Takorn); C-L. Chang (Chia-Lin); M.J. McAleer (Michael)

2017-01-01

textabstractOne of the most powerful internet communication channels is email. As employees and their clients communicate primarily via email, much crucial business data is conveyed via email content. Where businesses are understandably concerned, they need a sophisticated workflow management

CrossFlow: integrating workflow management and electronic commerce

NARCIS (Netherlands)

Hoffner, Y.; Ludwig, H.; Grefen, P.W.P.J.; Aberer, K.

2001-01-01

The CrossFlow architecture provides support for cross-organisational workflow management in dynamically established virtual enterprises. The creation of a business relationship between a service provider organisation performing a service on behalf of a consumer organisation can be made dynamic when

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.

A-Posteriori Detection of Sensor Infrastructure Errors in Correlated Sensor Data and Business Workflows

NARCIS (Netherlands)

Wombacher, Andreas

2011-01-01

Sensor data can be interpreted as a view on physical objects effected by business processes. Since both sensor infrastructures and business workflows must deal with imprecise information, the correlation of sensor data and business workflow data might be used a-posteriori to determine the source of

Workflow improvement and efficiency gain with near digitalization of a Radiology Department

International Nuclear Information System (INIS)

Langen, H.L.; Bielmeier, J.; Selbach, R.; Wittenberg, G.; Feustel, H.

2003-01-01

Purpose: To determine the temporal changes of the workflow caused by digitalization of the radiology department after installation of digital luminescence-radiography (DLR), a radiology information system (RIS) and picture archiving and communication system (PACS) at the Missionsaerztliche Klinik in April 2000. Materials and methods: In a comparative study, a workflow analysis by manual registration of different work steps was performed before (1999) and after (2001) digitalization of a radiology department. Results: The digitalization shortened the examination time for patients from a mean of 8 min to 5 min. The time the patient is absent from the emergency room did not change. Reporting radiographic examinations including comparison with previous studies begins earlier from a mean of 2 h 37 min to 17 min. Using PACS, 85.9% of all cases could be interpreted on the day of the examination (without PACS 41.2%) and 87.2% of the reports were completed the day after the examination (without PACS 64.5%). No time differences were found between reading conventional studies on the monitor or as soft-copy. Conclusion: Compared to conventional film-screen systems, complete digitalization of a radiology department is time saving at nearly all steps of the workflow, with expected positive effects on the workflow quality of the entire hospital. (orig.) [de

Omics Informatics: From Scattered Individual Software Tools to Integrated Workflow Management Systems.

Science.gov (United States)

Ma, Tianle; Zhang, Aidong

2017-01-01

Omic data analyses pose great informatics challenges. As an emerging subfield of bioinformatics, omics informatics focuses on analyzing multi-omic data efficiently and effectively, and is gaining momentum. There are two underlying trends in the expansion of omics informatics landscape: the explosion of scattered individual omics informatics tools with each of which focuses on a specific task in both single- and multi- omic settings, and the fast-evolving integrated software platforms such as workflow management systems that can assemble multiple tools into pipelines and streamline integrative analysis for complicated tasks. In this survey, we give a holistic view of omics informatics, from scattered individual informatics tools to integrated workflow management systems. We not only outline the landscape and challenges of omics informatics, but also sample a number of widely used and cutting-edge algorithms in omics data analysis to give readers a fine-grained view. We survey various workflow management systems (WMSs), classify them into three levels of WMSs from simple software toolkits to integrated multi-omic analytical platforms, and point out the emerging needs for developing intelligent workflow management systems. We also discuss the challenges, strategies and some existing work in systematic evaluation of omics informatics tools. We conclude by providing future perspectives of emerging fields and new frontiers in omics informatics.

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.

The Iqmulus Urban Showcase: Automatic Tree Classification and Identification in Huge Mobile Mapping Point Clouds

Science.gov (United States)

Böhm, J.; Bredif, M.; Gierlinger, T.; Krämer, M.; Lindenberg, R.; Liu, K.; Michel, F.; Sirmacek, B.

2016-06-01

Current 3D data capturing as implemented on for example airborne or mobile laser scanning systems is able to efficiently sample the surface of a city by billions of unselective points during one working day. What is still difficult is to extract and visualize meaningful information hidden in these point clouds with the same efficiency. This is where the FP7 IQmulus project enters the scene. IQmulus is an interactive facility for processing and visualizing big spatial data. In this study the potential of IQmulus is demonstrated on a laser mobile mapping point cloud of 1 billion points sampling ~ 10 km of street environment in Toulouse, France. After the data is uploaded to the IQmulus Hadoop Distributed File System, a workflow is defined by the user consisting of retiling the data followed by a PCA driven local dimensionality analysis, which runs efficiently on the IQmulus cloud facility using a Spark implementation. Points scattering in 3 directions are clustered in the tree class, and are separated next into individual trees. Five hours of processing at the 12 node computing cluster results in the automatic identification of 4000+ urban trees. Visualization of the results in the IQmulus fat client helps users to appreciate the results, and developers to identify remaining flaws in the processing workflow.

Designing Flexible E-Business Workflow Systems

OpenAIRE

Cătălin Silvestru; Codrin Nisioiu; Marinela Mircea; Bogdan Ghilic-Micu; Marian Stoica

2010-01-01

In today’s business environment organizations must cope with complex interactions between actors adapt fast to frequent market changes and be innovative. In this context, integrating knowledge with processes and Business Intelligenceis a major step towards improving organization agility. Therefore, traditional environments for workflow design have been adapted to answer the new business models and current requirements in the field of collaborative processes. This paper approaches the design o...

A Hybrid Task Graph Scheduler for High Performance Image Processing Workflows.

Science.gov (United States)

Blattner, Timothy; Keyrouz, Walid; Bhattacharyya, Shuvra S; Halem, Milton; Brady, Mary

2017-12-01

Designing applications for scalability is key to improving their performance in hybrid and cluster computing. Scheduling code to utilize parallelism is difficult, particularly when dealing with data dependencies, memory management, data motion, and processor occupancy. The Hybrid Task Graph Scheduler (HTGS) improves programmer productivity when implementing hybrid workflows for multi-core and multi-GPU systems. The Hybrid Task Graph Scheduler (HTGS) is an abstract execution model, framework, and API that increases programmer productivity when implementing hybrid workflows for such systems. HTGS manages dependencies between tasks, represents CPU and GPU memories independently, overlaps computations with disk I/O and memory transfers, keeps multiple GPUs occupied, and uses all available compute resources. Through these abstractions, data motion and memory are explicit; this makes data locality decisions more accessible. To demonstrate the HTGS application program interface (API), we present implementations of two example algorithms: (1) a matrix multiplication that shows how easily task graphs can be used; and (2) a hybrid implementation of microscopy image stitching that reduces code size by ≈ 43% compared to a manually coded hybrid workflow implementation and showcases the minimal overhead of task graphs in HTGS. Both of the HTGS-based implementations show good performance. In image stitching the HTGS implementation achieves similar performance to the hybrid workflow implementation. Matrix multiplication with HTGS achieves 1.3× and 1.8× speedup over the multi-threaded OpenBLAS library for 16k × 16k and 32k × 32k size matrices, respectively.

Adaptación de Workflows basada en Ontologías

Directory of Open Access Journals (Sweden)

Álvaro E. Prieto

2014-12-01

Full Text Available Los workflows para procesos administrativos son utilizados en empresas e instituciones públicas pero, para poder utilizarlos adecuadamente en sus distintas áreas y departamentos, deben ser adaptados a las características propias de cada uno de ellos, respetando las normas que regulan el proceso a nivel general. Este problema, llamado Problema de la Adaptación Jerárquica, también implica establecer las medidas que se deben tomar cuando la normativa general cambia, para mantener la consistencia entre los distintos niveles mediante la propagación de los cambios a todas las adaptaciones. Para resolver este problema, en este trabajo se presenta el Método de Adaptación Jerárquica. Un método basado en ontologías que define las reglas que debe satisfacer un workflow genérico para ser considerado adaptable a diferentes casos de aplicación y las reglas que deben satisfacer las adaptaciones. Además, proporciona las operaciones que facilitan tanto la adaptación de los workflows administrativos como la propagación de los cambios

SHIWA workflow interoperability solutions for neuroimaging data analysis

NARCIS (Netherlands)

Korkhov, Vladimir; Krefting, Dagmar; Montagnat, Johan; Truong Huu, Tram; Kukla, Tamas; Terstyanszky, Gabor; Manset, David; Caan, Matthan; Olabarriaga, Silvia

2012-01-01

Neuroimaging is a field that benefits from distributed computing infrastructures (DCIs) to perform data- and compute-intensive processing and analysis. Using grid workflow systems not only automates the processing pipelines, but also enables domain researchers to implement their expertise on how to

CrossFlow: Integrating Workflow Management and Electronic Commerce

NARCIS (Netherlands)

Hoffner, Y.; Ludwig, H.; Grefen, P.W.P.J.; Aberer, K.

2001-01-01

The CrossFlow1 architecture provides support for cross-organisational workflow management in dynamically established virtual enterprises. The creation of a business relationship between a service provider organisation performing a service on behalf of a consumer organisation can be made dynamic when

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.

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.

SU-E-T-362: Automatic Catheter Reconstruction of Flap Applicators in HDR Surface Brachytherapy

International Nuclear Information System (INIS)

Buzurovic, I; Devlin, P; Hansen, J; O'Farrell, D; Bhagwat, M; Friesen, S; Damato, A; Lewis, J; Cormack, R

2014-01-01

Purpose: Catheter reconstruction is crucial for the accurate delivery of radiation dose in HDR brachytherapy. The process becomes complicated and time-consuming for large superficial clinical targets with a complex topology. A novel method for the automatic catheter reconstruction of flap applicators is proposed in this study. Methods: We have developed a program package capable of image manipulation, using C++class libraries of The-Visualization-Toolkit(VTK) software system. The workflow for automatic catheter reconstruction is: a)an anchor point is placed in 3D or in the axial view of the first slice at the tip of the first, last and middle points for the curved surface; b)similar points are placed on the last slice of the image set; c)the surface detection algorithm automatically registers the points to the images and applies the surface reconstruction filter; d)then a structured grid surface is generated through the center of the treatment catheters placed at a distance of 5mm from the patient's skin. As a result, a mesh-style plane is generated with the reconstructed catheters placed 10mm apart. To demonstrate automatic catheter reconstruction, we used CT images of patients diagnosed with cutaneous T-cell-lymphoma and imaged with Freiburg-Flap-Applicators (Nucletron™-Elekta, Netherlands). The coordinates for each catheter were generated and compared to the control points selected during the manual reconstruction for 16catheters and 368control point Results: The variation of the catheter tip positions between the automatically and manually reconstructed catheters was 0.17mm(SD=0.23mm). The position difference between the manually selected catheter control points and the corresponding points obtained automatically was 0.17mm in the x-direction (SD=0.23mm), 0.13mm in the y-direction (SD=0.22mm), and 0.14mm in the z-direction (SD=0.24mm). Conclusion: This study shows the feasibility of the automatic catheter reconstruction of flap applicators with a high

Automatic analysis (aa: efficient neuroimaging workflows and parallel processing using Matlab and XML

Directory of Open Access Journals (Sweden)

Rhodri eCusack

2015-01-01

Full Text Available Recent years have seen neuroimaging data becoming richer, with larger cohorts of participants, a greater variety of acquisition techniques, and increasingly complex analyses. These advances have made data analysis pipelines complex to set up and run (increasing the risk of human error and time consuming to execute (restricting what analyses are attempted. Here we present an open-source framework, automatic analysis (aa, to address these concerns. Human efficiency is increased by making code modular and reusable, and managing its execution with a processing engine that tracks what has been completed and what needs to be (redone. Analysis is accelerated by optional parallel processing of independent tasks on cluster or cloud computing resources. A pipeline comprises a series of modules that each perform a specific task. The processing engine keeps track of the data, calculating a map of upstream and downstream dependencies for each module. Existing modules are available for many analysis tasks, such as SPM-based fMRI preprocessing, individual and group level statistics, voxel-based morphometry, tractography, and multi-voxel pattern analyses (MVPA. However, aa also allows for full customization, and encourages efficient management of code: new modules may be written with only a small code overhead. aa has been used by more than 50 researchers in hundreds of neuroimaging studies comprising thousands of subjects. It has been found to be robust, fast and efficient, for simple single subject studies up to multimodal pipelines on hundreds of subjects. It is attractive to both novice and experienced users. aa can reduce the amount of time neuroimaging laboratories spend performing analyses and reduce errors, expanding the range of scientific questions it is practical to address.

Automatic analysis (aa): efficient neuroimaging workflows and parallel processing using Matlab and XML.

Science.gov (United States)

Cusack, Rhodri; Vicente-Grabovetsky, Alejandro; Mitchell, Daniel J; Wild, Conor J; Auer, Tibor; Linke, Annika C; Peelle, Jonathan E

2014-01-01

Recent years have seen neuroimaging data sets becoming richer, with larger cohorts of participants, a greater variety of acquisition techniques, and increasingly complex analyses. These advances have made data analysis pipelines complicated to set up and run (increasing the risk of human error) and time consuming to execute (restricting what analyses are attempted). Here we present an open-source framework, automatic analysis (aa), to address these concerns. Human efficiency is increased by making code modular and reusable, and managing its execution with a processing engine that tracks what has been completed and what needs to be (re)done. Analysis is accelerated by optional parallel processing of independent tasks on cluster or cloud computing resources. A pipeline comprises a series of modules that each perform a specific task. The processing engine keeps track of the data, calculating a map of upstream and downstream dependencies for each module. Existing modules are available for many analysis tasks, such as SPM-based fMRI preprocessing, individual and group level statistics, voxel-based morphometry, tractography, and multi-voxel pattern analyses (MVPA). However, aa also allows for full customization, and encourages efficient management of code: new modules may be written with only a small code overhead. aa has been used by more than 50 researchers in hundreds of neuroimaging studies comprising thousands of subjects. It has been found to be robust, fast, and efficient, for simple-single subject studies up to multimodal pipelines on hundreds of subjects. It is attractive to both novice and experienced users. aa can reduce the amount of time neuroimaging laboratories spend performing analyses and reduce errors, expanding the range of scientific questions it is practical to address.

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.

ESO Reflex: a graphical workflow engine for data reduction

Science.gov (United States)

Hook, Richard; Ullgrén, Marko; Romaniello, Martino; Maisala, Sami; Oittinen, Tero; Solin, Otto; Savolainen, Ville; Järveläinen, Pekka; Tyynelä, Jani; Péron, Michèle; Ballester, Pascal; Gabasch, Armin; Izzo, Carlo

ESO Reflex is a prototype software tool that provides a novel approach to astronomical data reduction by integrating a modern graphical workflow system (Taverna) with existing legacy data reduction algorithms. Most of the raw data produced by instruments at the ESO Very Large Telescope (VLT) in Chile are reduced using recipes. These are compiled C applications following an ESO standard and utilising routines provided by the Common Pipeline Library (CPL). Currently these are run in batch mode as part of the data flow system to generate the input to the ESO/VLT quality control process and are also exported for use offline. ESO Reflex can invoke CPL-based recipes in a flexible way through a general purpose graphical interface. ESO Reflex is based on the Taverna system that was originally developed within the UK life-sciences community. Workflows have been created so far for three VLT/VLTI instruments, and the GUI allows the user to make changes to these or create workflows of their own. Python scripts or IDL procedures can be easily brought into workflows and a variety of visualisation and display options, including custom product inspection and validation steps, are available. Taverna is intended for use with web services and experiments using ESO Reflex to access Virtual Observatory web services have been successfully performed. ESO Reflex is the main product developed by Sampo, a project led by ESO and conducted by a software development team from Finland as an in-kind contribution to joining ESO. The goal was to look into the needs of the ESO community in the area of data reduction environments and to create pilot software products that illustrate critical steps along the road to a new system. Sampo concluded early in 2008. This contribution will describe ESO Reflex and show several examples of its use both locally and using Virtual Observatory remote web services. ESO Reflex is expected to be released to the community in early 2009.

ESO Reflex: A Graphical Workflow Engine for Data Reduction

Science.gov (United States)

Hook, R.; Romaniello, M.; Péron, M.; Ballester, P.; Gabasch, A.; Izzo, C.; Ullgrén, M.; Maisala, S.; Oittinen, T.; Solin, O.; Savolainen, V.; Järveläinen, P.; Tyynelä, J.

2008-08-01

Sampo {http://www.eso.org/sampo} (Hook et al. 2005) is a project led by ESO and conducted by a software development team from Finland as an in-kind contribution to joining ESO. The goal is to assess the needs of the ESO community in the area of data reduction environments and to create pilot software products that illustrate critical steps along the road to a new system. Those prototypes will not only be used to validate concepts and understand requirements but will also be tools of immediate value for the community. Most of the raw data produced by ESO instruments can be reduced using CPL {http://www.eso.org/cpl} recipes: compiled C programs following an ESO standard and utilizing routines provided by the Common Pipeline Library. Currently reduction recipes are run in batch mode as part of the data flow system to generate the input to the ESO VLT/VLTI quality control process and are also made public for external users. Sampo has developed a prototype application called ESO Reflex {http://www.eso.org/sampo/reflex/} that integrates a graphical user interface and existing data reduction algorithms. ESO Reflex can invoke CPL-based recipes in a flexible way through a dedicated interface. ESO Reflex is based on the graphical workflow engine Taverna {http://taverna.sourceforge.net} that was originally developed by the UK eScience community, mostly for work in the life sciences. Workflows have been created so far for three VLT/VLTI instrument modes ( VIMOS/IFU {http://www.eso.org/instruments/vimos/}, FORS spectroscopy {http://www.eso.org/instruments/fors/} and AMBER {http://www.eso.org/instruments/amber/}), and the easy-to-use GUI allows the user to make changes to these or create workflows of their own. Python scripts and IDL procedures can be easily brought into workflows and a variety of visualisation and display options, including custom product inspection and validation steps, are available.

Improving data collection, documentation, and workflow in a dementia screening study.

Science.gov (United States)

Read, Kevin B; LaPolla, Fred Willie Zametkin; Tolea, Magdalena I; Galvin, James E; Surkis, Alisa

2017-04-01

A clinical study team performing three multicultural dementia screening studies identified the need to improve data management practices and facilitate data sharing. A collaboration was initiated with librarians as part of the National Library of Medicine (NLM) informationist supplement program. The librarians identified areas for improvement in the studies' data collection, entry, and processing workflows. The librarians' role in this project was to meet needs expressed by the study team around improving data collection and processing workflows to increase study efficiency and ensure data quality. The librarians addressed the data collection, entry, and processing weaknesses through standardizing and renaming variables, creating an electronic data capture system using REDCap, and developing well-documented, reproducible data processing workflows. NLM informationist supplements provide librarians with valuable experience in collaborating with study teams to address their data needs. For this project, the librarians gained skills in project management, REDCap, and understanding of the challenges and specifics of a clinical research study. However, the time and effort required to provide targeted and intensive support for one study team was not scalable to the library's broader user community.

New on-line separation workflow of microbial metabolites via hyphenation of analytical and preparative comprehensive two-dimensional liquid chromatography.

Science.gov (United States)

Yan, Xia; Wang, Li-Juan; Wu, Zhen; Wu, Yun-Long; Liu, Xiu-Xiu; Chang, Fang-Rong; Fang, Mei-Juan; Qiu, Ying-Kun

2016-10-15

Microbial metabolites represent an important source of bioactive natural products, but always exhibit diverse of chemical structures or complicated chemical composition with low active ingredients content. Traditional separation methods rely mainly on off-line combination of open-column chromatography and preparative high performance liquid chromatography (HPLC). However, the multi-step and prolonged separation procedure might lead to exposure to oxygen and structural transformation of metabolites. In the present work, a new two-dimensional separation workflow for fast isolation and analysis of microbial metabolites from Chaetomium globosum SNSHI-5, a cytotoxic fungus derived from extreme environment. The advantage of this analytical comprehensive two-dimensional liquid chromatography (2D-LC) lies on its ability to analyze the composition of the metabolites, and to optimize the separation conditions for the preparative 2D-LC. Furthermore, gram scale preparative 2D-LC separation of the crude fungus extract could be performed on a medium-pressure liquid chromatograph×preparative high-performance liquid chromatography system, under the optimized condition. Interestingly, 12 cytochalasan derivatives, including two new compounds named cytoglobosin Ab (3) and isochaetoglobosin Db (8), were successfully obtained with high purity in a short period of time. The structures of the isolated metabolites were comprehensively characterized by HR ESI-MS and NMR. To be highlighted, this is the first report on the combination of analytical and preparative 2D-LC for the separation of microbial metabolites. The new workflow exhibited apparent advantages in separation efficiency and sample treatment capacity compared with conventional methods. Copyright © 2016 Elsevier B.V. All rights reserved.