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.

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.

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

KAUST Repository

Ikeda, Robert; Cho, Junsang; Fang, Charlie; Salihoglu, Semih; Torikai, Satoshi; Widom, Jennifer

2012-01-01

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

Concentration distribution of trace elements: from normal distribution to Levy flights

International Nuclear Information System (INIS)

Kubala-Kukus, A.; Banas, D.; Braziewicz, J.; Majewska, U.; Pajek, M.

2003-01-01

The paper discusses a nature of concentration distributions of trace elements in biomedical samples, which were measured by using the X-ray fluorescence techniques (XRF, TXRF). Our earlier observation, that the lognormal distribution well describes the measured concentration distribution is explained here on a more general ground. Particularly, the role of random multiplicative process, which models the concentration distributions of trace elements in biomedical samples, is discussed in detail. It is demonstrated that the lognormal distribution, appearing when the multiplicative process is driven by normal distribution, can be generalized to the so-called log-stable distribution. Such distribution describes the random multiplicative process, which is driven, instead of normal distribution, by more general stable distribution, being known as the Levy flights. The presented ideas are exemplified by the results of the study of trace element concentration distributions in selected biomedical samples, obtained by using the conventional (XRF) and (TXRF) X-ray fluorescence methods. Particularly, the first observation of log-stable concentration distribution of trace elements is reported and discussed here in detail

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.

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

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 method to mine workflows from provenance for assisting scientific workflow composition

NARCIS (Netherlands)

Zeng, R.; He, X.; 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 and complicated due to the large quantities of data

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...

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

Workflow-enabled distributed component-based information architecture for digital medical imaging enterprises.

Science.gov (United States)

Wong, Stephen T C; Tjandra, Donny; Wang, Huili; Shen, Weimin

2003-09-01

Few information systems today offer a flexible means to define and manage the automated part of radiology processes, which provide clinical imaging services for the entire healthcare organization. Even fewer of them provide a coherent architecture that can easily cope with heterogeneity and inevitable local adaptation of applications and can integrate clinical and administrative information to aid better clinical, operational, and business decisions. We describe an innovative enterprise architecture of image information management systems to fill the needs. Such a system is based on the interplay of production workflow management, distributed object computing, Java and Web techniques, and in-depth domain knowledge in radiology operations. Our design adapts the approach of "4+1" architectural view. In this new architecture, PACS and RIS become one while the user interaction can be automated by customized workflow process. Clinical service applications are implemented as active components. They can be reasonably substituted by applications of local adaptations and can be multiplied for fault tolerance and load balancing. Furthermore, the workflow-enabled digital radiology system would provide powerful query and statistical functions for managing resources and improving productivity. This paper will potentially lead to a new direction of image information management. We illustrate the innovative design with examples taken from an implemented system.

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.

Distributed late-binding micro-scheduling and data caching for data-intensive workflows

International Nuclear Information System (INIS)

Delgado Peris, A.

2015-01-01

Today's world is flooded with vast amounts of digital information coming from innumerable sources. Moreover, it seems clear that this trend will only intensify in the future. Industry, society and remarkably science are not indifferent to this fact. On the contrary, they are struggling to get the most out of this data, which means that they need to capture, transfer, store and process it in a timely and efficient manner, using a wide range of computational resources. And this task is not always simple. A very representative example of the challenges posed by the management and processing of large quantities of data is that of the Large Hadron Collider experiments, which handle tens of petabytes of physics information every year. Based on the experience of one of these collaborations, we have studied the main issues involved in the management of huge volumes of data and in the completion of sizeable workflows that consume it. In this context, we have developed a general-purpose architecture for the scheduling and execution of workflows with heavy data requirements: the Task Queue. This new system builds on the late-binding overlay model, which has helped experiments to successfully overcome the problems associated to the heterogeneity and complexity of large computational grids. Our proposal introduces several enhancements to the existing systems. The execution agents of the Task Queue architecture share a Distributed Hash Table (DHT) and perform job matching and assignment cooperatively. In this way, scalability problems of centralized matching algorithms are avoided and workflow execution times are improved. Scalability makes fine-grained micro-scheduling possible and enables new functionalities, like the implementation of a distributed data cache on the execution nodes and the integration of data location information in the scheduling decisions...(Author)

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...

Foundations for Survivable System Development: Service Traces, Intrusion Traces, and Evaluation Models

National Research Council Canada - National Science Library

Linger, Richard

2001-01-01

.... On the system side, survivability specifications can be defined by essential-service traces that map essential-service workflows, derived from user requirements, into system component dependencies...

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.

Log-stable concentration distributions of trace elements in biomedical samples

International Nuclear Information System (INIS)

Kubala-Kukus, A.; Kuternoga, E.; Braziewicz, J.; Pajek, M.

2004-01-01

In the present paper, which follows our earlier observation that the asymmetric and long-tailed concentration distributions of trace elements in biomedical samples, measured by the X-ray fluorescence techniques, can be modeled by the log-stable distributions, further specific aspects of this observation are discussed. First, we demonstrate that, typically, for a quite substantial fraction (10-20%) of trace elements studied in different kinds of biomedical samples, the measured concentration distributions are described in fact by the 'symmetric' log-stable distributions, i.e. the asymmetric distributions which are described by the symmetric stable distributions. This observation is, in fact, expected for the random multiplicative process, which models the concentration distributions of trace elements in the biomedical samples. The log-stable nature of concentration distribution of trace elements results in several problems of statistical nature, which have to be addressed in XRF data analysis practice. Consequently, in the present paper, the following problems, namely (i) the estimation of parameters for stable distributions and (ii) the testing of the log-stable nature of the concentration distribution by using the Anderson-Darling (A 2 ) test, especially for symmetric stable distributions, are discussed in detail. In particular, the maximum likelihood estimation and Monte Carlo simulation techniques were used, respectively, for estimation of stable distribution parameters and calculation of the critical values for the Anderson-Darling test. The discussed ideas are exemplified by the results of the study of trace element concentration distributions in selected biomedical samples, which were obtained by using the X-ray fluorescence (XRF, TXRF) methods

Data distribution method of workflow in the cloud environment

Science.gov (United States)

Wang, Yong; Wu, Junjuan; Wang, Ying

2017-08-01

Cloud computing for workflow applications provides the required high efficiency calculation and large storage capacity and it also brings challenges to the protection of trade secrets and other privacy data. Because of privacy data will cause the increase of the data transmission time, this paper presents a new data allocation algorithm based on data collaborative damage degree, to improve the existing data allocation strategy? Safety and public cloud computer algorithm depends on the private cloud; the static allocation method in the initial stage only to the non-confidential data division to improve the original data, in the operational phase will continue to generate data to dynamically adjust the data distribution scheme. The experimental results show that the improved method is effective in reducing the data transmission time.

DIaaS: Data-Intensive workflows as a service - Enabling easy composition and deployment of data-intensive workflows on Virtual Research Environments

Science.gov (United States)

Filgueira, R.; Ferreira da Silva, R.; Deelman, E.; Atkinson, M.

2016-12-01

We present the Data-Intensive workflows as a Service (DIaaS) model for enabling easy data-intensive workflow composition and deployment on clouds using containers. DIaaS model backbone is Asterism, an integrated solution for running data-intensive stream-based applications on heterogeneous systems, which combines the benefits of dispel4py with Pegasus workflow systems. The stream-based executions of an Asterism workflow are managed by dispel4py, while the data movement between different e-Infrastructures, and the coordination of the application execution are automatically managed by Pegasus. DIaaS combines Asterism framework with Docker containers to provide an integrated, complete, easy-to-use, portable approach to run data-intensive workflows on distributed platforms. Three containers integrate the DIaaS model: a Pegasus node, and an MPI and an Apache Storm clusters. Container images are described as Dockerfiles (available online at http://github.com/dispel4py/pegasus_dispel4py), linked to Docker Hub for providing continuous integration (automated image builds), and image storing and sharing. In this model, all required software (workflow systems and execution engines) for running scientific applications are packed into the containers, which significantly reduces the effort (and possible human errors) required by scientists or VRE administrators to build such systems. The most common use of DIaaS will be to act as a backend of VREs or Scientific Gateways to run data-intensive applications, deploying cloud resources upon request. We have demonstrated the feasibility of DIaaS using the data-intensive seismic ambient noise cross-correlation application (Figure 1). The application preprocesses (Phase1) and cross-correlates (Phase2) traces from several seismic stations. The application is submitted via Pegasus (Container1), and Phase1 and Phase2 are executed in the MPI (Container2) and Storm (Container3) clusters respectively. Although both phases could be executed

The Archive Solution for Distributed Workflow Management Agents of the CMS Experiment at LHC

Energy Technology Data Exchange (ETDEWEB)

Kuznetsov, Valentin [Cornell U.; Fischer, Nils Leif [Heidelberg U.; Guo, Yuyi [Fermilab

2018-03-19

The CMS experiment at the CERN LHC developed the Workflow Management Archive system to persistently store unstructured framework job report documents produced by distributed workflow management agents. In this paper we present its architecture, implementation, deployment, and integration with the CMS and CERN computing infrastructures, such as central HDFS and Hadoop Spark cluster. The system leverages modern technologies such as a document oriented database and the Hadoop eco-system to provide the necessary flexibility to reliably process, store, and aggregate $\\mathcal{O}$(1M) documents on a daily basis. We describe the data transformation, the short and long term storage layers, the query language, along with the aggregation pipeline developed to visualize various performance metrics to assist CMS data operators in assessing the performance of the CMS computing system.

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.

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%.

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.

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

HisT/PLIER: A two-fold Provenance Approach for Grid-enabled Scientific Workflows using WS-VLAM

NARCIS (Netherlands)

Gerhards, M.; Sander, V.; Belloum, A.; Vasunin, D.; Benabdelkader, A.; Jha, S.; Felde, N.G.; Buyya, R.; Fedak, G.

2011-01-01

Large scale scientific applications are frequently modeled as a workflow that is executed under the control of a workflow management system. One crucial requirement is the validation of the generated results, e.g. The trace ability of the experiment execution path. The automated tracking and storage

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

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.

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.

Oceanic distribution and geochemistry of several trace elements at GEOSECS stations

International Nuclear Information System (INIS)

Robertson, D.E.

1975-01-01

The biogeochemical and physical processes operating in the oceans create substantial geographical and vertical variations in the oceanic distribution of many trace elements. These variations are brought about by diverse mechanisms and involve trace elements of a wide spectrum of physicochemical and biological behavior. Thus, a knowledge of these trace element distributions can help characterize some of the ocean processes in which they participate. (auth)

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)

DISTRIBUTION OF TRACE ELEMENTS IN MUSCLE AND ORGANS ...

African Journals Online (AJOL)

a

revealed organ specific distribution of trace metals in Tilapia, which has been discussed .... The concentrations of copper (Table 2) varied from 1.68–4.95 in muscle, .... The lead concentrations in muscle and organs of Tilapia from both lakes were comparable. ... A, D and K, trace minerals, and essential fats and amino acids.

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...

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.

Overcoming the Challenges of Implementing a Multi-Mission Distributed Workflow System

Science.gov (United States)

Sayfi, Elias; Cheng, Cecilia; Lee, Hyun; Patel, Rajesh; Takagi, Atsuya; Yu, Dan

2009-01-01

A multi-mission approach to solving the same problems for various projects is enticing. However, the multi-mission approach leads to the need to develop a configurable, adaptable and distributed system to meet unique project requirements. That, in turn, leads to a set of challenges varying from handling synchronization issues to coming up with a smart design that allows the "unknowns" to be decided later. This paper discusses the challenges that the Multi-mission Automated Task Invocation Subsystem (MATIS) team has come up against while designing the distributed workflow system, as well as elaborates on the solutions that were implemented. The first is to design an easily adaptable system that requires no code changes as a result of configuration changes. The number of formal deliveries is often limited because each delivery costs time and money. Changes such as the sequence of programs being called, a change of a parameter value in the program that is being automated should not result in code changes or redelivery.

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...

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.

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

Trace element distribution in the rat cerebellum

International Nuclear Information System (INIS)

Kwiatek, W.M.; Long, G.J.; Pounds, J.G.; Reuhl, K.R.; Hanson, A.L.; Jones, K.W.

1989-10-01

Spatial distributions and concentrations of trace elements (TE) in the brain are important because TE perform catalytic structural functions in enzymes which regulate brain function and development. We have investigated the distributions of TE in rat cerebellum. Structures were sectioned and analyzed by the Synchrotron Radiation Induced X-ray Emission (SRIXE) method using the NSLS X-26 white-light microprobe facility. Advantages important for TE analysis of biological specimens with x-ray microscopy include short time of measurement, high brightness and flux, good spatial resolution, multielemental detection, good sensitivity, and non-destructive irradiation. Trace elements were measured in thin rat brain sections of 20-micrometers thickness. The analyses were performed on sample volumes as small as 0.2 nl with Minimum Detectable Limits (MDL) of 50 ppb wet weight for Fe, 100 ppb wet weight for Cu, and Zn, and 1 ppM wet weight for Pb. The distribution of TE in the molecular cell layer, granule cell layer and fiber tract of rat cerebella was investigated. Both point analyses and two-dimensional semi-quantitative mapping of the TE distribution in a section were used

Smallest eigenvalue distribution of the fixed-trace Laguerre beta-ensemble

International Nuclear Information System (INIS)

Chen Yang; Liu Dangzheng; Zhou Dasheng

2010-01-01

In this paper we study the entanglement of the reduced density matrix of a bipartite quantum system in a random pure state. It transpires that this involves the computation of the smallest eigenvalue distribution of the fixed-trace Laguerre ensemble of N x N random matrices. We showed that for finite N the smallest eigenvalue distribution may be expressed in terms of Jack polynomials. Furthermore, based on the exact results, we found a limiting distribution when the smallest eigenvalue is suitably scaled with N followed by a large N limit. Our results turn out to be the same as the smallest eigenvalue distribution of the classical Laguerre ensembles without the fixed-trace constraint. This suggests in a broad sense, the global constraint does not influence local correlations, at least, in the large N limit. Consequently, we have solved an open problem: the determination of the smallest eigenvalue distribution of the reduced density matrix-obtained by tracing out the environmental degrees of freedom-for a bipartite quantum system of unequal dimensions.

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.

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

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...

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.

A remote tracing facility for distributed systems

International Nuclear Information System (INIS)

Ehm, F.; Dworak, A.

2012-01-01

Today, CERN's control system is built upon a large number of C++ and Java services producing log events. In such a largely distributed environment these log messages are essential for problem recognition and tracing. Tracing is therefore vital for operation as understanding an issue in a subsystem means analysing log events in an efficient and fast manner. At present 3150 device servers are deployed on 1600 disk-less front-ends and they send their log messages via the network to an in-house developed central server which, in turn, saves them to files. However, this solution is not able to provide several highly desired features and has performance limitations which led to the development of a new solution. The new distributed tracing facility fulfills these requirements by taking advantage of the Streaming Text Oriented Messaging Protocol (STOMP) and ActiveMQ as the transport layer. The system not only allows storing critical log events centrally in files or in a database but also allows other clients (e.g. graphical interfaces) to read the same events concurrently by using the provided Java API. Thanks to the ActiveMQ broker technology the system can easily be extended to clients implemented in other languages and it is highly scalable in terms of performance. Long running tests have shown that the system can handle up to 10.000 messages/second. (authors)

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.

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

Trace elements distribution in environmental compartments

Energy Technology Data Exchange (ETDEWEB)

Queiroz, Juliana C. de; Peres, Sueli da Silva; Godoy, Maria Luiza D.P., E-mail: suelip@ird.gov.br [Instituto de Radioprotecao e Dosimetria (IRD/CNEN-RJ), Rio de Janeiro, RJ (Brazil)

2017-11-01

Trace elements term defines the presence of low concentrations metals at environment. Some of them are considered biologically essential, as Co, Cu and Mn. Others can cause detriment to environment and human health, as Pb, Cd, Hg, As, Ti and U. A large number of them have radioactive isotopes, implying the evaluation of risks for human health should be done considering the precepts of environmental radiological protection. The ecosystem pollution with trace elements generates changes at the geochemistry cycle of these elements and in environmental quality. Soils have single characteristics when compared with another components of biosphere (air, water and biota), cause they introduce themselves not only as a drain towards contaminants, but also as natural buffer that control the transport of chemical elements and other substances for atmosphere, hydrosphere and biota. The main purpose of environmental monitoring program is to evaluate the levels of contaminants in the various compartments of the environment: natural or anthropogenic, and to assess the contribution of a potential contaminant source on the environment. Elemental Composition for the collected samples was determined by inductively coupled plasma mass spectroscopy. The main objective of this work was to evaluate the map baseline of concentration of interest trace elements in environmental samples of water, sediment and soil from Environmental Monitoring Program of Instituto de Radioprotecao e Dosimetria (IRD). The samples were analyzed using an inductively coupled plasma mass spectrometer (ICP-MS) at IRD. >From the knowledge of trace elements concentrations, could be evaluated the environmental quality parameters at the studied ecosystems. The data allowed evaluating some relevant aspects of the study of trace elements in soil and aquatic systems, with emphasis at the distribution, concentration and identification of main anthropic sources of contamination at environment. (author)

Trace elements distribution in environmental compartments

International Nuclear Information System (INIS)

Queiroz, Juliana C. de; Peres, Sueli da Silva; Godoy, Maria Luiza D.P.

2017-01-01

Trace elements term defines the presence of low concentrations metals at environment. Some of them are considered biologically essential, as Co, Cu and Mn. Others can cause detriment to environment and human health, as Pb, Cd, Hg, As, Ti and U. A large number of them have radioactive isotopes, implying the evaluation of risks for human health should be done considering the precepts of environmental radiological protection. The ecosystem pollution with trace elements generates changes at the geochemistry cycle of these elements and in environmental quality. Soils have single characteristics when compared with another components of biosphere (air, water and biota), cause they introduce themselves not only as a drain towards contaminants, but also as natural buffer that control the transport of chemical elements and other substances for atmosphere, hydrosphere and biota. The main purpose of environmental monitoring program is to evaluate the levels of contaminants in the various compartments of the environment: natural or anthropogenic, and to assess the contribution of a potential contaminant source on the environment. Elemental Composition for the collected samples was determined by inductively coupled plasma mass spectroscopy. The main objective of this work was to evaluate the map baseline of concentration of interest trace elements in environmental samples of water, sediment and soil from Environmental Monitoring Program of Instituto de Radioprotecao e Dosimetria (IRD). The samples were analyzed using an inductively coupled plasma mass spectrometer (ICP-MS) at IRD. >From the knowledge of trace elements concentrations, could be evaluated the environmental quality parameters at the studied ecosystems. The data allowed evaluating some relevant aspects of the study of trace elements in soil and aquatic systems, with emphasis at the distribution, concentration and identification of main anthropic sources of contamination at environment. (author)

Particulate trace metals in Cochin backwaters: Distribution of seasonal indices

Digital Repository Service at National Institute of Oceanography (India)

Sankaranarayanan, V.N.; Jayalakshmy, K.V.; Joseph, T.

that surface distribution pattern of the trace metal concentration of cobalt, nickel and iron was almost similar at the four stations thereby stressing the fact that seasonal fluctuations contributed a major part in the surface distribution of these metals...

A lightweight messaging-based distributed processing and workflow execution framework for real-time and big data analysis

Science.gov (United States)

Laban, Shaban; El-Desouky, Aly

2014-05-01

To achieve a rapid, simple and reliable parallel processing of different types of tasks and big data processing on any compute cluster, a lightweight messaging-based distributed applications processing and workflow execution framework model is proposed. The framework is based on Apache ActiveMQ and Simple (or Streaming) Text Oriented Message Protocol (STOMP). ActiveMQ , a popular and powerful open source persistence messaging and integration patterns server with scheduler capabilities, acts as a message broker in the framework. STOMP provides an interoperable wire format that allows framework programs to talk and interact between each other and ActiveMQ easily. In order to efficiently use the message broker a unified message and topic naming pattern is utilized to achieve the required operation. Only three Python programs and simple library, used to unify and simplify the implementation of activeMQ and STOMP protocol, are needed to use the framework. A watchdog program is used to monitor, remove, add, start and stop any machine and/or its different tasks when necessary. For every machine a dedicated one and only one zoo keeper program is used to start different functions or tasks, stompShell program, needed for executing the user required workflow. The stompShell instances are used to execute any workflow jobs based on received message. A well-defined, simple and flexible message structure, based on JavaScript Object Notation (JSON), is used to build any complex workflow systems. Also, JSON format is used in configuration, communication between machines and programs. The framework is platform independent. Although, the framework is built using Python the actual workflow programs or jobs can be implemented by any programming language. The generic framework can be used in small national data centres for processing seismological and radionuclide data received from the International Data Centre (IDC) of the Preparatory Commission for the Comprehensive Nuclear

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

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.

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.

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...

Trace elements distribution in the Amazon floodplain soils

International Nuclear Information System (INIS)

Fernandes, E.A.N.; Ferraz, E.S.B.; Oliveira, H.

1994-01-01

Neutron activation analysis was performed on aluvial soil samples from several sites on the foodplains of the Amazon River and its major tributaries for trace elements determination. The spatial and temporal variations of chemical composition of floodland sediments in the Amazon basin are discussed. No significant difference was found in trace elemental distribution in the floodland soils along the Amazon main channel, even after the source material has been progressively diluted with that from lowland draining tributaries. It was also seen that the average chemical composition of floodplain soils compares well with that of the suspended sedimets. (author) 12 refs.; 5 figs.; 2 tabs

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

Evaluation of distribution patterns and decision of distribution coefficients of trace elements in high-purity aluminium by INAA

International Nuclear Information System (INIS)

Hayakawa, Yasuhiro; Suzuki, Shogo; Hirai, Shoji

1986-01-01

Recently, a high-purity aluminium has been used in semi-coductor device, so on. It was required that trace impurities should be reduced and that its content should be quantitatively evaluated. In this study, distribution patterns of many trace impurities in 99.999 % aluminium ingots, which was purified using a normal freezing method, were evaluated by an INAA. The effective distribution coefficient k for each detected elements was calculated using a theoretical distribution equation in the normal freezing method. As a result, the elements of k 1 was Hf. Especially, La, Sm, U and Th could be effectively purified, but Sc and Hf could be scarcely purified. Further more, it was found that the slower freezing gave the effective distribution coefficient close to the equilibrium distribution coefficient, and that the effective distribution coefficient became smaller with the larger atomic radius. (author)

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

A Distributed Collaborative Workflow Based Approach to Data Collection and Analysis

National Research Council Canada - National Science Library

Gerecke, William; Enas, Douglas; Gottschlich, Susan

2004-01-01

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

Radioactivity and concentration of some trace elements in sponges distributed along the Syrian coast

International Nuclear Information System (INIS)

Al-Masri, M. S.; Mamish, S.; Haleem, M. A.; Ammar, I.

2009-07-01

natural and artificial radionuclides ( 210 Po, 210 Pb, 40 K, 137 Cs, 234 U, 238 U) and concentration of some trace elements (Zn, Cu, Pb, Cd) in several types of sponges distributed along the Syrian coast have been studied. The samples were collected from four stations distributed at the Syrian coast (Al-Basset, Lattakia, Banise, Tartous). Concentration factors (CF) for the studied radionuclides and trace elements have been calculated in order to determine the sponges types to be used as biomonitors for the radionuclides and trace elements. (authors)

Distributions of traces of metals on sorption from solutions of vanadium(V)

International Nuclear Information System (INIS)

Evseeva, N.K.; Turnaov, A.N.; Telegin, G.F.; Kremenskaya, I.N.

1983-01-01

A study is made of the distributions of traces of metals between aqueous solutions of vanadium(V) and a solid reagent made by introducing di-2-ethylhexylphosphoric acid into an inert matrix: a nonionic macroporous copolymer of polystyrene with divinyl benzene (wofatit Y 29). As regards degree of extraction, the trace components fall in the series zinc > cadmium > manganese > copper > cobalt, which resemble the extractability series. The vanadium content of the solution and the concentrations of the trace components have virtually no effect on the sorption. The process is effective in concentrating trace components from solutions containing vanadium(V)

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

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

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.

Ray tracing the Wigner distribution function for optical simulations

NARCIS (Netherlands)

Mout, B.M.; Wick, Michael; Bociort, F.; Petschulat, Joerg; Urbach, Paul

2018-01-01

We study a simulation method that uses the Wigner distribution function to incorporate wave optical effects in an established framework based on geometrical optics, i.e., a ray tracing engine. We use the method to calculate point spread functions and show that it is accurate for paraxial 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)

Distribution of uranium and some trace elements in groundwater of eastern delta, egypt

International Nuclear Information System (INIS)

Hamza, M.S.; Aly, A.I.M.; Swailem, F.M.; Elreedy, W.; Nada, A.

1986-01-01

The distribution pattern of uranium and some trace elements in groundwater of eastern Nile delta indicate general trend of increasing trace element concentration from west and south to North and east direction. This trend is most probably due to extensive leaching from the soil due to recharge from irrigation water. The geochemical correlation among trace elements was also investigated. Possible industrial pollution in bahtim area was detected.1 fig.,4 tab

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

Distribution of trace elements in the coastal sea sediments of Maslinica Bay, Croatia

Science.gov (United States)

Mikulic, Nenad; Orescanin, Visnja; Elez, Loris; Pavicic, Ljiljana; Pezelj, Durdica; Lovrencic, Ivanka; Lulic, Stipe

2008-02-01

Spatial distributions of trace elements in the coastal sea sediments and water of Maslinica Bay (Southern Adriatic), Croatia and possible changes in marine flora and foraminifera communities due to pollution were investigated. Macro, micro and trace elements’ distributions in five granulometric fractions were determined for each sediment sample. Bulk sediment samples were also subjected to leaching tests. Elemental concentrations in sediments, sediment extracts and seawater were measured by source excited energy dispersive X-ray fluorescence (EDXRF). Concentrations of the elements Cr, Cu, Zn, and Pb in bulk sediment samples taken in the Maslinica Bay were from 2.1 to over six times enriched when compared with the background level determined for coarse grained carbonate sediments. A low degree of trace elements leaching determined for bulk sediments pointed to strong bonding of trace elements to sediment mineral phases. The analyses of marine flora pointed to higher eutrophication, which disturbs the balance between communities and natural habitats.

Evaluation of Circle Diameter by Distributed Tactile Information in Active Tracing

Directory of Open Access Journals (Sweden)

Hiroyuki Nakamoto

2013-01-01

Full Text Available Active touch with voluntary movement on the surface of an object is important for human to obtain the local and detailed features on it. In addition, the active touch is considered to enhance the human spatial resolution. In order to improve dexterity performance of multifinger robotic hands, it is necessary to study an active touch method for robotic hands. In this paper, first, we define four requirements of a tactile sensor for active touch and design a distributed tactile sensor model, which can measure a distribution of compressive deformation. Second, we suggest a measurement process with the sensor model, a synthesis method of distributed deformations. In the experiments, a five-finger robotic hand with tactile sensors traces on the surface of cylindrical objects and evaluates the diameters. We confirm that the hand can obtain more information of the diameters by tracing the finger.

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.

Distribution of particulate trace metals in the western Bay of Bengal

Digital Repository Service at National Institute of Oceanography (India)

Satyanarayana, D.; Murty, P.V.S.P.; Sarma, V.V.

continuous increase from surface to bottom in the case ofFe, Ni, which appeared to be related to a combination offactors suchas authigenicprecipita tion/scavenging, rcsuspension of bottom rich sediments, and diffusion followed by precipitation at sedimcnt... ), most of these studies do not provide information onthe interaction of trace elements with particulate matter. The present study deals with the distribution of particulate trace metals (Fe, Mn, Co, Ni, Cu, Pb, Zn and Cd) and their possible interactions...

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

Science.gov (United States)

Plale, B.

2009-05-01

under high-volume conditions, or the searchability and manageability of the resulting data products is disappointingly low. The provenance of a data product is a record of its lineage, or trace of the execution history that resulted in the product. The provenance of a forecast model result, e.g., captures information about the executable version of the model, configuration parameters, input data products, execution environment, and owner. Provenance enables data to be properly attributed and captures critical parameters about the model run so the quality of the result can be ascertained. Proper provenance is essential to providing reproducible scientific computing results. Workflow languages used in science discovery are complete programming languages, and in theory can support any logic expressible by a programming language. The execution environments supporting the workflow engines, on the other hand, are subject to constraints on physical resources, and hence in practice the workflow task graphs used in science utilize relatively few of the cataloged workflow patterns. It is important to note that these workflows are executed on demand, and are executed once. Into this context is introduced the need for science discovery that is responsive to real time information. If we can use simple programming models and abstractions to make scientific discovery involving real-time data accessible to specialists who share and utilize data across scientific domains, we bring science one step closer to solving the largest of human problems.

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.

Distribution of Selected Trace Elements in the Bayer Process

Directory of Open Access Journals (Sweden)

Johannes Vind

2018-05-01

Full Text Available The aim of this work was to achieve an understanding of the distribution of selected bauxite trace elements (gallium (Ga, vanadium (V, arsenic (As, chromium (Cr, rare earth elements (REEs, scandium (Sc in the Bayer process. The assessment was designed as a case study in an alumina plant in operation to provide an overview of the trace elements behaviour in an actual industrial setup. A combination of analytical techniques was used, mainly inductively coupled plasma mass spectrometry and optical emission spectroscopy as well as instrumental neutron activation analysis. It was found that Ga, V and As as well as, to a minor extent, Cr are principally accumulated in Bayer process liquors. In addition, Ga is also fractionated to alumina at the end of the Bayer processing cycle. The rest of these elements pass to bauxite residue. REEs and Sc have the tendency to remain practically unaffected in the solid phases of the Bayer process and, therefore, at least 98% of their mass is transferred to bauxite residue. The interest in such a study originates from the fact that many of these trace constituents of bauxite ore could potentially become valuable by-products of the Bayer process; therefore, the understanding of their behaviour needs to be expanded. In fact, Ga and V are already by-products of the Bayer process, but their distribution patterns have not been provided in the existing open literature.

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.

Distribution of trace and minor elements in Hungarian spice paprika plants

Energy Technology Data Exchange (ETDEWEB)

Sziklai, I L; Oerdoegh, M; Szabo, E; Molnar, E

1988-06-01

Detailed investigations were carried out to study the distribution of trace and minor elements in different parts (fruit, seed and rib, peduncle, stem, leaf, root) of ripe Hungarian spice paprika plants. Two varieties were analyzed for their Cl, Co, Fe, K, Mg, Mn, Na, Rb, Sc, V and Zn content by non-destructive neutron activation analysis. The results showed that the iron contents of the samples were much higher than those of the other trace elements. For trace elements Co, Fe, Mn, Sc, V and Zn a considerable enrichment was observed in the leaf, while the Rb and K, Na, Mg showed accumulation mainly in the peduncle. (author) 8 refs.; 3 tabs.

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

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

Wireless remote control of clinical image workflow: using a PDA for off-site distribution and disaster recovery.

Science.gov (United States)

Documet, Jorge; Liu, Brent J; Documet, Luis; Huang, H K

2006-07-01

This paper describes a picture archiving and communication system (PACS) tool based on Web technology that remotely manages medical images between a PACS archive and remote destinations. Successfully implemented in a clinical environment and also demonstrated for the past 3 years at the conferences of various organizations, including the Radiological Society of North America, this tool provides a very practical and simple way to manage a PACS, including off-site image distribution and disaster recovery. The application is robust and flexible and can be used on a standard PC workstation or a Tablet PC, but more important, it can be used with a personal digital assistant (PDA). With a PDA, the Web application becomes a powerful wireless and mobile image management tool. The application's quick and easy-to-use features allow users to perform Digital Imaging and Communications in Medicine (DICOM) queries and retrievals with a single interface, without having to worry about the underlying configuration of DICOM nodes. In addition, this frees up dedicated PACS workstations to perform their specialized roles within the PACS workflow. This tool has been used at Saint John's Health Center in Santa Monica, California, for 2 years. The average number of queries per month is 2,021, with 816 C-MOVE retrieve requests. Clinical staff members can use PDAs to manage image workflow and PACS examination distribution conveniently for off-site consultations by referring physicians and radiologists and for disaster recovery. This solution also improves radiologists' effectiveness and efficiency in health care delivery both within radiology departments and for off-site clinical coverage.

A study about trace element distribution in cancer tissue and serum of cancer patients

International Nuclear Information System (INIS)

Lee, Jong In; Lee, Eun Joo; Jung, Young Joo

1993-01-01

Authers analyzed the trace element distribution of cancer tissue and its corresponding normal tissue and serum of preoperative and postoperative stage in gastric, colon, breast cancer patients. Zinc and rubidium were higher in concentration in breast cancer tissue than in normal tissue. As for the distribution of trace element in serum, bromine became about 10 times higher after gastric resection. This result can be applied to experimental carcinogenesis and to relationship with other prognostic factors. (Author)

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.

CMS data and workflow management system

CERN Document Server

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

2008-01-01

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

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.

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.

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

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

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.

Main-, minor- and trace elements distribution in human brain

International Nuclear Information System (INIS)

Zoeger, N.; Streli, C.; Wobrauschek, P.; Jokubonis, C.; Pepponi, G.; Roschger, P.; Bohic, S.; Osterode, W.

2004-01-01

Lead (Pb) is known to induce adverse health effects in humans. In fact, cognitive deficits are repeatedly described with Pb exposure, but little is known about the distribution of lead in brain. Measurements of the distribution of Pb in human brain and to study if Pb is associated with the distribution of other chemical elements such as zinc (Zn), iron (Fe) is of great interest and could reveal some hints about the metabolism of Pb in brain. To determine the local distribution of lead (Pb) and other trace elements x-ray fluorescence spectroscopy (XRF) measurements have been performed, using a microbeam setup and highest flux synchrotron radiation. Experiments have been carried out at ID-22, ESRF, Grenoble, France. The installed microprobe setup provides a monochromatic beam (17 keV) from an undulator station focused by Kirkpatrick-Baez x-ray optics to a spot size of 5 μm x 3μm. Brain slices (20 μm thickness, imbedded in paraffin and mounted on Kapton foils) from areas of the frontal cortex, thalamus and hippocampus have been investigated. Generally no significant increase in fluorescence intensities could be detected in one of the investigated brain compartments. However Pb and other (trace) elements (e.g. S, Ca, Fe, Cu, Zn, Br) could be detected in all samples and showed strong inhomogeneities across the analyzed areas. While S, Ca, Fe, Cu, Zn and Br could be clearly assigned to the investigated brain structures (vessels, etc.) Pb showed a very different behavior. In some cases (e.g. plexus choroidei) Pb was located at the walls of the vessel, whereas with other structures (e.g. blood vessel) this correlation was not found. Moreover, the detected Pb in different brain areas was individually correlated with various elements. The local distribution of the detected elements in various brain structures will be discussed in this work. (author)

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.

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.

Distribution and Potential Toxicity of Trace Metals in the Surface Sediments of Sundarban Mangrove Ecosystem, Bangladesh

Science.gov (United States)

Kumar, A.; Ramanathan, A.; Mathukumalli, B. K. P.; Datta, D. K.

2014-12-01

The distribution, enrichment and ecotoxocity potential of Bangladesh part of Sundarban mangrove was investigated for eight trace metals (As, Cd, Cr, Cu, Fe, Mn, Pb and Zn) using sediment quality assessment indices. The average concentration of trace metals in the sediments exceeded the crustal abundance suggesting sources other than natural in origin. Additionally, the trace metals profile may be a reflection of socio-economic development in the vicinity of Sundarban which further attributes trace metals abundance to the anthropogenic inputs. Geoaccumulation index suggests moderately polluted sediment quality w.r.t. Ni and As and background concentrations for Al, Fe, Mn, Cu, Zn, Pb, Co, As and Cd. Contamination factor analysis suggested low contamination by Zn, Cr, Co and Cd, moderate by Fe, Mn, Cu and Pb while Ni and As show considerable and high contamination, respectively. Enrichment factors for Ni, Pb and As suggests high contamination from either biota or anthropogenic inputs besides natural enrichment. As per the three sediment quality guidelines, Fe, Mn, Cu, Ni, Co and As would be more of a concern with respect to ecotoxicological risk in the Sundarban mangroves. The correlation between various physiochemical variables and trace metals suggested significant role of fine grained particles (clay) in trace metal distribution whereas owing to low organic carbon content in the region the organic complexation may not be playing significant role in trace metal distribution in the Sundarban mangroves.

Using SensorML to describe scientific workflows in distributed web service environments

CSIR Research Space (South Africa)

Van Zyl, TL

2009-07-01

Full Text Available for increased collaboration through workflow sharing. The Sensor Web is an open complex adaptive system the pervades the internet and provides access to sensor resources. One mechanism for describing sensor resources is through the use of Sensor ML. It is shown...

Using SensorML to describe scientific workflows in distributed web service environments

CSIR Research Space (South Africa)

Van Zyl, TL

2009-07-01

Full Text Available for increased collaboration through workflow sharing. The Sensor Web is an open complex adaptive system the pervades the internet and provides access to sensor resources. One mechanism for describing sensor resources is through the use of SensorML. It is shown...

Ray tracing the Wigner distribution function for optical simulations

Science.gov (United States)

Mout, Marco; Wick, Michael; Bociort, Florian; Petschulat, Joerg; Urbach, Paul

2018-01-01

We study a simulation method that uses the Wigner distribution function to incorporate wave optical effects in an established framework based on geometrical optics, i.e., a ray tracing engine. We use the method to calculate point spread functions and show that it is accurate for paraxial systems but produces unphysical results in the presence of aberrations. The cause of these anomalies is explained using an analytical model.

Direct observation of two dimensional trace gas distributions with an airborne Imaging DOAS instrument

Directory of Open Access Journals (Sweden)

K.-P. Heue

2008-11-01

Full Text Available In many investigations of tropospheric chemistry information about the two dimensional distribution of trace gases on a small scale (e.g. tens to hundreds of metres is highly desirable. An airborne instrument based on imaging Differential Optical Absorption Spectroscopy has been built to map the two dimensional distribution of a series of relevant trace gases including NO₂, HCHO, C₂H₂O₂, H₂O, O₄, SO₂, and BrO on a scale of 100 m.

Here we report on the first tests of the novel aircraft instrument over the industrialised South African Highveld, where large variations in NO₂ column densities in the immediate vicinity of several sources e.g. power plants or steel works, were measured. The observed patterns in the trace gas distribution are interpreted with respect to flux estimates, and it is seen that the fine resolution of the measurements allows separate sources in close proximity to one another to be distinguished.

An Adaptable Seismic Data Format for Modern Scientific Workflows

Science.gov (United States)

Smith, J. A.; Bozdag, E.; Krischer, L.; Lefebvre, M.; Lei, W.; Podhorszki, N.; Tromp, J.

2013-12-01

Data storage, exchange, and access play a critical role in modern seismology. Current seismic data formats, such as SEED, SAC, and SEG-Y, were designed with specific applications in mind and are frequently a major bottleneck in implementing efficient workflows. We propose a new modern parallel format that can be adapted for a variety of seismic workflows. The Adaptable Seismic Data Format (ASDF) features high-performance parallel read and write support and the ability to store an arbitrary number of traces of varying sizes. Provenance information is stored inside the file so that users know the origin of the data as well as the precise operations that have been applied to the waveforms. The design of the new format is based on several real-world use cases, including earthquake seismology and seismic interferometry. The metadata is based on the proven XML schemas StationXML and QuakeML. Existing time-series analysis tool-kits are easily interfaced with this new format so that seismologists can use robust, previously developed software packages, such as ObsPy and the SAC library. ADIOS, netCDF4, and HDF5 can be used as the underlying container format. At Princeton University, we have chosen to use ADIOS as the container format because it has shown superior scalability for certain applications, such as dealing with big data on HPC systems. In the context of high-performance computing, we have implemented ASDF into the global adjoint tomography workflow on Oak Ridge National Laboratory's supercomputer Titan.

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...

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.

Evaluation of trace elements distribution in water, sediment, soil and cassava plant in Muria peninsula environment by NAA method

International Nuclear Information System (INIS)

Muryono, H.; Sumining; Agus Taftazani; Kris Tri Basuki; Sukarman, A.

1999-01-01

The evaluation of trace elements distribution in water, sediment, soil and cassava plant in Muria peninsula by NAA method were done. The nuclear power plant (NPP) and the coal power plant (CPP) will be built in Muria peninsula, so, the Muria peninsula is an important site for samples collection and monitoring of environment. River-water, sediment, dryland-soil and cassava plant were choosen as specimens samples from Muria peninsula environment. The analysis result of trace elements were used as a contributed data for environment monitoring before and after NPP was built. The trace elements in specimens of river-water, sediment, dryland-soil and cassava plant samples were analyzed by INAA method. It was found that the trace elements distribution were not evenly distributed. Percentage of trace elements distribution in river-water, sediment, dryland-soil and cassava leaves were 0.00026-0.037% in water samples, 0.49-62.7% in sediment samples, 36.29-99.35% in soil samples and 0.21-99.35% in cassava leaves. (author)

Evaluation of trace elements distribution in water, sediment, soil and cassava plant in Muria peninsula environment by NAA method

Energy Technology Data Exchange (ETDEWEB)

Muryono, H.; Sumining; Agus Taftazani; Kris Tri Basuki; Sukarman, A. [Yogyakarta Nuclear Research Center, Yogyakarta (Indonesia)

1999-10-01

The evaluation of trace elements distribution in water, sediment, soil and cassava plant in Muria peninsula by NAA method were done. The nuclear power plant (NPP) and the coal power plant (CPP) will be built in Muria peninsula, so, the Muria peninsula is an important site for samples collection and monitoring of environment. River-water, sediment, dryland-soil and cassava plant were choosen as specimens samples from Muria peninsula environment. The analysis result of trace elements were used as a contributed data for environment monitoring before and after NPP was built. The trace elements in specimens of river-water, sediment, dryland-soil and cassava plant samples were analyzed by INAA method. It was found that the trace elements distribution were not evenly distributed. Percentage of trace elements distribution in river-water, sediment, dryland-soil and cassava leaves were 0.00026-0.037% in water samples, 0.49-62.7% in sediment samples, 36.29-99.35% in soil samples and 0.21-99.35% in cassava leaves. (author)

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.

ERROR HANDLING IN INTEGRATION WORKFLOWS

Directory of Open Access Journals (Sweden)

Alexey M. Nazarenko

2017-01-01

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

Snakemake-a scalable bioinformatics workflow engine

NARCIS (Netherlands)

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

2012-01-01

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

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.)

Can liming change root anatomy, biomass allocation and trace element distribution among plant parts of Salix × smithiana in trace element-polluted soils?

Science.gov (United States)

Vondráčková, Stanislava; Tlustoš, Pavel; Száková, Jiřina

2017-08-01

Willows (Salix spp.) are considered to be effective for the phytoremediation of trace elements from contaminated soils, but their efficiency is limited in heavily polluted soils because of poor growth. Liming can be a desirable measure to decrease the plant availability of elements, resulting in improved plant development. Notably, large root area and maximum soil penetration are basic parameters that improve the efficiency of phytoremediation. The impact of soil chemical properties on willow root anatomy and the distribution of trace elements below-ground have rarely been studied. The effect of liming on root parameters, biomass allocation and trace element distribution in non-harvestable (coarse roots, fine roots, stumps) and harvestable plant parts (twigs and leaves) of Salix × smithiana was assessed at the end of a 4-year pot experiment with two trace element-polluted soils that differed in terms of soil pH. Stump biomass predominated in weakly acidic soil. In neutral soil, the majority of biomass was located in fine roots and stumps; the difference from other plant parts was minor. Trace elements were the most concentrated in fine roots. Translocation to above-ground biomass increased as follows: Pb roots roots). Lime application decreased the concentrations of mobile Cd and Zn and related levels in plants, improved biomass production and root parameters and increased the removal of all trace elements in weakly acidic soil. None or minimum differences in the monitored parameters were recorded for dolomite treatments in both soils. The dose and source of liming had crucial effects on root anatomy. Growing willows in limed trace element-polluted soils is a suitable measure for combination of two remediation strategies, i.e. phytoextraction of Cd and Zn and assisted phytostabilization of As and Pb.

Trace element distributions in aquatic sediments of Danang - Hoian area, Vietnam

Energy Technology Data Exchange (ETDEWEB)

Thuy, H.T.T.; Tobschall, H.J. [Erlangen-Nuernberg Univ., Erlangen (Germany). Inst. fuer Geologie und Mineralogie; An, P.V. [University of Mining and Geology, Hanoi (Viet Nam)

2000-05-01

Distribution of the trace elements Cr, Cu, Ni, Pb and Zn in surficial sediments of the river/sea environment in Danang - Hoian area (Vietnam) was investigated to examine the degree of metal pollution caused by anthropogenic activities. Point sources from domestic and industrial wastes are identified as dominant contributors of trace element accumulation. Surficial sediments of Hoian River show extremely high total concentrations of Cu (Average Concentration 295 {mu}g/g), Ni (AC 112 {mu}g/g), Pb (AC 396 {mu}g/g) and Zn (AC 429 mug/g) that exceed assigned safety levels ER-M. Similarly, the sediments of Han River show high Pb (AC 188 {mu}g/g) and Zn (AC 282 {mu}g/g) contents. In marine sediments of Thanhbinh beach Pb is also enriched (138 {mu}g/g) above guideline levels. In contrast the sediments of the Cude River are dominated by trace element concentrations close to background values. (orig.)

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...

Distributed trace using central performance counter memory

Science.gov (United States)

Satterfield, David L.; Sexton, James C.

2013-01-22

A plurality of processing cores, are central storage unit having at least memory connected in a daisy chain manner, forming a daisy chain ring layout on an integrated chip. At least one of the plurality of processing cores places trace data on the daisy chain connection for transmitting the trace data to the central storage unit, and the central storage unit detects the trace data and stores the trace data in the memory co-located in with the central storage unit.

Spatial Distribution of Trace Elements in Rice Field at Prafi District Manokwari

Directory of Open Access Journals (Sweden)

Aplena Elen S. Bless

2016-08-01

Full Text Available Mapping spatial variability of trace elements in rice Ḁeld is necessary to obtain soil quality information to en-hance rice production. ἀis study was aimed to measure concentration and distribution of Zn, Cu, Fe, Pb, and Cd in two diᴀerent sites (SP1, SP2 of PraḀ rice Ḁeld in Manokwari West Papua. ἀe representative 26 soil samples were analysed for their available trace metal concentration (DTPA, soil pH, and C-organic and soil texture. ἀe result indicated that Fe toxicity and Zn deḀcient problems were encountered in both sites.  Rice Ḁeld in SP2 was more deḀcient in Zn than SP1. Site with the highest trace elements (Zn, Fe, Cu, and Cd concentration had low soil pH and high C-organic. Acidic soil has higher solubility of metals; while high C-organic could improve the formation of dissolve organic carbon-metal binding, hence it improving the trace metals concentration in soil solution.

A semi-automated workflow for biodiversity data retrieval, cleaning, and quality control

Directory of Open Access Journals (Sweden)

Cherian Mathew

2014-12-01

Full Text Available The compilation and cleaning of data needed for analyses and prediction of species distributions is a time consuming process requiring a solid understanding of data formats and service APIs provided by biodiversity informatics infrastructures. We designed and implemented a Taverna-based Data Refinement Workflow which integrates taxonomic data retrieval, data cleaning, and data selection into a consistent, standards-based, and effective system hiding the complexity of underlying service infrastructures. The workflow can be freely used both locally and through a web-portal which does not require additional software installations by users.

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.)

Reproducible Bioconductor workflows using browser-based interactive notebooks and containers.

Science.gov (United States)

Almugbel, Reem; Hung, Ling-Hong; Hu, Jiaming; Almutairy, Abeer; Ortogero, Nicole; Tamta, Yashaswi; Yeung, Ka Yee

2018-01-01

Bioinformatics publications typically include complex software workflows that are difficult to describe in a manuscript. We describe and demonstrate the use of interactive software notebooks to document and distribute bioinformatics research. We provide a user-friendly tool, BiocImageBuilder, that allows users to easily distribute their bioinformatics protocols through interactive notebooks uploaded to either a GitHub repository or a private server. We present four different interactive Jupyter notebooks using R and Bioconductor workflows to infer differential gene expression, analyze cross-platform datasets, process RNA-seq data and KinomeScan data. These interactive notebooks are available on GitHub. The analytical results can be viewed in a browser. Most importantly, the software contents can be executed and modified. This is accomplished using Binder, which runs the notebook inside software containers, thus avoiding the need to install any software and ensuring reproducibility. All the notebooks were produced using custom files generated by BiocImageBuilder. BiocImageBuilder facilitates the publication of workflows with a point-and-click user interface. We demonstrate that interactive notebooks can be used to disseminate a wide range of bioinformatics analyses. The use of software containers to mirror the original software environment ensures reproducibility of results. Parameters and code can be dynamically modified, allowing for robust verification of published results and encouraging rapid adoption of new methods. Given the increasing complexity of bioinformatics workflows, we anticipate that these interactive software notebooks will become as necessary for documenting software methods as traditional laboratory notebooks have been for documenting bench protocols, and as ubiquitous. © The Author 2017. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Study of particle size and trace metal distribution in atmospheric aerosols of islamabad

International Nuclear Information System (INIS)

Shah, M.H.; Shaheen, N.

2009-01-01

Atmospheric aerosol samples were collected on glass fibre filters using high volume air samplers Half of each aerosol sample was solubilized in nitric acid/hydrochloric acid based wet digestion method and the concentration of trace metals was determined through flame atomic absorption spectrophotometer. Among the eight trace metals analyzed, mean concentration recorded for Zn (844 ng/m3), Fe (642 ng/m3) and Pb (253 ng/m3), was found to be higher than mean levels of Mn, Cr and Co. The size distribution of the collected particulate samples was carried out on mastersizer, which revealed PM/sub 100-10/ as the major fraction (55 %) followed by PM/sub 2.5-10/ (28 %). The correlation study evidenced a strong tendency of trace metals to be associated with fine particulate fractions. The atmospheric trace metal levels showed that the mean metal concentrations in the atmosphere of Islamabad are far higher than background and European urban sites mainly due to the anthropogenic emissions. (author)

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.

Distribution of trace species in power plant streams: A European perspective

International Nuclear Information System (INIS)

Meij, R.

1994-01-01

In the Netherlands only pulverized coal-fired dry bottom boilers are installed. The flue gases are cleaned by high-efficiency cold-side electrostatic precipitators (ESPs) and in all large coal-fired power plants by flue-gas desulfurization (FGD) installations of the lime(stone)/gypsum process. KEMA has performed a large research program on the fate of (trace) elements at coal-fired power plants. A great deal of attention has been paid to the concentrations and distribution of trace elements in coal, in ash and in the vapor phase in the flue gases. Sixteen balance studies of coal-fired power plants, where coal imported from various countries is fired, have been performed. With the information provided by these studies the enrichment factors for the trace elements in ash and the vaporization percentage of the minor and trace elements in the flue gases have been calculated. Using these enrichment factors and vaporization percentages combined with data on the concentration in the coal, the concentrations in the ash and in the vapor phase in the flue gases can be predicted. The emission into the air of trace elements occurs in the solid state (fly ash) and in the gaseous state. The emissions in the solid state are low due to the high degree of removal in the ESPs. The emissions in the gaseous phase are, relatively speaking, more important. In an FGD both emissions are further diminished. In the next section the behavior of elements in the boiler and ESP will be discussed. The influence of the electrostatic precipitators will be reviewed the section thereafter, followed by the fate of gaseous minor and trace elements. And finally the behavior of elements in the FGD will be treated in the last section

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.

The failure trace archive : enabling comparative analysis of failures in diverse distributed systems

NARCIS (Netherlands)

Kondo, D.; Javadi, B.; Iosup, A.; Epema, D.H.J.

2010-01-01

With the increasing functionality and complexity of distributed systems, resource failures are inevitable. While numerous models and algorithms for dealing with failures exist, the lack of public trace data sets and tools has prevented meaningful comparisons. To facilitate the design, validation,

Distribution characteristics of available trace elements in soil from a reclaimed land in a mining area of north Shaanxi, China

Directory of Open Access Journals (Sweden)

Li Zhanbin

2013-06-01

Full Text Available Through field and laboratory tests we studied the temporal and spatial variation in the soil content of four available trace elements :copper(Cu, iron(Fe, manganese(Mn and zinc (Zn, to analyze their distribution characteristics in reclaimed mining land under different reclamation conditions. The available trace elements content varied considerably with different land reclamation patterns. Extended reclamation time was helpful for the recovery of the available trace element content in the soil, and after more than eight years of soil reclamation, the content of available trace elements was closer to or greater than that in soil under natural conditions. Various treatment measures significantly influenced the content and distribution of available trace elements in the soil, and reasonable artificial treatments, including covering the soil and growing shrubs and herbaceous plants, increased the content of available trace elements.

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

A performance study of grid workflow engines

NARCIS (Netherlands)

Stratan, C.; Iosup, A.; Epema, D.H.J.

2008-01-01

To benefit from grids, scientists require grid workflow engines that automatically manage the execution of inter-related jobs on the grid infrastructure. So far, the workflows community has focused on scheduling algorithms and on interface tools. Thus, while several grid workflow engines have been

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...

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

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

Sources and distribution of trace elements in Estonian peat

Science.gov (United States)

Orru, Hans; Orru, Mall

2006-10-01

This paper presents the results of the distribution of trace elements in Estonian mires. Sixty four mires, representative of the different landscape units, were analyzed for the content of 16 trace elements (Cr, Mn, Ni, Cu, Zn, and Pb using AAS; Cd by GF-AAS; Hg by the cold vapour method; and V, Co, As, Sr, Mo, Th, and U by XRF) as well as other peat characteristics (peat type, degree of humification, pH and ash content). The results of the research show that concentrations of trace elements in peat are generally low: V 3.8 ± 0.6, Cr 3.1 ± 0.2, Mn 35.1 ± 2.7, Co 0.50 ± 0.05, Ni 3.7 ± 0.2, Cu 4.4 ± 0.3, Zn 10.0 ± 0.7, As 2.4 ± 0.3, Sr 21.9 ± 0.9, Mo 1.2 ± 0.2, Cd 0.12 ± 0.01, Hg 0.05 ± 0.01, Pb 3.3 ± 0.2, Th 0.47 ± 0.05, U 1.3 ± 0.2 μg g - 1 and S 0.25 ± 0.02%. Statistical analyses on these large database showed that Co has the highest positive correlations with many elements and ash content. As, Ni, Mo, ash content and pH are also significantly correlated. The lowest abundance of most trace elements was recorded in mires fed only by precipitation (ombrotrophic), and the highest in mires fed by groundwater and springs (minerotrophic), which are situated in the flood plains of river valleys. Concentrations usually differ between the superficial, middle and bottom peat layers, but the significance decreases depending on the type of mire in the following order: transitional mires - raised bogs - fens. Differences among mire types are highest for the superficial but not significant for the basal peat layers. The use of peat with high concentrations of trace elements in agriculture, horticulture, as fuel, for water purification etc., may pose a risk for humans: via the food chain, through inhalation, drinking water etc.

Dissolved trace metal (Cu, Cd, Co, Ni, and Ag) distribution and Cu speciation in the southern Yellow Sea and Bohai Sea, China

Science.gov (United States)

Li, Li; Xiaojing, Wang; Jihua, Liu; Xuefa, Shi

2017-02-01

Trace metals play an important role in biogeochemical cycling in ocean systems. However, because the use of trace metal clean sampling and analytical techniques has been limited in coastal China, there are few accurate trace metal data for that region. This work studied spatial distribution of selected dissolved trace metals (Ag, Cu, Co, Cd, and Ni) and Cu speciation in the southern Yellow Sea (SYS) and Bohai Sea (BS). In general, the average metal (Cu, Co, Cd, and Ni) concentrations found in the SYS were lower by a factor of two than those in BS, and they are comparable to dissolved trace metal concentrations in coastal seawater of the United States and Europe. Possible sources and sinks and physical and biological processes that influenced the distribution of these trace metals in the study region were further examined. Close relationships were found between the trace metal spatial distribution with local freshwater discharge and processes such as sediment resuspension and biological uptake. Ag, owing to its extremely low concentrations, exhibited a unique distribution pattern that magnified the influences from the physical and biological processes. Cu speciation in the water column showed that, in the study region, Cu was strongly complexed with organic ligands and concentrations of free cupric ion were in the range of 10-12.6-10-13.2 mol L-1. The distribution of Cu-complexing ligand, indicated by values of the side reaction coefficient α', was similar to the Chl a distribution, suggesting that in situ biota production may be one main source of Cu-complexing organic ligand.

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...

Resident Workflow and Psychiatric Emergency Consultation: Identifying Factors for Quality Improvement in a Training Environment.

Science.gov (United States)

Blair, Thomas; Wiener, Zev; Seroussi, Ariel; Tang, Lingqi; O'Hora, Jennifer; Cheung, Erick

2017-06-01

Quality improvement to optimize workflow has the potential to mitigate resident burnout and enhance patient care. This study applied mixed methods to identify factors that enhance or impede workflow for residents performing emergency psychiatric consultations. The study population consisted of all psychiatry program residents (55 eligible, 42 participating) at the Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles. The authors developed a survey through iterative piloting, surveyed all residents, and then conducted a focus group. The survey included elements hypothesized to enhance or impede workflow, and measures pertaining to self-rated efficiency and stress. Distributional and bivariate analyses were performed. Survey findings were clarified in focus group discussion. This study identified several factors subjectively associated with enhanced or impeded workflow, including difficulty with documentation, the value of personal organization systems, and struggles to communicate with patients' families. Implications for resident education are discussed.

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.

Distribution of trace elements in the brain of EL (epilepsy) mice.

Science.gov (United States)

Hirate, Maki; Takeda, Atsushi; Tamano, Haruna; Enomoto, Shuichi; Oku, Naoto

2002-09-01

The association of essential trace elements with epileptic seizures is poorly understood. On the basis of the evidences that the release of zinc from the brain of epilepsy (EL) mice, an animal model of genetically determined epilepsy, is enhanced by the induction of seizures and that alteration of zinc homeostasis is responsive to susceptibility to seizures, the distribution of trace elements in the brain was studied using EL mice and ddY mice, which form the genetic background for the inbred EL mice. The multitracer technique was applied to determine the distribution of trace elements. Twenty-four hours after intravenous injection of the multitracer, the concentration of 65Zn and 56Co in the brain of untreated EL mice was higher than in ddY mice, while the concentration of 65Zn and 56Co in the brain was decreased in seized EL mice. 75Se concentration in the hippocampus, cerebral cortex and cerebellum of untreated EL mice was lower than in ddY mice, while 75Se concentration in the hippocampus was increased in seized EL mice. 83Rb, an element of homologous series to potassium, concentration in the hippocampus and cerebral cortex of untreated EL mice was lower than in ddY mice, and 83Rb concentration in the cerebral cortex was decreased in seized EL mice. The movement of zinc, cobalt and selenium in the brain may be altered by enhancement of susceptibility to seizures. These results suggest that alteration of homeostasis of zinc, cobalt and selenium in the brain may be involved in the susceptibility, development or termination of seizures in EL mice. Copyright 2002 Elsevier Science B.V.

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.

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

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.

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.

Echoes of Semiotically-Based Design in the Development and Testing of a Workflow System

Directory of Open Access Journals (Sweden)

Clarisse Sieckenius de Souza

2001-05-01

Full Text Available Workflow systems are information-intensive task-oriented computer applications that typically involve a considerable number of users playing a wide variety of roles. Since communication, coordination and decision-making processes are essential for such systems, representing, interpreting and negotiating collective meanings are a crucial issue for software design and development processes. In this paper, we report and discuss our experience in implementing Qualitas, a web-based workflow system. Semiotic theory was extensively used to support design decisions and negotiations with users about technological signs. Taking scenarios as a type-sign exchanged throughout the whole process, we could trace the theoretic underpinnings of our experience and draw some revealing conclusions about the product and the process of technologically reified discourse. Although it is present in all information technology applications, this kind of discourse is seldom analyzed by software designers and developers. Our conjecture is that outside semiotic theory, professionals involved with human-computer interaction and software engineering practices have difficulty to coalesce concepts derived from such different disciplines as psychology, anthropology, linguistics and sociology, to name a few. Semiotics, however, can by itself provide a unifying ontological basis for interdisciplinary nowledge, raising issues and proposing alternatives, that may help professionals gain insights at lower learning costs. eywords: semiotic engineering, workflow systems, information-intensive task-oriented systems, scenario based design and development of computer systems, human-computer interaction

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

A Validation Approach of an End-to-End Whole Genome Sequencing Workflow for Source Tracking of Listeria monocytogenes and Salmonella enterica

Directory of Open Access Journals (Sweden)

Anne-Catherine Portmann

2018-03-01

Full Text Available Whole genome sequencing (WGS, using high throughput sequencing technology, reveals the complete sequence of the bacterial genome in a few days. WGS is increasingly being used for source tracking, pathogen surveillance and outbreak investigation due to its high discriminatory power. In the food industry, WGS used for source tracking is beneficial to support contamination investigations. Despite its increased use, no standards or guidelines are available today for the use of WGS in outbreak and/or trace-back investigations. Here we present a validation of our complete (end-to-end WGS workflow for Listeria monocytogenes and Salmonella enterica including: subculture of isolates, DNA extraction, sequencing and bioinformatics analysis. This end-to-end WGS workflow was evaluated according to the following performance criteria: stability, repeatability, reproducibility, discriminatory power, and epidemiological concordance. The current study showed that few single nucleotide polymorphism (SNPs were observed for L. monocytogenes and S. enterica when comparing genome sequences from five independent colonies from the first subculture and five independent colonies after the tenth subculture. Consequently, the stability of the WGS workflow for L. monocytogenes and S. enterica was demonstrated despite the few genomic variations that can occur during subculturing steps. Repeatability and reproducibility were also demonstrated. The WGS workflow was shown to have a high discriminatory power and has the ability to show genetic relatedness. Additionally, the WGS workflow was able to reproduce published outbreak investigation results, illustrating its capability of showing epidemiological concordance. The current study proposes a validation approach comprising all steps of a WGS workflow and demonstrates that the workflow can be applied to L. monocytogenes or S. enterica.

Trace metal distribution in sediments of the Pearl River Estuary and the surrounding coastal area, South China

International Nuclear Information System (INIS)

Ip, Carman C.M.; Li Xiangdong; Zhang Gan; Wai, Onyx W.H.; Li, Y.-S.

2007-01-01

Surface sediments and sediment cores collected at the Pearl River Estuary (PRE) and its surrounding coastal area were analysed for total metal concentrations, chemical partitioning, and Pb isotopic compositions. The distribution of Cu, Cr, Pb, and Zn demonstrated a typical diffusion pattern from the land to the direction of the sea. Two hotspots of trace metal contamination were located at the mixed zone between freshwater and marine waters. The enrichment of metals in the sediments could be attributed to the deposition of the dissolved and particulate trace metals in the water column at the estuarine area. The similar Pb isotopic signatures of the sediments at the PRE and its surrounding coastal area offered strong evidence that the PRE was a major source of trace metals to the adjacent coastal area. Slightly lower 206 Pb/ 207 Pb ratios in the coastal sediments may indicate other inputs of Pb in addition to the PRE sources, including the inputs from Hong Kong and other parts of the region. - The distribution of trace metals in sediments reflected contaminant sources, physical and chemical deposition processes

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

Selected trace elements in the Sacramento River, California: Occurrence and distribution

Science.gov (United States)

Taylor, Howard E.; Antweiler, Ronald C.; Roth, David A.; Dileanis, Peter D.; Alpers, Charles N.

2012-01-01

The impact of trace elements from the Iron Mountain Superfund site on the Sacramento River and selected tributaries is examined. The concentration and distribution of many trace elements—including aluminum, arsenic, boron, barium, beryllium, bismuth, cadmium, cerium, cobalt, chromium, cesium, copper, dysprosium, erbium, europium, iron, gadolinium, holmium, potassium, lanthanum, lithium, lutetium, manganese, molybdenum, neodymium, nickel, lead, praseodymium, rubidium, rhenium, antimony, selenium, samarium, strontium, terbium, thallium, thulium, uranium, vanadium, tungsten, yttrium, ytterbium, zinc, and zirconium—were measured using a combination of inductively coupled plasma-mass spectrometry and inductively coupled plasma-atomic emission spectrometry. Samples were collected using ultraclean techniques at selected sites in tributaries and the Sacramento River from below Shasta Dam to Freeport, California, at six separate time periods from mid-1996 to mid-1997. Trace-element concentrations in dissolved (ultrafiltered [0.005-μm pore size]) and colloidal material, isolated at each site from large volume samples, are reported. For example, dissolved Zn ranged from 900 μg/L at Spring Creek (Iron Mountain acid mine drainage into Keswick Reservoir) to 0.65 μg/L at the Freeport site on the Sacramento River. Zn associated with colloidal material ranged from 4.3 μg/L (colloid-equivalent concentration) in Spring Creek to 21.8 μg/L at the Colusa site on the Sacramento River. Virtually all of the trace elements exist in Spring Creek in the dissolved form. On entering Keswick Reservoir, the metals are at least partially converted by precipitation or adsorption to the particulate phase. Despite this observation, few of the elements are removed by settling; instead the majority is transported, associated with colloids, downriver, at least to the Bend Bridge site, which is 67 km from Keswick Dam. Most trace elements are strongly associated with the colloid phase going

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

Science.gov (United States)

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

2017-04-01

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

ADVANCED APPROACH TO PRODUCTION WORKFLOW COMPOSITION ON ENGINEERING KNOWLEDGE PORTALS

OpenAIRE

Novogrudska, Rina; Kot, Tatyana; Globa, Larisa; Schill, Alexander

2016-01-01

Background. In the environment of engineering knowledge portals great amount of partial workflows is concentrated. Such workflows are composed into general workflow aiming to perform real complex production task. Characteristics of partial workflows and general workflow structure are not studied enough, that affects the impossibility of general production workflowdynamic composition.Objective. Creating an approach to the general production workflow dynamic composition based on the partial wor...

Preliminary investigation on determination of radionuclide distribution in field tracing test site

International Nuclear Information System (INIS)

Tanaka, Tadao; Mukai, Masayuki; Takebe, Shinichi; Guo Zede; Li Shushen; Kamiyama, Hideo.

1993-12-01

Field tracing tests for radionuclide migration have been conducted by using 3 H, 60 Co, 85 Sr and 134 Cs, in the natural unsaturated loess zone at field test site of China Institute for Radiation Protection. It is necessary to obtain confidable distribution data of the radionuclides in the test site, in order to evaluate exactly the migration behavior of the radionuclides in situ. An available method to determine the distribution was proposed on the basis of preliminary discussing results on sampling method of soils from the test site and analytical method of radioactivity in the soils. (author)

A STRUCTURAL MODEL OF AN EXCAVATOR WORKFLOW CONTROL SYSTEM

Directory of Open Access Journals (Sweden)

A. Gurko

2016-12-01

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

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

Trace element composition and distribution in micron area of dinosaur eggshell fossils determined by proton microprobe

International Nuclear Information System (INIS)

Chen Youhong; Zhu Jieqing; Wang Xiaohong; Wang Yimin

1997-01-01

The scanning proton microprobe and micro-PIXE quantitative analysis technique have been used to determine composition and distribution of the trace elements in micron areas of dinosaur eggshell fossils from the stratum of Upper Cretaceous system at Nanxiong Basin in Guangdong Province, China. The study shows that the trace elements mainly include Ti, V, Cr, Mn, Co, Ni, Cu, Zn, As, Rb, Sr, Y, Zr, Sb, Ba and Pb in the micron area, but they present different distributions. While the element Sr is mainly enriched in the near surface layer, others mainly reside in the near inner layer. A preliminary discussion on the reason of the dinosaur extinction is given based on the above study

Trace element composition and distribution in micron area of dinosaur eggshell fossils determined by proton microprobe

International Nuclear Information System (INIS)

Chen Youhong; Zhu Jieqing; Wang Xiaohong; Wang Yimin

1997-01-01

The scanning proton microprobe and micro-PIXE quantitative analysis technique have been used to determine composition and distribution of the trace elements in micron areas of dinosaur eggshell fossils from the stratum of Upper Cretaceous system at Nanxiong Basin in Guangdong Province, China. The study shows that the trace elements mainly include Ti, V, Cr, Mn, Co, Ni, Cu, Zn, As, Rb, Sr, Y, Zr, Sb, Ba and Pb in the micron area, but they present different distributions. While the elements Sr is mainly enriched in the near surface layer, others mainly reside in the near inner layer. A preliminary discussion on the reason of the dinosaur extinction is given based on the above study

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...

A workflow learning model to improve geovisual analytics utility.

Science.gov (United States)

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

2009-01-01

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

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

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.

Automated Finite State Workflow for Distributed Data Production

Science.gov (United States)

Hajdu, L.; Didenko, L.; Lauret, J.; Amol, J.; Betts, W.; Jang, H. J.; Noh, S. Y.

2016-10-01

In statistically hungry science domains, data deluges can be both a blessing and a curse. They allow the narrowing of statistical errors from known measurements, and open the door to new scientific opportunities as research programs mature. They are also a testament to the efficiency of experimental operations. However, growing data samples may need to be processed with little or no opportunity for huge increases in computing capacity. A standard strategy has thus been to share resources across multiple experiments at a given facility. Another has been to use middleware that “glues” resources across the world so they are able to locally run the experimental software stack (either natively or virtually). We describe a framework STAR has successfully used to reconstruct a ~400 TB dataset consisting of over 100,000 jobs submitted to a remote site in Korea from STAR's Tier 0 facility at the Brookhaven National Laboratory. The framework automates the full workflow, taking raw data files from tape and writing Physics-ready output back to tape without operator or remote site intervention. Through hardening we have demonstrated 97(±2)% efficiency, over a period of 7 months of operation. The high efficiency is attributed to finite state checking with retries to encourage resilience in the system over capricious and fallible infrastructure.

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

Workflow efficiency of two 1.5 T MR scanners with and without an automated user interface for head examinations.

Science.gov (United States)

Moenninghoff, Christoph; Umutlu, Lale; Kloeters, Christian; Ringelstein, Adrian; Ladd, Mark E; Sombetzki, Antje; Lauenstein, Thomas C; Forsting, Michael; Schlamann, Marc

2013-06-01

Workflow efficiency and workload of radiological technologists (RTs) were compared in head examinations performed with two 1.5 T magnetic resonance (MR) scanners equipped with or without an automated user interface called "day optimizing throughput" (Dot) workflow engine. Thirty-four patients with known intracranial pathology were examined with a 1.5 T MR scanner with Dot workflow engine (Siemens MAGNETOM Aera) and with a 1.5 T MR scanner with conventional user interface (Siemens MAGNETOM Avanto) using four standardized examination protocols. The elapsed time for all necessary work steps, which were performed by 11 RTs within the total examination time, was compared for each examination at both MR scanners. The RTs evaluated the user-friendliness of both scanners by a questionnaire. Normality of distribution was checked for all continuous variables by use of the Shapiro-Wilk test. Normally distributed variables were analyzed by Student's paired t-test, otherwise Wilcoxon signed-rank test was used to compare means. Total examination time of MR examinations performed with Dot engine was reduced from 24:53 to 20:01 minutes (P user interface (P = .001). According to this preliminary study, the Dot workflow engine is a time-saving user assistance software, which decreases the RTs' effort significantly and may help to automate neuroradiological examinations for a higher workflow efficiency. Copyright © 2013 AUR. Published by Elsevier Inc. All rights reserved.

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...

A Semi-Automated Workflow Solution for Data Set Publication

Directory of Open Access Journals (Sweden)

Suresh Vannan

2016-03-01

Full Text Available To address the need for published data, considerable effort has gone into formalizing the process of data publication. From funding agencies to publishers, data publication has rapidly become a requirement. Digital Object Identifiers (DOI and data citations have enhanced the integration and availability of data. The challenge facing data publishers now is to deal with the increased number of publishable data products and most importantly the difficulties of publishing diverse data products into an online archive. The Oak Ridge National Laboratory Distributed Active Archive Center (ORNL DAAC, a NASA-funded data center, faces these challenges as it deals with data products created by individual investigators. This paper summarizes the challenges of curating data and provides a summary of a workflow solution that ORNL DAAC researcher and technical staffs have created to deal with publication of the diverse data products. The workflow solution presented here is generic and can be applied to data from any scientific domain and data located at any data center.

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

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.

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...

The flux distribution from a 1.25m2 target aligned heliostat: comparison of ray tracing and experimental results

CSIR Research Space (South Africa)

Maliage, M

2012-05-01

Full Text Available The purpose of this paper is to validate SolTrace for concentrating solar investigations at CSIR by means of a test case: the comparison of the flux distribution in the focal spot of a 1.25 m2 target aligned heliostat predicted by the ray tracing...

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.

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.

Automated Finite State Workflow for Distributed Data Production

International Nuclear Information System (INIS)

Hajdu, L; Didenko, L; Lauret, J; Betts, W; Amol, J; Jang, H J; Noh, S Y

2016-01-01

In statistically hungry science domains, data deluges can be both a blessing and a curse. They allow the narrowing of statistical errors from known measurements, and open the door to new scientific opportunities as research programs mature. They are also a testament to the efficiency of experimental operations. However, growing data samples may need to be processed with little or no opportunity for huge increases in computing capacity. A standard strategy has thus been to share resources across multiple experiments at a given facility. Another has been to use middleware that “glues” resources across the world so they are able to locally run the experimental software stack (either natively or virtually). We describe a framework STAR has successfully used to reconstruct a ∼400 TB dataset consisting of over 100,000 jobs submitted to a remote site in Korea from STAR's Tier 0 facility at the Brookhaven National Laboratory. The framework automates the full workflow, taking raw data files from tape and writing Physics-ready output back to tape without operator or remote site intervention. Through hardening we have demonstrated 97(±2)% efficiency, over a period of 7 months of operation. The high efficiency is attributed to finite state checking with retries to encourage resilience in the system over capricious and fallible infrastructure. (paper)

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

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....

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.

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

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.

Design Tools and Workflows for Braided Structures

DEFF Research Database (Denmark)

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

2017-01-01

and merits of our method, demonstrated though four example design and analysis workflows. The workflows frame specific aspects of enquiry for the ongoing research project flora robotica. These include modelling target geometries, automatically producing instructions for fabrication, conducting structural...

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

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

A Model of Workflow Composition for Emergency Management

Science.gov (United States)

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

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

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...

A Hybrid Metaheuristic for Multi-Objective Scientific Workflow Scheduling in a Cloud Environment

Directory of Open Access Journals (Sweden)

Nazia Anwar

2018-03-01

Full Text Available Cloud computing has emerged as a high-performance computing environment with a large pool of abstracted, virtualized, flexible, and on-demand resources and services. Scheduling of scientific workflows in a distributed environment is a well-known NP-complete problem and therefore intractable with exact solutions. It becomes even more challenging in the cloud computing platform due to its dynamic and heterogeneous nature. The aim of this study is to optimize multi-objective scheduling of scientific workflows in a cloud computing environment based on the proposed metaheuristic-based algorithm, Hybrid Bio-inspired Metaheuristic for Multi-objective Optimization (HBMMO. The strong global exploration ability of the nature-inspired metaheuristic Symbiotic Organisms Search (SOS is enhanced by involving an efficient list-scheduling heuristic, Predict Earliest Finish Time (PEFT, in the proposed algorithm to obtain better convergence and diversity of the approximate Pareto front in terms of reduced makespan, minimized cost, and efficient load balance of the Virtual Machines (VMs. The experiments using different scientific workflow applications highlight the effectiveness, practicality, and better performance of the proposed algorithm.

Trace element distribution in geological crystals

Energy Technology Data Exchange (ETDEWEB)

Den Besten, J.L.; Jamieson, D.N.; Weiser, P.S. [Melbourne Univ., Parkville, VIC (Australia). School of Physics

1996-12-31

Channelling is a useful microprobe technique for determining the structure of crystals, but until now has not been performed on geological crystals. The composition has been investigated rather than the structure, which can further explain the origin of the crystal and provide useful information on the substitutionality of trace elements. This may then lead to applications of extraction of valuable metals and semiconductor electronics. Natural crystals of pyrite, FeS{sub 2}, which contains a substantial concentration of gold were channeled and examined to identify the channel axis orientation. Rutherford Backscattering (RBS) and Particle Induced X-Ray Emission (PIXE) spectra using MeV ions were obtained in the experiment to provide a comparison of lattice and non-lattice trace elements. 3 figs.

Trace element distribution in geological crystals

Energy Technology Data Exchange (ETDEWEB)

Den Besten, J L; Jamieson, D N; Weiser, P S [Melbourne Univ., Parkville, VIC (Australia). School of Physics

1997-12-31

Channelling is a useful microprobe technique for determining the structure of crystals, but until now has not been performed on geological crystals. The composition has been investigated rather than the structure, which can further explain the origin of the crystal and provide useful information on the substitutionality of trace elements. This may then lead to applications of extraction of valuable metals and semiconductor electronics. Natural crystals of pyrite, FeS{sub 2}, which contains a substantial concentration of gold were channeled and examined to identify the channel axis orientation. Rutherford Backscattering (RBS) and Particle Induced X-Ray Emission (PIXE) spectra using MeV ions were obtained in the experiment to provide a comparison of lattice and non-lattice trace elements. 3 figs.

Molecular simulation workflows as parallel algorithms: the execution engine of Copernicus, a distributed high-performance computing platform.

Science.gov (United States)

Pronk, Sander; Pouya, Iman; Lundborg, Magnus; Rotskoff, Grant; Wesén, Björn; Kasson, Peter M; Lindahl, Erik

2015-06-09

Computational chemistry and other simulation fields are critically dependent on computing resources, but few problems scale efficiently to the hundreds of thousands of processors available in current supercomputers-particularly for molecular dynamics. This has turned into a bottleneck as new hardware generations primarily provide more processing units rather than making individual units much faster, which simulation applications are addressing by increasingly focusing on sampling with algorithms such as free-energy perturbation, Markov state modeling, metadynamics, or milestoning. All these rely on combining results from multiple simulations into a single observation. They are potentially powerful approaches that aim to predict experimental observables directly, but this comes at the expense of added complexity in selecting sampling strategies and keeping track of dozens to thousands of simulations and their dependencies. Here, we describe how the distributed execution framework Copernicus allows the expression of such algorithms in generic workflows: dataflow programs. Because dataflow algorithms explicitly state dependencies of each constituent part, algorithms only need to be described on conceptual level, after which the execution is maximally parallel. The fully automated execution facilitates the optimization of these algorithms with adaptive sampling, where undersampled regions are automatically detected and targeted without user intervention. We show how several such algorithms can be formulated for computational chemistry problems, and how they are executed efficiently with many loosely coupled simulations using either distributed or parallel resources with Copernicus.

Provenance for Runtime Workflow Steering and Validation in Computational Seismology

Science.gov (United States)

Spinuso, A.; Krischer, L.; Krause, A.; Filgueira, R.; Magnoni, F.; Muraleedharan, V.; David, M.

2014-12-01

Provenance systems may be offered by modern workflow engines to collect metadata about the data transformations at runtime. If combined with effective visualisation and monitoring interfaces, these provenance recordings can speed up the validation process of an experiment, suggesting interactive or automated interventions with immediate effects on the lifecycle of a workflow run. For instance, in the field of computational seismology, if we consider research applications performing long lasting cross correlation analysis and high resolution simulations, the immediate notification of logical errors and the rapid access to intermediate results, can produce reactions which foster a more efficient progress of the research. These applications are often executed in secured and sophisticated HPC and HTC infrastructures, highlighting the need for a comprehensive framework that facilitates the extraction of fine grained provenance and the development of provenance aware components, leveraging the scalability characteristics of the adopted workflow engines, whose enactment can be mapped to different technologies (MPI, Storm clusters, etc). This work looks at the adoption of W3C-PROV concepts and data model within a user driven processing and validation framework for seismic data, supporting also computational and data management steering. Validation needs to balance automation with user intervention, considering the scientist as part of the archiving process. Therefore, the provenance data is enriched with community-specific metadata vocabularies and control messages, making an experiment reproducible and its description consistent with the community understandings. Moreover, it can contain user defined terms and annotations. The current implementation of the system is supported by the EU-Funded VERCE (http://verce.eu). It provides, as well as the provenance generation mechanisms, a prototypal browser-based user interface and a web API built on top of a NoSQL storage

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....

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

Science.gov (United States)

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

2013-01-01

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

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.

DataSpaces: An Interaction and Coordination Framework for Coupled Simulation Workflows

International Nuclear Information System (INIS)

Docan, Ciprian; Klasky, Scott A.; Parashar, Manish

2010-01-01

Emerging high-performance distributed computing environments are enabling new end-to-end formulations in science and engineering that involve multiple interacting processes and data-intensive application workflows. For example, current fusion simulation efforts are exploring coupled models and codes that simultaneously simulate separate application processes, such as the core and the edge turbulence, and run on different high performance computing resources. These components need to interact, at runtime, with each other and with services for data monitoring, data analysis and visualization, and data archiving. As a result, they require efficient support for dynamic and flexible couplings and interactions, which remains a challenge. This paper presents Data-Spaces, a flexible interaction and coordination substrate that addresses this challenge. DataSpaces essentially implements a semantically specialized virtual shared space abstraction that can be associatively accessed by all components and services in the application workflow. It enables live data to be extracted from running simulation components, indexes this data online, and then allows it to be monitored, queried and accessed by other components and services via the space using semantically meaningful operators. The underlying data transport is asynchronous, low-overhead and largely memory-to-memory. The design, implementation, and experimental evaluation of DataSpaces using a coupled fusion simulation workflow is presented.

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.

Effects of statistical distribution of joint trace length on the stability of tunnel excavated in jointed rock mass

Directory of Open Access Journals (Sweden)

Kayvan Ghorbani

2015-12-01

Full Text Available The rock masses in a construction site of underground cavern are generally not continuous, due to the presence of discontinuities, such as bedding, joints, faults, and fractures. The performance of an underground cavern is principally ruled by the mechanical behaviors of the discontinuities in the vicinity of the cavern. During underground excavation, many surrounding rock failures have close relationship with joints. The stability study on tunnel in jointed rock mass is of importance to rock engineering, especially tunneling and underground space development. In this study, using the probability density distribution functions of negative exponential, log-normal and normal, we investigated the effect of joint trace length on the stability parameters such as stress and displacement of tunnel constructed in rock mass using UDEC (Universal Distinct Element Code. It was obtained that normal distribution function of joint trace length is more critical on the stability of tunnel, and exponential distribution function has less effect on the tunnel stability compared to the two other distribution functions.

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

Science.gov (United States)

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

2013-12-01

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

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.

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

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.

Facilitating Scientific Research through Workflows and Provenance on the DataONE Cyberinfrastructure (Invited)

Science.gov (United States)

Ludaescher, B.; Cuevas-Vicenttín, V.; Missier, P.; Dey, S.; Kianmajd, P.; Wei, Y.; Koop, D.; Chirigati, F.; Altintas, I.; Belhajjame, K.; Bowers, S.

2013-12-01

ONE CI to be 'provenance-aware'. DataONE Member Nodes manage packages containing the data along with their science/system metadata, indexing them to facilitate search by the tools of the Information Toolkit (ITK) such as ONEMercury. Our extension is based on PBase, which can manage D-PROV provenance data efficiently. D-PROV extends the W3C PROV standard by enabling the explicit representation of workflows along with traces in a standardized manner. PBase consists of components for storage, indexing, and querying. First, it has a provenance data repository capable of dealing with the scalability and availability requirements expected from large datasets. A graph database such as Neo4j could fulfill this role. Second, PBase has a specialized index enabling efficient data access, built based on but also extending the indexing capabilities furnished by the underlying database. Finally, PBase contains a querying engine supported by the provenance index. This engine will enable easy and efficient access to the provenance data, primarily through a declarative language.

Vertical distribution of particulate trace elements in a street canyon determined by PIXE analysis

International Nuclear Information System (INIS)

Raunemaa, T.; Hautojaervi, A.; Kaisla, K.; Gerlander, M.

1981-01-01

Suspended particles in a street canyon were investigated by collecting air particulate matter on thin filters at heigths 2.3 to 20.5 m. The weather parameters and traffic characteristics were registered during the collection. Quantitative analysis of 15 trace elements from AI to Pb was carried out by the PIXE method using 1.8-2.0 MeV protons. The concentration of lead was found to decrease exponentially when going from street level to roof level. Almost all the trace elements analyzed were found to fall into two groups with different vertical distributions. The collected matter above 10 m height was found to be due mainly to combustion originated motor vehicle exhaust, the matter below 10 m to soil originated dust. (orig.)

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

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.

Enhanced reproducibility of SADI web service workflows with Galaxy and Docker.

Science.gov (United States)

Aranguren, Mikel Egaña; Wilkinson, Mark D

2015-01-01

Semantic Web technologies have been widely applied in the life sciences, for example by data providers such as OpenLifeData and through web services frameworks such as SADI. The recently reported OpenLifeData2SADI project offers access to the vast OpenLifeData data store through SADI services. This article describes how to merge data retrieved from OpenLifeData2SADI with other SADI services using the Galaxy bioinformatics analysis platform, thus making this semantic data more amenable to complex analyses. This is demonstrated using a working example, which is made distributable and reproducible through a Docker image that includes SADI tools, along with the data and workflows that constitute the demonstration. The combination of Galaxy and Docker offers a solution for faithfully reproducing and sharing complex data retrieval and analysis workflows based on the SADI Semantic web service design patterns.

Geometry-invariant GRIN lens: finite ray tracing.

Science.gov (United States)

Bahrami, Mehdi; Goncharov, Alexander V

2014-11-17

The refractive index distribution of the geometry-invariant gradient refractive index lens (GIGL) model is derived as a function of Cartesian coordinates. The adjustable external geometry of the GIGL model aims to mimic the shape of the human and animal crystalline lens. The refractive index distribution is based on an adjustable power-law profile, which provides additional flexibility of the model. An analytical method for layer-by-layer finite ray tracing through the GIGL model is developed and used to calculate aberrations of the GIGL model. The result of the finite ray tracing aberrations of the GIGL model are compared to those obtained with paraxial ray tracing. The derived analytical expression for the refractive index distribution can be employed in the reconstruction processes of the eye using the conventional ray tracing methods. The layer-by-layer finite ray tracing approach would be an asset in ray tracing through a modified GIGL model, where the refractive index distribution cannot be described analytically. Using the layer-by-layer finite ray-tracing method, the potential of the GIGL model in representing continuous as well as shell-like layered structures is illustrated and the results for both cases are presented and analysed.

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.

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.

Altitudinal patterns and controls of trace metal distribution in soils of a remote high mountain, Southwest China.

Science.gov (United States)

Li, Rui; Bing, Haijian; Wu, Yanhong; Zhou, Jun; Xiang, Zhongxiang

2018-02-01

The aim of this study is to reveal the effects of regional human activity on trace metal accumulation in remote alpine ecosystems under long-distance atmospheric transport. Trace metals (Cd, Pb, and Zn) in soils of the Mt. Luoji, Southwest China, were investigated along a large altitudinal gradient [2200-3850 m above sea level (a.s.l.)] to elaborate the key factors controlling their distribution by Pb isotopic composition and statistical models. The concentrations of Cd, Pb, and Zn in the surface soils (O and A horizons) were relatively low at the altitudes of 3500-3700 m a.s.l. The enrichment factors of trace metals in the surface soils increased with altitude. After normalization for soil organic matter, the concentrations of Cd still increased with altitude, whereas those of Pb and Zn did not show a clear altitudinal trend. The effects of vegetation and cold trapping (CTE) (pollutant enrichment by decreasing temperature with increasing altitude) mainly determined the distribution of Cd and Pb in the O horizon, whereas CTE and bedrock weathering (BW) controlled that of Zn. In the A horizon, the distribution of Cd and Pb depended on the vegetation regulation, whereas that of Zn was mainly related to BW. Human activity, including ores mining and fossil fuels combustion, increased the trace metal deposition in the surface soils. The anthropogenic percentage of Cd, Pb, and Zn quantified 92.4, 67.8, and 42.9% in the O horizon, and 74.5, 33.9, and 24.9% in the A horizon, respectively. The anthropogenic metals deposited at the high altitudes of Mt. Luoji reflected the impact of long-range atmospheric transport on this remote alpine ecosystem from southern and southwestern regions.

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.

A Workflow to Investigate Exposure and Pharmacokinetic Influences on High-Throughput in Vitro Chemical Screening Based on Adverse Outcome Pathways

Science.gov (United States)

Phillips, Martin B.; Leonard, Jeremy A.; Grulke, Christopher M.; Chang, Daniel T.; Edwards, Stephen W.; Brooks, Raina; Goldsmith, Michael-Rock; El-Masri, Hisham; Tan, Yu-Mei

2015-01-01

Background Adverse outcome pathways (AOPs) link adverse effects in individuals or populations to a molecular initiating event (MIE) that can be quantified using in vitro methods. Practical application of AOPs in chemical-specific risk assessment requires incorporation of knowledge on exposure, along with absorption, distribution, metabolism, and excretion (ADME) properties of chemicals. Objectives We developed a conceptual workflow to examine exposure and ADME properties in relation to an MIE. The utility of this workflow was evaluated using a previously established AOP, acetylcholinesterase (AChE) inhibition. Methods Thirty chemicals found to inhibit human AChE in the ToxCast™ assay were examined with respect to their exposure, absorption potential, and ability to cross the blood–brain barrier (BBB). Structures of active chemicals were compared against structures of 1,029 inactive chemicals to detect possible parent compounds that might have active metabolites. Results Application of the workflow screened 10 “low-priority” chemicals of 30 active chemicals. Fifty-two of the 1,029 inactive chemicals exhibited a similarity threshold of ≥ 75% with their nearest active neighbors. Of these 52 compounds, 30 were excluded due to poor absorption or distribution. The remaining 22 compounds may inhibit AChE in vivo either directly or as a result of metabolic activation. Conclusions The incorporation of exposure and ADME properties into the conceptual workflow eliminated 10 “low-priority” chemicals that may otherwise have undergone additional, resource-consuming analyses. Our workflow also increased confidence in interpretation of in vitro results by identifying possible “false negatives.” Citation Phillips MB, Leonard JA, Grulke CM, Chang DT, Edwards SW, Brooks R, Goldsmith MR, El-Masri H, Tan YM. 2016. A workflow to investigate exposure and pharmacokinetic influences on high-throughput in vitro chemical screening based on adverse outcome pathways. Environ

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.

Workflow-Oriented Cyberinfrastructure for Sensor Data Analytics

Science.gov (United States)

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

2015-12-01

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

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?

wft4galaxy: a workflow testing tool for galaxy.

Science.gov (United States)

Piras, Marco Enrico; Pireddu, Luca; Zanetti, Gianluigi

2017-12-01

Workflow managers for scientific analysis provide a high-level programming platform facilitating standardization, automation, collaboration and access to sophisticated computing resources. The Galaxy workflow manager provides a prime example of this type of platform. As compositions of simpler tools, workflows effectively comprise specialized computer programs implementing often very complex analysis procedures. To date, no simple way to automatically test Galaxy workflows and ensure their correctness has appeared in the literature. With wft4galaxy we offer a tool to bring automated testing to Galaxy workflows, making it feasible to bring continuous integration to their development and ensuring that defects are detected promptly. wft4galaxy can be easily installed as a regular Python program or launched directly as a Docker container-the latter reducing installation effort to a minimum. Available at https://github.com/phnmnl/wft4galaxy under the Academic Free License v3.0. marcoenrico.piras@crs4.it. © The Author 2017. Published by Oxford University Press.

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

The MPO system for automatic workflow documentation

Energy Technology Data Exchange (ETDEWEB)

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

2016-11-15

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

The MPO system for automatic workflow documentation

International Nuclear Information System (INIS)

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

2016-01-01

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

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

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.

A Scheduling Algorithm for the Distributed Student Registration System in Transaction-Intensive Environment

Science.gov (United States)

Li, Wenhao

2011-01-01

Distributed workflow technology has been widely used in modern education and e-business systems. Distributed web applications have shown cross-domain and cooperative characteristics to meet the need of current distributed workflow applications. In this paper, the author proposes a dynamic and adaptive scheduling algorithm PCSA (Pre-Calculated…

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

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.

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.

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

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...

Provenance for distributed biomedical workflow execution

NARCIS (Netherlands)

Madougou, S.; Santcroos, M.; Benabdelkader, A.; van Schaik, B.D.; Shahand, S.; Korkhov, V.; van Kampen, A.H.C.; Olabarriaga, S.D.

2012-01-01

Scientific research has become very data and compute intensive because of the progress in data acquisition and measurement devices, which is particularly true in Life Sciences. To cope with this deluge of data, scientists use distributed computing and storage infrastructures. The use of such

Concentrations and distributions of trace and minor elements in Chinese and Canadian coals and ashes

International Nuclear Information System (INIS)

Sun Jingxin; Jervis, R.E.

1987-01-01

A total of 35 trace and minor elements including some of environmental significance were determined in each of a selection of 15 Chinese and 6 Canadian thermal coals and their ashes by using the SLOWPOKE-2 nuclear reactor facility of the University of Toronto. The concentrations and distributions of these constituents among the coals and their combustion products (viz. ash and volatile matter) are presented. The detailed results showed wide variations in trace impurity concentrations (up to a factor of 100 and more) among the coals studied. Values for elemental enrichment factors (EF) relative to normal crustal abundances indicated that only As(EF=13), Br(5.7), I(16), S(230), Sb(11) and Se(320) were appreciably enriched in coal. (author) 14 refs.; 5 tabs

Effects of cooking and subcellular distribution on the bioaccessibility of trace elements in two marine fish species.

Science.gov (United States)

He, Mei; Ke, Cai-Huan; Wang, Wen-Xiong

2010-03-24

In current human health risk assessment, the maximum acceptable concentrations of contaminants in food are mostly based on the total concentrations. However, the total concentration of contaminants may not always reflect the available amount. Bioaccessibility determination is thus required to improve the risk assessment of contaminants. This study used an in vitro digestion model to assess the bioaccessibility of several trace elements (As, Cd, Cu, Fe, Se, and Zn) in the muscles of two farmed marine fish species (seabass Lateolabrax japonicus and red seabream Pagrosomus major ) of different body sizes. The total concentrations and subcellular distributions of these trace elements in fish muscles were also determined. Bioaccessibility of these trace elements was generally high (>45%), and the lowest bioaccessibility was observed for Fe. Cooking processes, including boiling, steaming, frying, and grilling, generally decreased the bioaccessibility of these trace elements, especially for Cu and Zn. The influences of frying and grilling were greater than those of boiling and steaming. The relationship of bioaccessibility and total concentration varied with the elements. A positive correlation was found for As and Cu and a negative correlation for Fe, whereas no correlation was found for Cd, Se, and Zn. A significant positive relationship was demonstrated between the bioaccessibility and the elemental partitioning in the heat stable protein fraction and in the trophically available fraction, and a negative correlation was observed between the bioaccessibility and the elemental partitioning in metal-rich granule fraction. Subcellular distribution may thus affect the bioaccessibility of metals and should be considered in the risk assessment for seafood safety.

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.

Distribution and seasonal variation of trace metals in surface sediments of the Mandovi estuary, west coast of India

Digital Repository Service at National Institute of Oceanography (India)

Alagarsamy, R.

The concentration and distribution of selected trace metals in surface sediments of the Mandovi estuary were studied to determine the extent of anthropogenic inputs from mining activities and to estimate the effects of monsoon on geochemical...

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.

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...

A workflow for sub-/seismic structure and deformation quantification of 3-D reflection seismic data sets across different scales

Energy Technology Data Exchange (ETDEWEB)

Krawczyk, C.M.; Lohr, T.; Oncken, O. [GFZ Potsdam (Germany); Tanner, D.C. [Goettingen Univ. (Germany). GZG; Endres, H. [RWTH Aachen (Germany)]|[TEEC, Isernhagen (Germany); Trappe, H.; Kukla, P. [TEEC, Isernhagen (Germany)

2007-09-13

The evolution of a sedimentary basin is mostly affected by deformation. Large-scale, subsurface deformation is typically identified by seismic data, sub-seismic small-scale fractures by well data. Between these two methods, we lack a deeper understanding of how deformation scales. We analysed a 3-D reflection seismic data set in the North German Basin, in order to determine the magnitude and distribution of deformation and its accumulation in space and time. A five-step approach is introduced for quantitative deformation and fracture prediction. An increased resolution of subtle tectonic lineaments is achieved by coherency processing, allowing to unravel the kinematics in the North German Basin from structural interpretation. Extensional events during basin initiation and later inversion are evident. 3-D retrodeformation shows major-strain magnitudes between 0-20% up to 1.3 km away from a fault trace, and variable deviations of associated extensional fractures. Good correlation of FMI data, strain distribution from retro-deformation and from geostatistic tools (see also Trappe et al., this volume) allows the validation of the results and makes the prediction of small-scale faults/fractures possible. The temporal component will be gained in the future by analogue models. The suggested workflow is applicable to reflection seismic surveys and yields in great detail both the tectonic history of a region as well as predictions for hydrocarbon plays or deep groundwater or geothermal reservoirs. (orig.)

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.

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.

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.

Spatial distribution and potential sources of trace metals in insoluble particles of snow from Urumqi, China.

Science.gov (United States)

Li, Xiaolan; Jiang, Fengqing; Wang, Shaoping; Turdi, Muyesser; Zhang, Zhaoyong

2015-01-01

The purpose of this work is to characterize trace elements in snow in urban-suburb gradient over Urumqi city, China. The spatial distribution patterns of 11 trace metals in insoluble particulate matters of snow were revealed by using 102 snow samples collected in and around urban areas of Urumqi, a city suffering from severe wintertime air pollution in China. Similar spatial distribution for Mn, Cu, Zn, Ni, and Pb was found and their two significant high-value areas located in the west and east, respectively, and a high-value area in the south, which were correlated with factory emissions, traffic activities, and construction fugitive dust. The high-value areas of Cr, Ni, and V occurred in the northeast corner and along main traffic paths, which were linked to oil refinery and vehicular emissions. High value of Be presented in the west of the city. The high-value area of Co in the northeast could be related to local soil. Cd and U displayed relatively even spatial patterns in the urban area. In view of distance from the urban center, e.g., from the first circular belt to the fourth circular belt, except Be, V, Cd, and U, the contents of other metals generally decreased from the first circular belt to the forth circular belt, implying the effect of human activity clearly. Additionally, prevailing northwesterly winds and occasionally southeasterly winds in winter were associated with decreased, generally, concentrations of trace metal in snow from the urban center to the southern suburb along a northwest and southeast transect. The information on concentrations and spatial distributions of these metals in insoluble particles of snow in winter will be valuable for further environmental protection and planning.

The cobas p 630 instrument: a dedicated pre-analytic solution to optimize COBAS® AmpliPrep/COBAS® TaqMan® system workflow and turn-around-time.

Science.gov (United States)

Vallefuoco, L; Sorrentino, R; Spalletti Cernia, D; Colucci, G; Portella, G

2012-12-01

The cobas p 630, a fully automated pre-analytical instrument for primary tube handling recently introduced to complete the Cobas(®) TaqMan systems portfolio, was evaluated in conjunction with: the COBAS(®) AmpliPrep/COBAS(®) TaqMan HBV Test, v2.0, COBAS(®) AmpliPrep/COBAS(®) TaqMan HCV Test, v1.0 and COBAS(®) AmpliPrep/COBAS(®) TaqMan HIV Test, v2.0. The instrument performance in transferring samples from primary to secondary tubes, its impact in improving COBAS(®) AmpliPrep/COBAS(®) TaqMan workflow and hands-on reduction and the risk of possible cross-contamination were assessed. Samples from 42 HBsAg positive, 42 HCV and 42 HIV antibody (Ab) positive patients as well as 21 healthy blood donors were processed with or without automated primary tubes. HIV, HCV and HBsAg positive samples showed a correlation index of 0.999, 0.987 and of 0.994, respectively. To assess for cross-contamination, high titer HBV DNA positive samples, HCV RNA and HIV RNA positive samples were distributed in the cobas p 630 in alternate tube positions, adjacent to negative control samples within the same rack. None of the healthy donor samples showed any reactivity. Based on these results, the cobas p 630 can improve workflow and sample tracing in laboratories performing molecular tests, and reduce turnaround time, errors, and risks. Copyright © 2012 Elsevier B.V. All rights reserved.

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.

Distribution of trace elements in land plants and botanical taxonomy with special reference to rare earth elements and actinium

International Nuclear Information System (INIS)

Koyama, Mutsuo

1989-01-01

Distribution profiles of trace elements in land plants were studied by neutron activation analysis and radioactivity measurements without activation. Number of botanical samples analyzed were more than three thousand in which more than three hundred botanical species were included. New accumulator plants of Co, Cr, Zn, Cd, rare earth elements, Ac, U, etc., were found. Capabilities of accumulating trace elements can be related to the botanical taxonomy. Discussions are given from view points of inorganic chemistry as well as from botanical physiology

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 novel approach to optimize workflow in grid-based teleradiology applications.

Science.gov (United States)

Yılmaz, Ayhan Ozan; Baykal, Nazife

2016-01-01

This study proposes an infrastructure with a reporting workflow optimization algorithm (RWOA) in order to interconnect facilities, reporting units and radiologists on a single access interface, to increase the efficiency of the reporting process by decreasing the medical report turnaround time and to increase the quality of medical reports by determining the optimum match between the inspection and radiologist in terms of subspecialty, workload and response time. Workflow centric network architecture with an enhanced caching, querying and retrieving mechanism is implemented by seamlessly integrating Grid Agent and Grid Manager to conventional digital radiology systems. The inspection and radiologist attributes are modelled using a hierarchical ontology structure. Attribute preferences rated by radiologists and technical experts are formed into reciprocal matrixes and weights for entities are calculated utilizing Analytic Hierarchy Process (AHP). The assignment alternatives are processed by relation-based semantic matching (RBSM) and Integer Linear Programming (ILP). The results are evaluated based on both real case applications and simulated process data in terms of subspecialty, response time and workload success rates. Results obtained using simulated data are compared with the outcomes obtained by applying Round Robin, Shortest Queue and Random distribution policies. The proposed algorithm is also applied to a real case teleradiology application process data where medical reporting workflow was performed based on manual assignments by the chief radiologist for 6225 inspections. RBSM gives the highest subspecialty success rate and integrating ILP with RBSM ratings as RWOA provides a better response time and workload distribution success rate. RWOA based image delivery also prevents bandwidth, storage or hardware related stuck and latencies. When compared with a real case teleradiology application where inspection assignments were performed manually, the proposed

Access Control with Delegated Authorization Policy Evaluation for Data-Driven Microservice Workflows

Directory of Open Access Journals (Sweden)

Davy Preuveneers

2017-09-01

Full Text Available Microservices offer a compelling competitive advantage for building data flow systems as a choreography of self-contained data endpoints that each implement a specific data processing functionality. Such a ‘single responsibility principle’ design makes them well suited for constructing scalable and flexible data integration and real-time data flow applications. In this paper, we investigate microservice based data processing workflows from a security point of view, i.e., (1 how to constrain data processing workflows with respect to dynamic authorization policies granting or denying access to certain microservice results depending on the flow of the data; (2 how to let multiple microservices contribute to a collective data-driven authorization decision and (3 how to put adequate measures in place such that the data within each individual microservice is protected against illegitimate access from unauthorized users or other microservices. Due to this multifold objective, enforcing access control on the data endpoints to prevent information leakage or preserve one’s privacy becomes far more challenging, as authorization policies can have dependencies and decision outcomes cross-cutting data in multiple microservices. To address this challenge, we present and evaluate a workflow-oriented authorization framework that enforces authorization policies in a decentralized manner and where the delegated policy evaluation leverages feature toggles that are managed at runtime by software circuit breakers to secure the distributed data processing workflows. The benefit of our solution is that, on the one hand, authorization policies restrict access to the data endpoints of the microservices, and on the other hand, microservices can safely rely on other data endpoints to collectively evaluate cross-cutting access control decisions without having to rely on a shared storage backend holding all the necessary information for the policy evaluation.

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

Scientific Workflows and the Sensor Web for Virtual Environmental Observatories

Science.gov (United States)

Simonis, I.; Vahed, A.

2008-12-01

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

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.

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

Microwave transport in EBT distribution manifolds using Monte Carlo ray-tracing techniques

International Nuclear Information System (INIS)

Lillie, R.A.; White, T.L.; Gabriel, T.A.; Alsmiller, R.G. Jr.

1983-01-01

Ray tracing Monte Carlo calculations have been carried out using an existing Monte Carlo radiation transport code to obtain estimates of the microsave power exiting the torus coupling links in EPT microwave manifolds. The microwave power loss and polarization at surface reflections were accounted for by treating the microwaves as plane waves reflecting off plane surfaces. Agreement on the order of 10% was obtained between the measured and calculated output power distribution for an existing EBT-S toroidal manifold. A cost effective iterative procedure utilizing the Monte Carlo history data was implemented to predict design changes which could produce increased manifold efficiency and improved output power uniformity

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.

Distribution of trace levels of therapeutic gallium in bone as mapped by synchrotron X-ray microscopy

International Nuclear Information System (INIS)

Bockman, R.S.; Repo, M.A.; Warrell, R.P. Jr.; Pounds, J.G.; Schidlovsky, G.; Gordon, B.M.; Jones, K.W.

1990-01-01

Gallium nitrate, a drug that inhibits calcium release from bone, has been proven a safe and effective treatment for the accelerated bone resorption associated with cancer. Though bone is a target organ for gallium, the kinetics, sites, and effects of gallium accumulation in bone are not known. The authors have used synchrotron X-ray microscopy to map the distribution of trace levels of gallium in bone. After short-term in vivo administration of gallium nitrate to rats, trace (nanogram) amounts of gallium preferentially localized to the metabolically active regions in the metaphysis as well as the endosteal and periosteal surfaces of diaphyseal bone, regions where new bone formation and modeling were occurring. The amounts measured were well below the levels known to be cytotoxic. Iron and zinc, trace elements normally found in bone, were decreased in amount after in vivo administration of gallium. These studies represent a first step toward understanding the mechanism(s) of action of gallium in bone by suggesting the possible cellular, structural, and elemental targets of gallium

"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

Distribution of trace elements between clays and zeolites and aqueous solutions similar to sea water

International Nuclear Information System (INIS)

Berger, G.

1992-01-01

The mechanisms of solid-solution partitioning during mineral crystallization in sea water have been investigated for Rb, Cs, Co, Sr, U, Th and lanthanides as trace elements, and Fe, Mg-chlorite/smectites and Na-zeolites as solid phases. These minerals have been synthesized by alteration at 40 o C in saline solutions of silicate glasses of appropriate compositions. The variation of the distribution coefficients (D) with the concentration of the elements as well as competition mechanisms between elements of analogous crystallochemical properties have been studied. The ''trapping'' of trace elements is shown to be governed by two mechanisms, according to D values or to water-rock ratios. At low values of D the incorporation of elements is controlled only by D, whereas at high values it is controlled by the number of available crystallochemical sites. (Author)

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...

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.

Modeling Workflow Management in a Distributed Computing System ...

African Journals Online (AJOL)

Distributed computing is becoming increasingly important in our daily life. This is because it enables the people who use it to share information more rapidly and increases their productivity. A major characteristic feature or distributed computing is the explicit representation of process logic within a communication system, ...

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...

Distribution, provenance and early diagenesis of major and trace metals in sediment cores from the Mandovi estuary, western India

Digital Repository Service at National Institute of Oceanography (India)

Prajith, A.; Rao, V.P.; Chakraborty, P.

Major elements and trace metals were analyzed in four sediment cores recovered along a transect in the Mandovi estuary for their distribution, provenance and early diagenesis. The sediments were clayey silts in cores from the upper/lower estuary...

Spatial distribution of the trace elements zinc, strontium and lead in human bone tissue☆

Science.gov (United States)

Pemmer, B.; Roschger, A.; Wastl, A.; Hofstaetter, J.G.; Wobrauschek, P.; Simon, R.; Thaler, H.W.; Roschger, P.; Klaushofer, K.; Streli, C.

2013-01-01

Trace elements are chemical elements in minute quantities, which are known to accumulate in the bone. Cortical and trabecular bones consist of bone structural units (BSUs) such as osteons and bone packets of different mineral content and are separated by cement lines. Previous studies investigating trace elements in bone lacked resolution and therefore very little is known about the local concentration of zinc (Zn), strontium (Sr) and lead (Pb) in BSUs of human bone. We used synchrotron radiation induced micro X-ray fluorescence analysis (SR μ-XRF) in combination with quantitative backscattered electron imaging (qBEI) to determine the distribution and accumulation of Zn, Sr, and Pb in human bone tissue. Fourteen human bone samples (10 femoral necks and 4 femoral heads) from individuals with osteoporotic femoral neck fractures as well as from healthy individuals were analyzed. Fluorescence intensity maps were matched with BE images and correlated with calcium (Ca) content. We found that Zn and Pb had significantly increased levels in the cement lines of all samples compared to the surrounding mineralized bone matrix. Pb and Sr levels were found to be correlated with the degree of mineralization. Interestingly, Zn intensities had no correlation with Ca levels. We have shown for the first time that there is a differential accumulation of the trace elements Zn, Pb and Sr in BSUs of human bone indicating different mechanisms of accumulation. PMID:23932972

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

Rare earth element distributions in the West Pacific: Trace element sources and conservative vs. non-conservative behavior

Science.gov (United States)

Behrens, Melanie K.; Pahnke, Katharina; Paffrath, Ronja; Schnetger, Bernhard; Brumsack, Hans-Jürgen

2018-03-01

Recent studies suggest that transport and water mass mixing may play a dominant role in controlling the distribution of dissolved rare earth element concentrations ([REE]) at least in parts of the North and South Atlantic and the Pacific Southern Ocean. Here we report vertically and spatially high-resolution profiles of dissolved REE concentrations ([REE]) along a NW-SE transect in the West Pacific and examine the processes affecting the [REE] distributions in this area. Surface water REE patterns reveal sources of trace element (TE) input near South Korea and in the tropical equatorial West Pacific. Positive europium anomalies and middle REE enrichments in surface and subsurface waters are indicative of TE input from volcanic islands and fingerprint in detail small-scale equatorial zonal eastward transport of TEs to the iron-limited tropical East Pacific. The low [REE] of North and South Pacific Tropical Waters and Antarctic Intermediate Water are a long-range (i.e., preformed) laterally advected signal, whereas increasing [REE] with depth within North Pacific Intermediate Water result from release from particles. Optimum multiparameter analysis of deep to bottom waters indicates a dominant control of lateral transport and mixing on [REE] at the depth of Lower Circumpolar Deep Water (≥3000 m water depth; ∼75-100% explained by water mass mixing), allowing the northward tracing of LCDW to ∼28°N in the Northwest Pacific. In contrast, scavenging in the hydrothermal plumes of the Lau Basin and Tonga-Fiji area at 1500-2000 m water depth leads to [REE] deficits (∼40-60% removal) and marked REE fractionation in the tropical West Pacific. Overall, our data provide evidence for active trace element input both near South Korea and Papua New Guinea, and for a strong lateral transport component in the distribution of dissolved REEs in large parts of the West Pacific.

Distributed late-binding micro-scheduling and data caching for data-intensive workflows; Microplanificación de asignación tardía y almacenamiento temporal distribuidos para flujos de trabajo intensivos en datos

Energy Technology Data Exchange (ETDEWEB)

Delgado Peris, A.

2015-07-01

Today's world is flooded with vast amounts of digital information coming from innumerable sources. Moreover, it seems clear that this trend will only intensify in the future. Industry, society and remarkably science are not indifferent to this fact. On the contrary, they are struggling to get the most out of this data, which means that they need to capture, transfer, store and process it in a timely and efficient manner, using a wide range of computational resources. And this task is not always simple. A very representative example of the challenges posed by the management and processing of large quantities of data is that of the Large Hadron Collider experiments, which handle tens of petabytes of physics information every year. Based on the experience of one of these collaborations, we have studied the main issues involved in the management of huge volumes of data and in the completion of sizeable workflows that consume it. In this context, we have developed a general-purpose architecture for the scheduling and execution of workflows with heavy data requirements: the Task Queue. This new system builds on the late-binding overlay model, which has helped experiments to successfully overcome the problems associated to the heterogeneity and complexity of large computational grids. Our proposal introduces several enhancements to the existing systems. The execution agents of the Task Queue architecture share a Distributed Hash Table (DHT) and perform job matching and assignment cooperatively. In this way, scalability problems of centralized matching algorithms are avoided and workflow execution times are improved. Scalability makes fine-grained micro-scheduling possible and enables new functionalities, like the implementation of a distributed data cache on the execution nodes and the integration of data location information in the scheduling decisions...(Author)

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

VisTrails SAHM: visualization and workflow management for species habitat modeling

Science.gov (United States)

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

2013-01-01

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

Washability and Distribution Behaviors of Trace Elements of a High-Sulfur Coal, SW Guizhou, China

Directory of Open Access Journals (Sweden)

Wei Cheng

2018-02-01

Full Text Available The float-sink test is a commonly used technology for the study of coal washability, which determines optimal separation density for coal washing based on the desired sulfur and ash yield of the cleaned coal. In this study, the float-sink test is adopted for a high-sulfur Late Permian coal from Hongfa coalmine (No.26, southwestern Guizhou, China, to investigate its washability, and to analyze the organic affinities and distribution behaviors of some toxic and valuable trace elements. Results show that the coal is difficult to separate in terms of desulfurization. A cleaned coal could theoretically be obtained with a yield of 75.50%, sulfur 2.50%, and ash yield 11.33% when the separation density is 1.57 g/cm3. Trace elements’ distribution behaviors during the gravity separation were evaluated by correlation analysis and calculation. It was found that Cs, Ga, Ta, Th, Rb, Sb, Nb, Hf, Ba, Pb, In, Cu, and Zr are of significant inorganic affinity; while Sn, Co, Re, U, Mo, V, Cr, Ni, and Be are of relatively strong organic affinity. LREE (Light rare earth elements, however, seem to have weaker organic affinity than HREE (Heavy rare earth elements, which can probably be attributed to lanthanide contraction. When the separation density is 1.60 g/cm3, a large proportion of Sn, Be, Cr, U, V, Mo, Ni, Cd, Pb, and Cu migrate to the cleaned coal, but most of Mn, Sb and Th stay in the gangue. Coal preparation provides alternativity for either toxic elements removal or valuable elements preconcentration in addition to desulfurization and deashing. The enrichment of trace elements in the cleaned coal depends on the predetermined separation density which will influence the yields and ash yields of the cleaned coal.

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.

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.

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.

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.

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

Science.gov (United States)

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

2013-12-01

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

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

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.

Investigation of exposure rates and radionuclide and trace metal distributions along the Hanford Reach of the Columbia River

International Nuclear Information System (INIS)

Cooper, A.T.; Woodruff, R.K.

1993-09-01

Studies have been conducted to investigate exposure rates, and radionuclide and trace metal distributions along the Columbia River where it borders the Hanford Site. The last major field study was conducted in 1979. With recently renewed interest in various land use and resource protection alternatives, it is important to have data that represent current conditions. Radionuclides and trace metals were surveyed in Columbia River shoreline soils along the Hanford Site (Hanford Reach). The work was conducted as part of the Surface Environmental Surveillance Project, Pacific Northwest Laboratory. The survey consisted of taking exposure rate measurements and soil samples primarily at locations known or expected to have elevated exposure rates

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.

Task Balanced Workflow Scheduling Technique considering Task Processing Rate in Spot Market

Directory of Open Access Journals (Sweden)

Daeyong Jung

2014-01-01

Full Text Available Recently, the cloud computing is a computing paradigm that constitutes an advanced computing environment that evolved from the distributed computing. And the cloud computing provides acquired computing resources in a pay-as-you-go manner. For example, Amazon EC2 offers the Infrastructure-as-a-Service (IaaS instances in three different ways with different price, reliability, and various performances of instances. Our study is based on the environment using spot instances. Spot instances can significantly decrease costs compared to reserved and on-demand instances. However, spot instances give a more unreliable environment than other instances. In this paper, we propose the workflow scheduling scheme that reduces the out-of-bid situation. Consequently, the total task completion time is decreased. The simulation results reveal that, compared to various instance types, our scheme achieves performance improvements in terms of an average combined metric of 12.76% over workflow scheme without considering the processing rate. However, the cost in our scheme is higher than an instance with low performance and is lower than an instance with high performance.

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

The trace formula and the distribution of eigenvalues of Schroedinger operators on manifolds all of whose geodesics are closed

International Nuclear Information System (INIS)

Schubert, R.

1995-05-01

We investigate the behaviour of the remainder term R(E) in the Weyl formula {nvertical stroke E n ≤E}=Vol(M).E d/2 /[(4π) d/2 Γ(d/2+1)]+R(E) for the eigenvalues E n of a Schroedinger operator on a d-dimensional compact Riemannian manifold all of whose geodesics are closed. We show that R(E) is of the form E (d-1)/2 Θ(√E), where Θ(x) is an almost periodic function of Besicovitch class B 2 which has a limit distribution whose density is a box-shaped function. Furthermore we derive a trace formula and study higher order terms in the asymptotics of the coefficients related to the periodic orbits. The periodicity of the geodesic flow leads to a very simple structure of the trace formula which is the reason why the limit distribution can be computed explicitly. (orig.)

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.

Flexible Early Warning Systems with Workflows and Decision Tables

Science.gov (United States)

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

2012-04-01

An essential part of early warning systems and systems for crisis management are decision support systems that facilitate communication and collaboration. Often official policies specify how different organizations collaborate and what information is communicated to whom. For early warning systems it is crucial that information is exchanged dynamically in a timely manner and all participants get exactly the information they need to fulfil their role in the crisis management process. Information technology obviously lends itself to automate parts of the process. We have experienced however that in current operational systems the information logistics processes are hard-coded, even though they are subject to change. In addition, systems are tailored to the policies and requirements of a certain organization and changes can require major software refactoring. We seek to develop a system that can be deployed and adapted to multiple organizations with different dynamic runtime policies. A major requirement for such a system is that changes can be applied locally without affecting larger parts of the system. In addition to the flexibility regarding changes in policies and processes, the system needs to be able to evolve; when new information sources become available, it should be possible to integrate and use these in the decision process. In general, this kind of flexibility comes with a significant increase in complexity. This implies that only IT professionals can maintain a system that can be reconfigured and adapted; end-users are unable to utilise the provided flexibility. In the business world similar problems arise and previous work suggested using business process management systems (BPMS) or workflow management systems (WfMS) to guide and automate early warning processes or crisis management plans. However, the usability and flexibility of current WfMS are limited, because current notations and user interfaces are still not suitable for end-users, and workflows

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

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

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.)

Spatial distribution of the trace elements zinc, strontium and lead in human bone tissue.

Science.gov (United States)

Pemmer, B; Roschger, A; Wastl, A; Hofstaetter, J G; Wobrauschek, P; Simon, R; Thaler, H W; Roschger, P; Klaushofer, K; Streli, C

2013-11-01

Trace elements are chemical elements in minute quantities, which are known to accumulate in the bone. Cortical and trabecular bones consist of bone structural units (BSUs) such as osteons and bone packets of different mineral content and are separated by cement lines. Previous studies investigating trace elements in bone lacked resolution and therefore very little is known about the local concentration of zinc (Zn), strontium (Sr) and lead (Pb) in BSUs of human bone. We used synchrotron radiation induced micro X-ray fluorescence analysis (SR μ-XRF) in combination with quantitative backscattered electron imaging (qBEI) to determine the distribution and accumulation of Zn, Sr, and Pb in human bone tissue. Fourteen human bone samples (10 femoral necks and 4 femoral heads) from individuals with osteoporotic femoral neck fractures as well as from healthy individuals were analyzed. Fluorescence intensity maps were matched with BE images and correlated with calcium (Ca) content. We found that Zn and Pb had significantly increased levels in the cement lines of all samples compared to the surrounding mineralized bone matrix. Pb and Sr levels were found to be correlated with the degree of mineralization. Interestingly, Zn intensities had no correlation with Ca levels. We have shown for the first time that there is a differential accumulation of the trace elements Zn, Pb and Sr in BSUs of human bone indicating different mechanisms of accumulation. © 2013. Published by Elsevier Inc. All rights reserved.

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.

Data partitioning enables the use of standard SOAP Web Services in genome-scale workflows.

Science.gov (United States)

Sztromwasser, Pawel; Puntervoll, Pål; Petersen, Kjell

2011-07-26

Biological databases and computational biology tools are provided by research groups around the world, and made accessible on the Web. Combining these resources is a common practice in bioinformatics, but integration of heterogeneous and often distributed tools and datasets can be challenging. To date, this challenge has been commonly addressed in a pragmatic way, by tedious and error-prone scripting. Recently however a more reliable technique has been identified and proposed as the platform that would tie together bioinformatics resources, namely Web Services. In the last decade the Web Services have spread wide in bioinformatics, and earned the title of recommended technology. However, in the era of high-throughput experimentation, a major concern regarding Web Services is their ability to handle large-scale data traffic. We propose a stream-like communication pattern for standard SOAP Web Services, that enables efficient flow of large data traffic between a workflow orchestrator and Web Services. We evaluated the data-partitioning strategy by comparing it with typical communication patterns on an example pipeline for genomic sequence annotation. The results show that data-partitioning lowers resource demands of services and increases their throughput, which in consequence allows to execute in-silico experiments on genome-scale, using standard SOAP Web Services and workflows. As a proof-of-principle we annotated an RNA-seq dataset using a plain BPEL workflow engine.

Data partitioning enables the use of standard SOAP Web Services in genome-scale workflows

Directory of Open Access Journals (Sweden)

Sztromwasser Paweł

2011-06-01

Full Text Available Biological databases and computational biology tools are provided by research groups around the world, and made accessible on the Web. Combining these resources is a common practice in bioinformatics, but integration of heterogeneous and often distributed tools and datasets can be challenging. To date, this challenge has been commonly addressed in a pragmatic way, by tedious and error-prone scripting. Recently however a more reliable technique has been identified and proposed as the platform that would tie together bioinformatics resources, namely Web Services. In the last decade the Web Services have spread wide in bioinformatics, and earned the title of recommended technology. However, in the era of high-throughput experimentation, a major concern regarding Web Services is their ability to handle large-scale data traffic. We propose a stream-like communication pattern for standard SOAP Web Services, that enables efficient flow of large data traffic between a workflow orchestrator and Web Services. We evaluated the data-partitioning strategy by comparing it with typical communication patterns on an example pipeline for genomic sequence annotation. The results show that data-partitioning lowers resource demands of services and increases their throughput, which in consequence allows to execute in-silico experiments on genome-scale, using standard SOAP Web Services and workflows. As a proof-of-principle we annotated an RNA-seq dataset using a plain BPEL workflow engine.

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

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.

A Component Based Approach to Scientific Workflow Management

CERN Document Server

Le Goff, Jean-Marie; Baker, Nigel; Brooks, Peter; McClatchey, Richard

2001-01-01

CRISTAL is a distributed scientific workflow system used in the manufacturing and production phases of HEP experiment construction at CERN. The CRISTAL project has studied the use of a description driven approach, using meta- modelling techniques, to manage the evolving needs of a large physics community. Interest from such diverse communities as bio-informatics and manufacturing has motivated the CRISTAL team to re-engineer the system to customize functionality according to end user requirements but maximize software reuse in the process. The next generation CRISTAL vision is to build a generic component architecture from which a complete software product line can be generated according to the particular needs of the target enterprise. This paper discusses the issues of adopting a component product line based approach and our experiences of software reuse.

A component based approach to scientific workflow management

International Nuclear Information System (INIS)

Baker, N.; Brooks, P.; McClatchey, R.; Kovacs, Z.; LeGoff, J.-M.

2001-01-01

CRISTAL is a distributed scientific workflow system used in the manufacturing and production phases of HEP experiment construction at CERN. The CRISTAL project has studied the use of a description driven approach, using meta-modelling techniques, to manage the evolving needs of a large physics community. Interest from such diverse communities as bio-informatics and manufacturing has motivated the CRISTAL team to re-engineer the system to customize functionality according to end user requirements but maximize software reuse in the process. The next generation CRISTAL vision is to build a generic component architecture from which a complete software product line can be generated according to the particular needs of the target enterprise. This paper discusses the issues of adopting a component product line based approach and our experiences of software reuse

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.

Automated selected reaction monitoring data analysis workflow for large-scale targeted proteomic studies.

Science.gov (United States)

Surinova, Silvia; Hüttenhain, Ruth; Chang, Ching-Yun; Espona, Lucia; Vitek, Olga; Aebersold, Ruedi

2013-08-01

Targeted proteomics based on selected reaction monitoring (SRM) mass spectrometry is commonly used for accurate and reproducible quantification of protein analytes in complex biological mixtures. Strictly hypothesis-driven, SRM assays quantify each targeted protein by collecting measurements on its peptide fragment ions, called transitions. To achieve sensitive and accurate quantitative results, experimental design and data analysis must consistently account for the variability of the quantified transitions. This consistency is especially important in large experiments, which increasingly require profiling up to hundreds of proteins over hundreds of samples. Here we describe a robust and automated workflow for the analysis of large quantitative SRM data sets that integrates data processing, statistical protein identification and quantification, and dissemination of the results. The integrated workflow combines three software tools: mProphet for peptide identification via probabilistic scoring; SRMstats for protein significance analysis with linear mixed-effect models; and PASSEL, a public repository for storage, retrieval and query of SRM data. The input requirements for the protocol are files with SRM traces in mzXML format, and a file with a list of transitions in a text tab-separated format. The protocol is especially suited for data with heavy isotope-labeled peptide internal standards. We demonstrate the protocol on a clinical data set in which the abundances of 35 biomarker candidates were profiled in 83 blood plasma samples of subjects with ovarian cancer or benign ovarian tumors. The time frame to realize the protocol is 1-2 weeks, depending on the number of replicates used in the experiment.

Spatial Distribution and Fuzzy Health Risk Assessment of Trace Elements in Surface Water from Honghu Lake.

Science.gov (United States)

Li, Fei; Qiu, Zhenzhen; Zhang, Jingdong; Liu, Chaoyang; Cai, Ying; Xiao, Minsi

2017-09-04

Previous studies revealed that Honghu Lake was polluted by trace elements due to anthropogenic activities. This study investigated the spatial distribution of trace elements in Honghu Lake, and identified the major pollutants and control areas based on the fuzzy health risk assessment at screening level. The mean total content of trace elements in surface water decreased in the order of Zn (18.04 μg/L) > Pb (3.42 μg/L) > Cu (3.09 μg/L) > Cr (1.63 μg/L) > As (0.99 μg/L) > Cd (0.14 μg/L), within limits of Drinking Water Guidelines. The results of fuzzy health risk assessment indicated that there was no obvious non-carcinogenic risk to human health, while carcinogenic risk was observed in descending order of As > Cr > Cd > Pb. As was regarded to have the highest carcinogenic risk among selected trace elements because it generally accounted for 64% of integrated carcinogenic risk. Potential carcinogenic risk of trace elements in each sampling site was approximately at medium risk level (10 -5 to 10 -4 ). The areas in the south (S4, S13, and S16) and northeast (S8, S18, and S19) of Honghu Lake were regarded as the risk priority control areas. However, the corresponding maximum memberships of integrated carcinogenic risk in S1, S3, S10-S13, S15, and S18 were of relatively low credibility (50-60%), and may mislead the decision-makers in identifying the risk priority areas. Results of fuzzy assessment presented the subordinate grade and corresponding reliability of risk, and provided more full-scale results for decision-makers, which made up for the deficiency of certainty assessment to a certain extent.

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

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

Using the ion microprobe mass analyser for trace element analysis

International Nuclear Information System (INIS)

Schilling, J.H.

1978-01-01

Most techniques for the analysis of trace elements are capable of determining the concentrations in a bulk sample or solution, but without reflecting their distribution. In a bulk analysis therefore elements which occur in high concentration in a few precipitates would still be considered trace elements even though their local concentration greatly exceed the normally accepted trace elements concentration limit. Anomalous distribution is also shown by an oxide layer, a few hundred Angstrom thick, on an aluminium sample. A low oxide concentration would be reported if it were included in the bulk analysis, which contradicts the high surface concentration. The importance of a knowledge of the trace element distribution is therefore demonstrated. Distributional trace element analysis can be carried out using the ion microprobe mass analyser (IMMA). Since the analytical technique used in this instrument, namely secondary ion mass spectrometry (SIMS), is not universally appreciated, the instrument and its features will be described briefly followed by a discussion of quantitative analysis and the related subjects of detection limit and sample consumption. Finally, a few examples of the use of the instrument are given

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.

Study of trace elements distribution in various tissues structures

International Nuclear Information System (INIS)

Kwiatek, W.M.; Marczewska, E.

1994-01-01

Many papers have been written during the past ten years about TE study in cancer and normal tissues describing the use of different methods for detection of trace elements. Concentration of TE depends strongly on the sample measured. However, according to our knowledge, the role of TE in cancerous tissue is still known. Therefore, we propose to perform an experiment which will hopefully given us more information about the relationship between the concentration of elements in different tissues. The developing industry localised near Cracow becomes a serious danger for health of it's inhabitants. The negative influence of the air pollution to the living organisms is seen not only in the nature but also in humans. Therefore we want to analyse the trace element contents in the air. Such investigation will give the information about the pollution level in the City. The pollution has its obvious negative influence to health and toxic element concentration level in blood. It is interesting to check if placenta plays an effective role in foetus protection against toxic metals. In order to study this problem, the trace element analysis of placenta tissues will be done by means of synchrotron microbeam. (author). 1 ref

Tropospheric chemistry over the lower Great Plains of the United States. 2. Trace gas profiles and distributions

Science.gov (United States)

Luke, Winston T.; Dickerson, Russell R.; Ryan, William F.; Pickering, Kenneth E.; Nunnermacker, Linda J.

1992-12-01

Convective clouds and thunderstorms redistribute air pollutants vertically, and by altering the chemistry and radiative balance of the upper troposphere, these local actions can have global consequences. To study these effects, measurements of trace gases ozone, O3, carbon monoxide, CO, and odd nitrogen were made aboard the NCAR Sabreliner on 18 flights over the southern Great Plains during June 1985. To demonstrate chemical changes induced by vertical motions in the atmosphere and to facilitate comparison with computer model calculations, these data were categorized according to synoptic flow patterns. Part 1 of this two-part paper details the alternating pulses of polar and maritime air masses that dominate the vertical mixing in this region. In this paper, trace gas measurements are presented as altitude profiles (0-12 km) with statistical distributions of mixing ratios for each species in each flow pattern. The polar flow regime is characterized by northwesterly winds, subsiding air, and convective stability. Concentrations of CO and total odd nitrogen (NOy) are relatively high in the shallow planetary boundary layer (PBL) but decrease rapidly with altitude. Ozone, on the other hand, is uniformly distributed, suggesting limited photochemical production; in fact, nitric oxide, NO, mixing ratios fell below 10 ppt (parts per 1012 by volume) in the midtroposphere. The maritime regime is characterized by southerly surface winds, convective instability, and a deep PBL; uniformly high concentrations of trace gases were found up to 4 km on one flight. Severe storms occur in maritime flow, especially when capped by a dry layer, and they transport large amounts of CO, O3, and NOy into the upper troposphere. Median NO levels at high altitude exceeded 300 ppt. Lightning produces spikes of NO (but not CO) with mixing ratios sometimes exceeding 1000 ppt. This flow pattern tends to leave the midtroposphere relatively clean with concentrations of trace gases similar to those

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.

Trace element distribution in different chemical fractions of False Bay sediments

International Nuclear Information System (INIS)

Rosental, R.

1984-05-01

Trace metals in the aquatic environment are generally concentrated on solid geochemical phases which eventually become incorporated into estuarine and marine sediments. The mechanism of trace metal concentration is believed to be adsorption on various geochemical phases, such as hydrous metal oxides, clays and organic matter. Metals in estuarine sediments can thus be expected to be partitioned between different phases, depending on the concentration of the phase and the strength of the adsorption bond. The bioavailability of sediment-bound metals to deposit-feeding organisms will depend on trace metal partitioning and the kinetics of biological metal uptake from each geochemical phase. The major objective of this study was to establish an analytical procedure involving sequential chemical extractions for the partitioning of particulate trace metals in sediment samples, collected from False Bay. Eight metals were examined, i.e. Cd, Cu, Cr, Fe, Mn, Ni, Pb and Zn. X-ray diffraction was also used in the study

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...

SigWin-detector: a Grid-enabled workflow for discovering enriched windows of genomic features related to DNA sequences

Directory of Open Access Journals (Sweden)

Wibisono Adianto

2008-08-01

Full Text Available Abstract Background Chromosome location is often used as a scaffold to organize genomic information in both the living cell and molecular biological research. Thus, ever-increasing amounts of data about genomic features are stored in public databases and can be readily visualized by genome browsers. To perform in silico experimentation conveniently with this genomics data, biologists need tools to process and compare datasets routinely and explore the obtained results interactively. The complexity of such experimentation requires these tools to be based on an e-Science approach, hence generic, modular, and reusable. A virtual laboratory environment with workflows, workflow management systems, and Grid computation are therefore essential. Findings Here we apply an e-Science approach to develop SigWin-detector, a workflow-based tool that can detect significantly enriched windows of (genomic features in a (DNA sequence in a fast and reproducible way. For proof-of-principle, we utilize a biological use case to detect regions of increased and decreased gene expression (RIDGEs and anti-RIDGEs in human transcriptome maps. We improved the original method for RIDGE detection by replacing the costly step of estimation by random sampling with a faster analytical formula for computing the distribution of the null hypothesis being tested and by developing a new algorithm for computing moving medians. SigWin-detector was developed using the WS-VLAM workflow management system and consists of several reusable modules that are linked together in a basic workflow. The configuration of this basic workflow can be adapted to satisfy the requirements of the specific in silico experiment. Conclusion As we show with the results from analyses in the biological use case on RIDGEs, SigWin-detector is an efficient and reusable Grid-based tool for discovering windows enriched for features of a particular type in any sequence of values. Thus, SigWin-detector provides the

SigWin-detector: a Grid-enabled workflow for discovering enriched windows of genomic features related to DNA sequences.

Science.gov (United States)

Inda, Márcia A; van Batenburg, Marinus F; Roos, Marco; Belloum, Adam S Z; Vasunin, Dmitry; Wibisono, Adianto; van Kampen, Antoine H C; Breit, Timo M

2008-08-08

Chromosome location is often used as a scaffold to organize genomic information in both the living cell and molecular biological research. Thus, ever-increasing amounts of data about genomic features are stored in public databases and can be readily visualized by genome browsers. To perform in silico experimentation conveniently with this genomics data, biologists need tools to process and compare datasets routinely and explore the obtained results interactively. The complexity of such experimentation requires these tools to be based on an e-Science approach, hence generic, modular, and reusable. A virtual laboratory environment with workflows, workflow management systems, and Grid computation are therefore essential. Here we apply an e-Science approach to develop SigWin-detector, a workflow-based tool that can detect significantly enriched windows of (genomic) features in a (DNA) sequence in a fast and reproducible way. For proof-of-principle, we utilize a biological use case to detect regions of increased and decreased gene expression (RIDGEs and anti-RIDGEs) in human transcriptome maps. We improved the original method for RIDGE detection by replacing the costly step of estimation by random sampling with a faster analytical formula for computing the distribution of the null hypothesis being tested and by developing a new algorithm for computing moving medians. SigWin-detector was developed using the WS-VLAM workflow management system and consists of several reusable modules that are linked together in a basic workflow. The configuration of this basic workflow can be adapted to satisfy the requirements of the specific in silico experiment. As we show with the results from analyses in the biological use case on RIDGEs, SigWin-detector is an efficient and reusable Grid-based tool for discovering windows enriched for features of a particular type in any sequence of values. Thus, SigWin-detector provides the proof-of-principle for the modular e-Science based concept

Distribution of some artificial and natural radionuclides and trace elements in Syrian soils

International Nuclear Information System (INIS)

Al-Masri, M. S.; Shaik Khalil, H.; Amin, Y.; Ibrahim, S.; Hassan, M.

2004-07-01

Within the environmental monitoring program in Syria, about 115 surface soil and 38 profile soil samples were collected and analyzed during the period of 1998 to 2003 in order to determine the levels of natural and artificial radionuclides and some of trace elements (Cu, Zn, Cd, Pb). The concentrations of the natural radionuclides in the surface samples were found to vary from area to another and ranged from 2-50 Bq/kg, 4-228 Bq/kg, 4-55 Bq/kg, 1-143 Bq/kg and 96-672 Bq/kg for 224 Ra, 226 Ra, 228 Ra, 137 Cs and 04 K, respectively. While, the concentrations of the studied trace elements were varied between 0.5-5.6 mg/kg for U, 3.2-31.7 mg/kg for Pb, 14-141 mg/kg for Zn, 1.6-114 mg/kg for Cu and 0.25-2.7 mg/kg for Cd. Most of the reported values in this study were in the range of the natural uncontaminated surface soil concentrations and published values in many countries in the world. The results showed that the relation between the distribution of the natural radionuclides and depth was approximately the same for all radionuclides except for 137 Cs, which was extremely binded in the upper layers of soil. In addition, some differences in the concentrations of the studied trace elements with depth were observed. These differences may be due to the average of rainfall and the existence of some potential sources of contamination of such elements. However, the results of this study can be considered as a database for the natural background in Syria that helps to establish the radiation map of the country.(author)

CMS distributed analysis infrastructure and operations: experience with the first LHC data

International Nuclear Information System (INIS)

Vaandering, E W

2011-01-01

The CMS distributed analysis infrastructure represents a heterogeneous pool of resources distributed across several continents. The resources are harnessed using glite and glidein-based work load management systems (WMS). We provide the operational experience of the analysis workflows using CRAB-based servers interfaced with the underlying WMS. The automatized interaction of the server with the WMS provides a successful analysis workflow. We present the operational experience as well as methods used in CMS to analyze the LHC data. The interaction with CMS Run-registry for Run and luminosity block selections via CRAB is discussed. The variations of different workflows during the LHC data-taking period and the lessons drawn from this experience are also outlined.

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...

Nuclear traces in glass

International Nuclear Information System (INIS)

Segovia A, M. de N.

1978-01-01

The charged particles produce, in dielectric materials, physical and chemical effects which make evident the damaged zone along the trajectory of the particle. This damaged zone is known as the latent trace. The latent traces can be enlarged by an etching of the detector material. This treatment attacks preferently the zones of the material where the charged particles have penetrated, producing concavities which can be observed through a low magnification optical microscope. These concavities are known as developed traces. In this work we describe the glass characteristics as a detector of the fission fragments traces. In the first chapter we present a summary of the existing basic theories to explain the formation of traces in solids. In the second chapter we describe the etching method used for the traces development. In the following chapters we determine some chatacteristics of the traces formed on the glass, such as: the development optimum time; the diameter variation of the traces and their density according to the temperature variation of the detector; the glass response to a radiation more penetrating than that of the fission fragments; the distribution of the developed traces and the existing relation between this ditribution and the fission fragments of 252 Cf energies. The method which has been used is simple and cheap and can be utilized in laboratories whose resources are limited. The commercial glass which has been employed allows the registration of the fission fragments and subsequently the realization of experiments which involve the counting of the traces as well as the identification of particles. (author)

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.

Capturing sunlight into a photobioreactor: Ray tracing simulations of the propagation of light from capture to distribution into the reactor

NARCIS (Netherlands)

Zijffers, J.F.; Janssen, M.G.J.; Tramper, J.; Wijffels, R.H.; Salim, S.

2008-01-01

The Green Solar Collector (GSC), a photobioreactor designed for area efficient outdoor cultivation of microalgae uses Fresnel lenses and light guides to focus, transport and distribute direct light into the algae suspension. Calculating the path of rays of light, so-called ray tracing, is used to

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.

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

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

Integrated Automatic Workflow for Phylogenetic Tree Analysis Using Public Access and Local Web Services.

Science.gov (United States)

Damkliang, Kasikrit; Tandayya, Pichaya; Sangket, Unitsa; Pasomsub, Ekawat

2016-11-28

At the present, coding sequence (CDS) has been discovered and larger CDS is being revealed frequently. Approaches and related tools have also been developed and upgraded concurrently, especially for phylogenetic tree analysis. This paper proposes an integrated automatic Taverna workflow for the phylogenetic tree inferring analysis using public access web services at European Bioinformatics Institute (EMBL-EBI) and Swiss Institute of Bioinformatics (SIB), and our own deployed local web services. The workflow input is a set of CDS in the Fasta format. The workflow supports 1,000 to 20,000 numbers in bootstrapping replication. The workflow performs the tree inferring such as Parsimony (PARS), Distance Matrix - Neighbor Joining (DIST-NJ), and Maximum Likelihood (ML) algorithms of EMBOSS PHYLIPNEW package based on our proposed Multiple Sequence Alignment (MSA) similarity score. The local web services are implemented and deployed into two types using the Soaplab2 and Apache Axis2 deployment. There are SOAP and Java Web Service (JWS) providing WSDL endpoints to Taverna Workbench, a workflow manager. The workflow has been validated, the performance has been measured, and its results have been verified. Our workflow's execution time is less than ten minutes for inferring a tree with 10,000 replicates of the bootstrapping numbers. This paper proposes a new integrated automatic workflow which will be beneficial to the bioinformaticians with an intermediate level of knowledge and experiences. All local services have been deployed at our portal http://bioservices.sci.psu.ac.th.

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.

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.  

Speciation and Distribution of Trace Metals and Organic Matter in Marine Lake as In Situ Laboratory

Science.gov (United States)

Mlakar, M.; Fiket, Ž.; Cuculić, V.; Cukrov, N.; Geček, S.

2016-02-01

Marine lakes are unique, isolated marine systems, also recognized as in situ "laboratories" in which geochemical processes on a different scale compared to the open sea, can be observed. Impact of organic matter cycling on distribution of trace metals in the marine lake Mir, located on Dugi Otok Island, in the central part of the eastern Adriatic Sea, was investigated. Intense spatial and seasonal variations of physico-chemical parameters and organic matter concentrations in the water column of the Lake are governed predominantly by natural processes. Enhanced oxygen consumption in the Lake during summer season, high organic carbon concentrations and low redox potential result in occasional occurrence of anoxic conditions in the bottom layers. Speciation modelling showed that dissolved trace metals Cu, Pb and Zn, are mostly bound to organic matter, while Cd, Co and Ni are present predominantly as free ions and inorganic complexes. Trace metals removal from the water column and their retention in the sediment was found to depend on the nature of the relationship between specific metal and high proportion of organic matter (up to 9%) and inorganic phases, Fe-oxyhydroxydes or biogenic calcite. Surrounding karstic background, with occasional occurrences of red soil characterize deposited sediments as coarse grained and carbonate rich, whose elemental composition is affected by bathymetry of the basin and overall biological production.

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...

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

Major and trace element distribution in soil and sediments from the Egyptian central Nile Valley

Science.gov (United States)

Badawy, W. M.; Ghanim, E. H.; Duliu, O. G.; El Samman, H.; Frontasyeva, M. V.

2017-07-01

The distributions of 32 major and trace elements in 72 surface soil and sediment samples collected from the Asyut to Cairo Nile river section were determined by epithermal neutron activation analysis and compared with corresponding data for the Upper Continental Crust, North American Shale Composite, Average Soil and Average Sediment as well as suspended sediments from Congo and Upper Niger Rivers, in order to establish to which extent the Nile sedimentary material can be related to similar material all over the world as well as to local geology. Their relative distributions indicate the presence of detrital material of igneous origin, most probably resulting from weathering of the Ethiopian Highlands and transported by the Blue Nile, the Nile main tributary. The distributions of nickel, zinc, and arsenic contents suggest that the lower part of the Nile and its surroundings including the Nile Delta is not seriously polluted with heavy metals, so that, in spite of a human activity, which lasted four millennia, the Nile River continues to be less affected by any anthropogenic contamination.

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

Measuring trace gas emission from multi-distributed sources using vertical radial plume mapping (VRPM) and backward Lagrangian stochastic (bLS) techniques

Science.gov (United States)

Two micrometeorological techniques for measuring trace gas emission rates from distributed area sources were evaluated using a variety of synthetic area sources. The accuracy of the vertical radial plume mapping (VRPM) and the backward Lagrangian (bLS) techniques with an open-path optical spectrosco...

Distribution of trace metals in surface seawater and zooplankton of the Bay of Bengal, off Rushikulya estuary, East Coast of India

International Nuclear Information System (INIS)

Srichandan, Suchismita; Panigrahy, R.C.; Baliarsingh, S.K.; Srinivasa, Rao B.; Pati, Premalata; Sahu, Biraja K.; Sahu, K.C.

2016-01-01

Concentrations of trace metals such as iron (Fe), copper (Cu), zinc (Zn), cobalt (Co), nickel (Ni), manganese (Mn), lead (Pb), cadmium (Cd), chromium (Cr), arsenic (As), vanadium (V), and selenium (Se) were determined in seawater and zooplankton from the surface waters off Rushikulya estuary, north-western Bay of Bengal. During the study period, the concentration of trace metals in seawater and zooplankton showed significant spatio-temporal variation. Cu and Co levels in seawater mostly remained non-detectable. Other elements were found at higher concentrations and exhibited marked variations. The rank order distribution of trace metals in terms of their average concentration in seawater was observed as Fe > Ni > Mn > Pb > As > Zn > Cr > V > Se > Cd while in zooplankton it was Fe > Mn > Cd > As > Pb > Ni > Cr > Zn > V > Se. The bioaccumulation factor (BAF) of Fe was highest followed by Zn and the lowest value was observed with Ni. Results of correlation analysis discerned positive affinity and good relationship among the majority of the trace metals, both in seawater and zooplankton suggesting their strong affinity and coexistence. - Highlights: • First-hand report on trace metal concentration in zooplankton and seawater covering 2 years from this eco-sensitive region. • In seawater trace metals followed the rank order of Fe > Ni > Mn > Pb > As > Zn > Cr > V > Se > Cd. • In zooplankton the rank order was Fe > Mn > Cd > As > Pb > Ni > Cr > Zn > V > Se. • The bioaccumulation factor of Fe was highest followed by Zn. • Strong affinity, coexistence, and similar source of trace metals in the study area.

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.

Alert Messaging in the CMS Distributed Workflow System

International Nuclear Information System (INIS)

Maxa, Zdenek

2012-01-01

WMAgent is the core component of the CMS workload management system. One of the features of this job managing platform is a configurable messaging system aimed at generating, distributing and processing alerts: short messages describing a given alert-worthy information or pathological condition. Apart from the framework's sub-components running within the WMAgent instances, there is a stand-alone application collecting alerts from all WMAgent instances running across the CMS distributed computing environment. The alert framework has a versatile design that allows for receiving alert messages also from other CMS production applications, such as PhEDEx data transfer manager. We present implementation details of the system, including its Python implementation using ZeroMQ, CouchDB message storage and future visions as well as operational experiences. Inter-operation with monitoring platforms such as Dashboard or Lemon is described.

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.

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

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

Content and distribution of trace metals in pristine permafrost environments of Northeastern Siberia, Russia

Science.gov (United States)

Antcibor, I.; Eschenbach, A.; Kutzbach, L.; Bolshiyanov, D.; Pfeiffer, E.-M.

2012-04-01

Arctic regions are one of the most sensitive areas with respect to climatic changes and human impacts. Research is required to discover how the function of permafrost soils as a buffering system for metal pollutants could change in response to the predicted changes. The goal of this work is to determine the background levels of trace metals in the pristine arctic ecosystems of the Lena River Delta in Northeastern Siberia and to evaluate the possible effect of human impacts on this arctic region. The Lena River Delta represents areas with different dominating geomorphologic processes that can generally be divided between accumulation and erosion sites. Frequent changes of the river water level create different periods of sedimentation and result in the formation of stratified soils and sediment layers which are dominated either by mineral substrates with allochthonous organic matter or pure autochthonous peat. The deposited sediments that have formed the delta islands are mostly composed of sand fractions; therefore the buffering effects of clay materials can be neglected. Samoylov Island is representative of the south-central and eastern modern delta surfaces of the Lena River Delta and is selected as a pilot study site. We determined total element contents of Fe, Mn, Zn, Cd, Ni, Cu, As, Pb, Co and Hg in soil horizons from different polygonal elevated rims, polygonal depressed centers and the middle floodplain. High gravimetric concentrations (related to dry mass of soil material) of Mn and Fe are found within all soil profiles and vary from 0.14 to 1.39 g kg-1 and from 10.7 to 41.2 g kg-1, respectively. While the trace element concentrations do not exceed typical crustal abundances, the maximum values of most of the metals are observed within the soil profile situated at the middle floodplain. This finding suggests that apart from the parent material the second potential source of trace metals is due to allochthonous substance input during annual flooding of the

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...

Trace element metabolism in man and animals

International Nuclear Information System (INIS)

Kirchgessner, M.

1977-01-01

Uptake, distribution, storage, excretion of different trace elements and resulting disturbances are investigated in blood and organs in animal experiments and in human diagnostics with the aid of radioisotopes. Apart from this, untritional disturbances are mentioned. Finally, future aspects of physiological trace element examinations are listed. (AJ) 891 AJ [de

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....

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.

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.

Geochemical distribution of trace metals and organochlorine contaminants of a lake ontario shoreline marsh

Energy Technology Data Exchange (ETDEWEB)

Glooschenko, W A; Capocianco, J; Coburn, J; Glooschenko, V

1981-02-01

Rattray Marsh, an 8 ha marsh on the Lake Ontario shoreline at Mississauga, Ontario, is an important local habitat for waterfowl and shorebirds during spring and fall migration. A study was conducted to determine the distribution of nutrients (carbon, nitrogen, and phosphorus) and potential trace metal and organochlorine pollutants in the marsh as evidenced by the sedimentary concentrations of these compounds. Generally, copper, zinc, lead, and mercury were higher in concentration in local soils than in Lake Ontario sediments. Metals and organic carbon levels did not correlate, and the metals appeared to be associated with silts and clays. Organochlorine contaminants include p,p1-DDE, p,p1-DDD, p,p1-DDT, alpha-chlordane, PCB, mirex, and HCB.

Distribution of trace elements in whole blood of Syrian lymphomas patients using instrumental neutron activation analysis

International Nuclear Information System (INIS)

Bakir, M. A.; Serhil, A.; Mohammad, A.; Habil, K.

2013-12-01

In recent years, there had been much interest in the concentrations of trace metals occurring in human and animal tissues and in the manner in which these concentrations may alter in malignant and other diseases. Neutron activation analysis is consider one of several methods that have been described for the determination of trace elements in biological materials. This method possesses the sensitivity and specificity necessary for the estimation at the concentrations existing naturally in most tissues, particularly when only small samples are available for analysis. The purpose of this study was to compare blood concentrations of trace elements Co, Cr, Fe, Rb, Sc, Se, Th, and Zn of lymphomas Syrian patients with those of healthy volunteers. Also, determine the relationships between trace elements concentration and the histological type of lymphomas. The blood samples were collected from 39 healthy volunteers and 49 patients with histologically confirmed lymphomas (29 Hodgkin's HL and 20 non-Hodgkin's lymphomas NHL), and analyzed to obtain the concentration of the trace elements in blood. Then, comparison between the healthy volunteers and lymphomas patients (both HL and NHL) was made to elucidate differences of the concentration distributions of the elements in blood. However, statistical analysis using Student's t test revealed significantly high concentrations of Co, Cr, Sc, and Th in lymphoma patients. Whereas Fe and Rb were found significantly decreased in lymphomas patient comparing to control group. Increasing or decreasing concentrations of Se and Zn in lymphoma patients was found not significant. Comparison between the healthy volunteers and non-Hodgkin's lymphomas patients reveled that Co, Cr, Sc, and Th were significantly elevated whereas, Rb only one trace element was decreased and all change in concentrations (elevating or decreasing) of Se and Zn were not significant. Comparison between the healthy volunteers and Hodgkin

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...

Proceedings of the scientific meeting on 'behavior and distributions of trace substances in the environment'

International Nuclear Information System (INIS)

Fukui, M.; Matsuzuru, H.

1998-02-01

The scientific meeting was held at the Research Reactor Institute, Kyoto University on December 11-12, 1997. This single report covers all aspects concerning association of trace substances such as pesticides/herbicides, organic chemicals and radionuclides in the environment. The reason for having this meeting is to describe the distribution and behavior of trace substances in which the emphasis is directed towards the dynamic interaction between the soil-sediment-water system and the contaminants. The Chernobyl accident raised the attention on the fate of radionuclides released in the environment and stimulated many scientists, who carry out large scale 'field experiments' without using a tracer in a laboratory. Of course, fundamental laboratory studies are necessary to give direction to and to understand observations from field studies. These activities have brought a lot of knowledge and understanding towards revealing a part of the complexity of the transport processes. It is hoped that the assembled experts, will not only dwell on distinct scientific issues, but also be able to draw firm conclusions with respect to the effective environmental management of the ecological aspects of hazardous materials. The 25 of the presented papers are indexed individually. (J.P.N.)

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.

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.

DOMstudio: an integrated workflow for Digital Outcrop Model reconstruction and interpretation

Science.gov (United States)

Bistacchi, Andrea

2015-04-01

). This dataset can be used as-is (PC-DOM), or a 3D triangulated surface can be interpolated from the point cloud, and images can be used to associate a texture to this surface (TS-DOM). In the DOMstudio workflow we use both PC-DOMs and TS-DOMs. Particularly, the latter are obtained projecting the original images onto the triangulated surface, without any downsampling, thus retaining the original resolution and quality of images collected in the field. In the DOMstudio interpretation step, PC-DOM is considered the best option for fracture analysis in outcrops where facets corresponding to fractures are present. This allows obtaining orientation statistics (e.g. stereoplots, Fisher statistics, etc.) directly from a point cloud where, for each point, the unit vector normal to the outcrop surface has been calculated. A recent development in this kind of processing is represented by the possibility to automatically select (segment) subset point clouds representing single fracture surfaces, which can be used for studies on fracture length, spacing, etc., allowing to obtain parameters like the frequency-length distribution, P21, etc. PC-DOM interpretation can be combined or complemented, depending on the outcrop morphology, with an interpretation carried out on a TS-DOM in terms of traces, which are the linear intersection of "geological" surfaces (fractures, faults, bedding, etc.) with the outcrop surface. This kind of interpretation is very well suited for outcrops with smooth surfaces, and can be performed either by manual picking, or by applying image analysis techniques on the images associated with the DOM. In this case, a huge mass of data, with very high resolution, can be collected very effectively. If we consider applications like lithological or mineral map-ping, TS-DOM datasets are the only suitable support. Finally, the DOMstudio workflow produces output in formats that are compatible with all common geomodelling packages (e.g. Gocad/Skua, Petrel, Move), allowing

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

A terrestrial lidar-based workflow for determining three-dimensional slip vectors and associated uncertainties

Science.gov (United States)

Gold, Peter O.; Cowgill, Eric; Kreylos, Oliver; Gold, Ryan D.

2012-01-01

Three-dimensional (3D) slip vectors recorded by displaced landforms are difficult to constrain across complex fault zones, and the uncertainties associated with such measurements become increasingly challenging to assess as landforms degrade over time. We approach this problem from a remote sensing perspective by using terrestrial laser scanning (TLS) and 3D structural analysis. We have developed an integrated TLS data collection and point-based analysis workflow that incorporates accurate assessments of aleatoric and epistemic uncertainties using experimental surveys, Monte Carlo simulations, and iterative site reconstructions. Our scanning workflow and equipment requirements are optimized for single-operator surveying, and our data analysis process is largely completed using new point-based computing tools in an immersive 3D virtual reality environment. In a case study, we measured slip vector orientations at two sites along the rupture trace of the 1954 Dixie Valley earthquake (central Nevada, United States), yielding measurements that are the first direct constraints on the 3D slip vector for this event. These observations are consistent with a previous approximation of net extension direction for this event. We find that errors introduced by variables in our survey method result in <2.5 cm of variability in components of displacement, and are eclipsed by the 10–60 cm epistemic errors introduced by reconstructing the field sites to their pre-erosion geometries. Although the higher resolution TLS data sets enabled visualization and data interactivity critical for reconstructing the 3D slip vector and for assessing uncertainties, dense topographic constraints alone were not sufficient to significantly narrow the wide (<26°) range of allowable slip vector orientations that resulted from accounting for epistemic uncertainties.

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.

Dose distributions of a proton beam for eye tumor therapy: Hybrid pencil-beam ray-tracing calculations

International Nuclear Information System (INIS)

Rethfeldt, Ch.; Fuchs, H.; Gardey, K.-U.

2006-01-01

For the case of eye tumor therapy with protons, improvements are introduced compared to the standard dose calculation which implies straight-line optics and the constant-density assumption for the eye and its surrounding. The progress consists of (i) taking account of the lateral scattering of the protons in tissue by folding the entrance fluence distribution with the pencil beam distribution widening with growing depth in the tissue, (ii) rescaling the spread-out Bragg peak dose distribution in water with the radiological path length calculated voxel by voxel on ray traces through a realistic density matrix for the treatment geometry, yielding a trajectory dependence of the geometrical range. Distributions calculated for some specific situations are compared to measurements and/or standard calculations, and differences to the latter are discussed with respect to the requirements of therapy planning. The most pronounced changes appear for wedges placed in front of the eye, causing additional widening of the lateral falloff. The more accurate prediction of the dose dependence at the field borders is of interest with respect to side effects in the risk organs of the eye

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.

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....

Vegetation and Cold Trapping Modulating Elevation-dependent Distribution of Trace Metals in Soils of a High Mountain in Eastern Tibetan Plateau.

Science.gov (United States)

Bing, Haijian; Wu, Yanhong; Zhou, Jun; Li, Rui; Luo, Ji; Yu, Dong

2016-04-07

Trace metals adsorbed onto fine particles can be transported long distances and ultimately deposited in Polar Regions via the cold condensation effect. This study indicated the possible sources of silver (Ag), cadmium (Cd), copper (Cu), lead (Pb), antimony (Sb) and zinc (Zn) in soils on the eastern slope of Mt. Gongga, eastern Tibetan Plateau, and deciphered the effects of vegetation and mountain cold condensation on their distributions with elevation. The metal concentrations in the soils were comparable to other mountains worldwide except the remarkably high concentrations of Cd. Trace metals with high enrichment in the soils were influenced from anthropogenic contributions. Spatially, the concentrations of Cu and Zn in the surface horizons decreased from 2000 to 3700 m a.s.l., and then increased with elevation, whereas other metals were notably enriched in the mid-elevation area (approximately 3000 m a.s.l.). After normalization for soil organic carbon, high concentrations of Cd, Pb, Sb and Zn were observed above the timberline. Our results indicated the importance of vegetation in trace metal accumulation in an alpine ecosystem and highlighted the mountain cold trapping effect on trace metal deposition sourced from long-range atmospheric transport.

Distribution of trace metals in surface seawater and zooplankton of the Bay of Bengal, off Rushikulya estuary, East Coast of India.

Science.gov (United States)

Srichandan, Suchismita; Panigrahy, R C; Baliarsingh, S K; Rao B, Srinivasa; Pati, Premalata; Sahu, Biraja K; Sahu, K C

2016-10-15

Concentrations of trace metals such as iron (Fe), copper (Cu), zinc (Zn), cobalt (Co), nickel (Ni), manganese (Mn), lead (Pb), cadmium (Cd), chromium (Cr), arsenic (As), vanadium (V), and selenium (Se) were determined in seawater and zooplankton from the surface waters off Rushikulya estuary, north-western Bay of Bengal. During the study period, the concentration of trace metals in seawater and zooplankton showed significant spatio-temporal variation. Cu and Co levels in seawater mostly remained non-detectable. Other elements were found at higher concentrations and exhibited marked variations. The rank order distribution of trace metals in terms of their average concentration in seawater was observed as Fe>Ni>Mn>Pb>As>Zn>Cr>V>Se>Cd while in zooplankton it was Fe>Mn>Cd>As>Pb>Ni>Cr>Zn>V>Se. The bioaccumulation factor (BAF) of Fe was highest followed by Zn and the lowest value was observed with Ni. Results of correlation analysis discerned positive affinity and good relationship among the majority of the trace metals, both in seawater and zooplankton suggesting their strong affinity and coexistence. Copyright © 2016 Elsevier Ltd. All rights reserved.

Resilient data staging through MxN distributed transactions.

Energy Technology Data Exchange (ETDEWEB)

Schwan, Karsten (Georgia Institute of Technology, Atlanta, GA); Oldfield, Ron A.; Lofstead, Gerald Fredrick, II; Dayal, Jai (Georgia Institute of Technology, Atlanta, GA)

2011-11-01

Scientific computing-driven discoveries are frequently driven from workflows that use persistent storage as a staging area for data between operations. With the bad and progressively worse bandwidth vs. data size issues as we continue towards exascale, eliminating persistent storage through techniques like data staging will both enable these workflows to continue online, but also enable more interactive workflows reducing the time to scientific discoveries. Data staging has shown to be an effective way for applications running on high-end computing platforms to offload expensive I/O operations and to manage the tremendous amounts of data they produce. This data staging approach, however, lacks the ACID style guarantees traditional straight-to-disk methods provide. Distributed transactions are a proven way to add ACID properties to data movements, however distributed transactions follow 1xN data movement semantics, where our highly parallel HPC environments employ MxN data movement semantics. In this paper we present a novel protocol that extends distributed transaction terminology to include MxN semantics which allows our data staging areas to benefit from ACID properties. We show that with our protocol we can provide resilient data staging with a limited performance penalty over current data staging implementations.

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.

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.

Surface distribution of dissolved trace metals in the oligotrophic ocean and their influence on phytoplankton biomass and productivity

KAUST Repository

Pinedo-González, Paulina

2015-10-25

The distribution of bioactive trace metals has the potential to enhance or limit primary productivity and carbon export in some regions of the world ocean. To study these connections, the concentrations of Cd, Co, Cu, Fe, Mo, Ni, and V were determined for 110 surface water samples collected during the Malaspina 2010 Circumnavigation Expedition (MCE). Total dissolved Cd, Co, Cu, Fe, Mo, Ni, and V concentrations averaged 19.0 ± 5.4 pM, 21.4 ± 12 pM, 0.91 ± 0.4 nM, 0.66 ± 0.3 nM, 88.8 ± 12 nM, 1.72 ± 0.4 nM, and 23.4 ± 4.4 nM, respectively, with the lowest values detected in the Central Pacific and increased values at the extremes of all transects near coastal zones. Trace metal concentrations measured in surface waters of the Atlantic Ocean during the MCE were compared to previously published data for the same region. The comparison revealed little temporal changes in the distribution of Cd, Co, Cu, Fe, and Ni over the last 30 years. We utilized a multivariable linear regression model to describe potential relationships between primary productivity and the hydrological, biological, trace nutrient and macronutrient data collected during the MCE. Our statistical analysis shows that primary productivity in the Indian Ocean is best described by chlorophyll a, NO3, Ni, temperature, SiO4, and Cd. In the Atlantic Ocean, primary productivity is correlated with chlorophyll a, NO3, PO4, mixed layer depth, Co, Fe, Cd, Cu, V, and Mo. The variables salinity, temperature, SiO4, NO3, PO4, Fe, Cd, and V were found to best predict primary productivity in the Pacific Ocean. These results suggest that some of the lesser studied trace elements (e.g., Ni, V, Mo, and Cd) may play a more important role in regulating oceanic primary productivity than previously thought and point to the need for future experiments to verify their potential biological functions.

Surface distribution of dissolved trace metals in the oligotrophic ocean and their influence on phytoplankton biomass and productivity

KAUST Repository

Pinedo-Gonzá lez, Paulina; West, A. Joshua; Tovar-Sá nchez, Antonio; Duarte, Carlos M.; Marañ ó n, Emilio; Cermeñ o, Pedro; Gonzá lez, Natalia; Sobrino, Cristina; Huete-Ortega, Marí a; Ferná ndez, Ana; Ló pez-Sandoval, Daffne C.; Vidal, Montserrat; Blasco, Dolors; Estrada, Marta; Sañ udo-Wilhelmy, Sergio A.

2015-01-01

The distribution of bioactive trace metals has the potential to enhance or limit primary productivity and carbon export in some regions of the world ocean. To study these connections, the concentrations of Cd, Co, Cu, Fe, Mo, Ni, and V were determined for 110 surface water samples collected during the Malaspina 2010 Circumnavigation Expedition (MCE). Total dissolved Cd, Co, Cu, Fe, Mo, Ni, and V concentrations averaged 19.0 ± 5.4 pM, 21.4 ± 12 pM, 0.91 ± 0.4 nM, 0.66 ± 0.3 nM, 88.8 ± 12 nM, 1.72 ± 0.4 nM, and 23.4 ± 4.4 nM, respectively, with the lowest values detected in the Central Pacific and increased values at the extremes of all transects near coastal zones. Trace metal concentrations measured in surface waters of the Atlantic Ocean during the MCE were compared to previously published data for the same region. The comparison revealed little temporal changes in the distribution of Cd, Co, Cu, Fe, and Ni over the last 30 years. We utilized a multivariable linear regression model to describe potential relationships between primary productivity and the hydrological, biological, trace nutrient and macronutrient data collected during the MCE. Our statistical analysis shows that primary productivity in the Indian Ocean is best described by chlorophyll a, NO3, Ni, temperature, SiO4, and Cd. In the Atlantic Ocean, primary productivity is correlated with chlorophyll a, NO3, PO4, mixed layer depth, Co, Fe, Cd, Cu, V, and Mo. The variables salinity, temperature, SiO4, NO3, PO4, Fe, Cd, and V were found to best predict primary productivity in the Pacific Ocean. These results suggest that some of the lesser studied trace elements (e.g., Ni, V, Mo, and Cd) may play a more important role in regulating oceanic primary productivity than previously thought and point to the need for future experiments to verify their potential biological functions.

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

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.

Bridging the provenance gap: opportunities and challenges tracking in and ex silico provenance in sUAS workflows

Science.gov (United States)

Thomer, A.

2017-12-01

Data provenance - the record of the varied processes that went into the creation of a dataset, as well as the relationships between resulting data objects - is necessary to support the reusability, reproducibility and reliability of earth science data. In sUAS-based research, capturing provenance can be particularly challenging because of the breadth and distributed nature of the many platforms used to collect, process and analyze data. In any given project, multiple drones, controllers, computers, software systems, sensors, cameras, imaging processing algorithms and data processing workflows are used over sometimes long periods of time. These platforms and processing result in dozens - if not hundreds - of data products in varying stages of readiness-for-analysis and sharing. Provenance tracking mechanisms are needed to make the relationships between these many data products explicit, and therefore more reusable and shareable. In this talk, I discuss opportunities and challenges in tracking provenance in sUAS-based research, and identify gaps in current workflow-capture technologies. I draw on prior work conducted as part of the IMLS-funded Site-Based Data Curation project in which we developed methods of documenting in and ex silico (that is, computational and non-computation) workflows, and demonstrate this approaches applicability to research with sUASes. I conclude with a discussion of ontologies and other semantic technologies that have potential application in sUAS research.

A Metric and Workflow for Quality Control in the Analysis of Heterogeneity in Phenotypic Profiles and Screens