Large Scale Software Building with CMake in ATLAS

CERN Document Server

Elmsheuser, Johannes; The ATLAS collaboration; Obreshkov, Emil; Undrus, Alexander

2016-01-01

The offline software of the ATLAS experiment at the LHC (Large Hadron Collider) serves as the platform for detector data reconstruction, simulation and analysis. It is also used in the detector trigger system to select LHC collision events during data taking. ATLAS offline software consists of several million lines of C++ and Python code organized in a modular design of more than 2000 specialized packages. Because of different workflows many stable numbered releases are in parallel production use. To accommodate specific workflow requests, software patches with modified libraries are distributed on top of existing software releases on a daily basis. The different ATLAS software applications require a flexible build system that strongly supports unit and integration tests. Within the last year this build system was migrated to CMake. A CMake configuration has been developed that allows one to easily set up and build the mentioned software packages. This also makes it possible to develop and test new and modifi...

Large scale software building with CMake in ATLAS

CERN Document Server

AUTHOR|(INSPIRE)INSPIRE-00218447; The ATLAS collaboration; Elmsheuser, Johannes; Obreshkov, Emil; Undrus, Alexander

2017-01-01

The offline software of the ATLAS experiment at the LHC (Large Hadron Collider) serves as the platform for detector data reconstruction, simulation and analysis. It is also used in the detector trigger system to select LHC collision events during data taking. ATLAS offline software consists of several million lines of C++ and Python code organized in a modular design of more than 2000 specialized packages. Because of different workflows many stable numbered releases are in parallel production use. To accommodate specific workflow requests, software patches with modified libraries are distributed on top of existing software releases on a daily basis. The different ATLAS software applications require a flexible build system that strongly supports unit and integration tests. Within the last year this build system was migrated to CMake. A CMake configuration has been developed that allows one to easily set up and build the mentioned software packages. This also makes it possible to develop and test new and modifi...

A software-aided workflow for precinct-scale residential redevelopment

International Nuclear Information System (INIS)

Glackin, Stephen; Trubka, Roman; Dionisio, Maria Rita

2016-01-01

Growing urban populations, combined with environmental challenges, have placed significant pressure on urban planning to supply housing while addressing policy issues such as sustainability, affordability, and liveability. The interrelated nature of these issues, combined with the requirement of evidence-based planning, has made decision-making so complex that urban planners need to combine expertise on energy, water, carbon emissions, transport and economic development along with other bodies of knowledge necessary to make well-informed decisions. This paper presents two geospatial software systems that can assist in the mediation of complexity, by allowing users to assess a variety of planning metrics without expert knowledge in those disciplines. Using Envision and Envision Scenario Planner (ESP), both products of the Greening the Greyfields research project funded by the Cooperative Research Centre for Spatial Information (CRCSI) in Australia, we demonstrate a workflow for identifying potential redevelopment precincts and designing and assessing possible redevelopment scenarios to optimise planning outcomes.

A software-aided workflow for precinct-scale residential redevelopment

Energy Technology Data Exchange (ETDEWEB)

Glackin, Stephen, E-mail: sglackin@swin.edu.au [Swinburne University of Technology, Melbourne, Victoria (Australia); Trubka, Roman, E-mail: r.trubka@gmail.com [Curtin University, Perth, Western Australia (Australia); Dionisio, Maria Rita, E-mail: rita.dionisio@canterbury.ac.nz [University of Canterbury (New Zealand)

2016-09-15

Growing urban populations, combined with environmental challenges, have placed significant pressure on urban planning to supply housing while addressing policy issues such as sustainability, affordability, and liveability. The interrelated nature of these issues, combined with the requirement of evidence-based planning, has made decision-making so complex that urban planners need to combine expertise on energy, water, carbon emissions, transport and economic development along with other bodies of knowledge necessary to make well-informed decisions. This paper presents two geospatial software systems that can assist in the mediation of complexity, by allowing users to assess a variety of planning metrics without expert knowledge in those disciplines. Using Envision and Envision Scenario Planner (ESP), both products of the Greening the Greyfields research project funded by the Cooperative Research Centre for Spatial Information (CRCSI) in Australia, we demonstrate a workflow for identifying potential redevelopment precincts and designing and assessing possible redevelopment scenarios to optimise planning outcomes.

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

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?

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)

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

Ergatis: a web interface and scalable software system for bioinformatics workflows

Science.gov (United States)

Orvis, Joshua; Crabtree, Jonathan; Galens, Kevin; Gussman, Aaron; Inman, Jason M.; Lee, Eduardo; Nampally, Sreenath; Riley, David; Sundaram, Jaideep P.; Felix, Victor; Whitty, Brett; Mahurkar, Anup; Wortman, Jennifer; White, Owen; Angiuoli, Samuel V.

2010-01-01

Motivation: The growth of sequence data has been accompanied by an increasing need to analyze data on distributed computer clusters. The use of these systems for routine analysis requires scalable and robust software for data management of large datasets. Software is also needed to simplify data management and make large-scale bioinformatics analysis accessible and reproducible to a wide class of target users. Results: We have developed a workflow management system named Ergatis that enables users to build, execute and monitor pipelines for computational analysis of genomics data. Ergatis contains preconfigured components and template pipelines for a number of common bioinformatics tasks such as prokaryotic genome annotation and genome comparisons. Outputs from many of these components can be loaded into a Chado relational database. Ergatis was designed to be accessible to a broad class of users and provides a user friendly, web-based interface. Ergatis supports high-throughput batch processing on distributed compute clusters and has been used for data management in a number of genome annotation and comparative genomics projects. Availability: Ergatis is an open-source project and is freely available at http://ergatis.sourceforge.net Contact: jorvis@users.sourceforge.net PMID:20413634

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

Science.gov (United States)

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

2017-12-01

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

Special software for computing the special functions of wave catastrophes

Directory of Open Access Journals (Sweden)

Andrey S. Kryukovsky

2015-01-01

Full Text Available The method of ordinary differential equations in the context of calculating the special functions of wave catastrophes is considered. Complementary numerical methods and algorithms are described. The paper shows approaches to accelerate such calculations using capabilities of modern computing systems. Methods for calculating the special functions of wave catastrophes are considered in the framework of parallel computing and distributed systems. The paper covers the development process of special software for calculating of special functions, questions of portability, extensibility and interoperability.

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

Science.gov (United States)

Stockwell, Simon R; Mittnacht, Sibylle

2014-12-16

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

A practical data processing workflow for multi-OMICS projects.

Science.gov (United States)

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

2014-01-01

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

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.

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 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.

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

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

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

Science.gov (United States)

Stockton, David B; Santamaria, Fidel

2017-10-01

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

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.

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.

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

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

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

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.

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.

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

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.

Large Scale Software Building with CMake in ATLAS

Science.gov (United States)

Elmsheuser, J.; Krasznahorkay, A.; Obreshkov, E.; Undrus, A.; ATLAS Collaboration

2017-10-01

The offline software of the ATLAS experiment at the Large Hadron Collider (LHC) serves as the platform for detector data reconstruction, simulation and analysis. It is also used in the detector’s trigger system to select LHC collision events during data taking. The ATLAS offline software consists of several million lines of C++ and Python code organized in a modular design of more than 2000 specialized packages. Because of different workflows, many stable numbered releases are in parallel production use. To accommodate specific workflow requests, software patches with modified libraries are distributed on top of existing software releases on a daily basis. The different ATLAS software applications also require a flexible build system that strongly supports unit and integration tests. Within the last year this build system was migrated to CMake. A CMake configuration has been developed that allows one to easily set up and build the above mentioned software packages. This also makes it possible to develop and test new and modified packages on top of existing releases. The system also allows one to detect and execute partial rebuilds of the release based on single package changes. The build system makes use of CPack for building RPM packages out of the software releases, and CTest for running unit and integration tests. We report on the migration and integration of the ATLAS software to CMake and show working examples of this large scale project in production.

Transformación de procesos de desarrollo de software tipo SPEM a procesos workflow : Una propuesta de caso de estudio: SmallRUP

OpenAIRE

Zorzán, Fabio Andrés; Riesco, Daniel Eduardo; Szasz, Nora

2009-01-01

Esta línea de investigación pretende aportar a la mejora de los procesos de desarrollo de software, en particular los especificados con el Software Process Engineering Metamodel versión 2 (SPEM). El caso de estudio propuesto consiste en transformar la especificación en SPEM de la metodología de desarrollo SmallRUP a una especificación de procesos que pueda ser utilizada como entrada de un motor workflow estándar. Para realizar esta transformación, se utilizará una transformación definida en e...

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

Distributed Workflow Service Composition Based on CTR Technology

Science.gov (United States)

Feng, Zhilin; Ye, Yanming

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

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.

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 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.

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.

Assessment of osteoporotic vertebral fractures using specialized workflow software for 6-point morphometry

International Nuclear Information System (INIS)

Guglielmi, Giuseppe; Palmieri, Francesco; Placentino, Maria Grazia; D'Errico, Francesco; Stoppino, Luca Pio

2009-01-01

Purpose: To evaluate the time required, the accuracy and the precision of a model-based image analysis software tool for the diagnosis of osteoporotic fractures using a 6-point morphometry protocol. Materials and methods: Lateral dorsal and lumbar radiographs were performed on 92 elderly women (mean age 69.2 ± 5.7 years). Institutional review board approval and patient informed consent were obtained for all subjects. The semi-automated and the manual correct annotations of 6-point placement were compared to calculate the time consumed and the accuracy of the software. Twenty test images were randomly selected and the data obtained by multiple perturbed initialisation points on the same image were compared to assess the precision of the system. Results: The time requirement data of the semi-automated system (420 ± 67 s) were statistically different (p < 0.05) from that of manual placement (900 ± 77 s). In the accuracy test, the mean reproducibility error for semi-automatic 6-point placement was 2.50 ± 0.72% [95% CI] for the anterior-posterior reference and 2.16 ± 0.5% [95% CI] for the superior-inferior reference. In the precision test the mean error resulted averaged over all vertebrae was 2.6 ± 1.3% in terms of vertebral width. Conclusions: The technique is time effective, accurate and precise and can, therefore, be recommended in large epidemiological studies and pharmaceutical trials for reporting of osteoporotic vertebral fractures.

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.)

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.

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.

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.

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

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

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.

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.

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.

Introducing W.A.T.E.R.S.: a workflow for the alignment, taxonomy, and ecology of ribosomal sequences.

Science.gov (United States)

Hartman, Amber L; Riddle, Sean; McPhillips, Timothy; Ludäscher, Bertram; Eisen, Jonathan A

2010-06-12

For more than two decades microbiologists have used a highly conserved microbial gene as a phylogenetic marker for bacteria and archaea. The small-subunit ribosomal RNA gene, also known as 16 S rRNA, is encoded by ribosomal DNA, 16 S rDNA, and has provided a powerful comparative tool to microbial ecologists. Over time, the microbial ecology field has matured from small-scale studies in a select number of environments to massive collections of sequence data that are paired with dozens of corresponding collection variables. As the complexity of data and tool sets have grown, the need for flexible automation and maintenance of the core processes of 16 S rDNA sequence analysis has increased correspondingly. We present WATERS, an integrated approach for 16 S rDNA analysis that bundles a suite of publicly available 16 S rDNA analysis software tools into a single software package. The "toolkit" includes sequence alignment, chimera removal, OTU determination, taxonomy assignment, phylogentic tree construction as well as a host of ecological analysis and visualization tools. WATERS employs a flexible, collection-oriented 'workflow' approach using the open-source Kepler system as a platform. By packaging available software tools into a single automated workflow, WATERS simplifies 16 S rDNA analyses, especially for those without specialized bioinformatics, programming expertise. In addition, WATERS, like some of the newer comprehensive rRNA analysis tools, allows researchers to minimize the time dedicated to carrying out tedious informatics steps and to focus their attention instead on the biological interpretation of the results. One advantage of WATERS over other comprehensive tools is that the use of the Kepler workflow system facilitates result interpretation and reproducibility via a data provenance sub-system. Furthermore, new "actors" can be added to the workflow as desired and we see WATERS as an initial seed for a sizeable and growing repository of interoperable

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.

Laboratory Information Management Software for genotyping workflows: applications in high throughput crop genotyping

Directory of Open Access Journals (Sweden)

Prasanth VP

2006-08-01

Full Text Available Abstract Background With the advances in DNA sequencer-based technologies, it has become possible to automate several steps of the genotyping process leading to increased throughput. To efficiently handle the large amounts of genotypic data generated and help with quality control, there is a strong need for a software system that can help with the tracking of samples and capture and management of data at different steps of the process. Such systems, while serving to manage the workflow precisely, also encourage good laboratory practice by standardizing protocols, recording and annotating data from every step of the workflow. Results A laboratory information management system (LIMS has been designed and implemented at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT that meets the requirements of a moderately high throughput molecular genotyping facility. The application is designed as modules and is simple to learn and use. The application leads the user through each step of the process from starting an experiment to the storing of output data from the genotype detection step with auto-binning of alleles; thus ensuring that every DNA sample is handled in an identical manner and all the necessary data are captured. The application keeps track of DNA samples and generated data. Data entry into the system is through the use of forms for file uploads. The LIMS provides functions to trace back to the electrophoresis gel files or sample source for any genotypic data and for repeating experiments. The LIMS is being presently used for the capture of high throughput SSR (simple-sequence repeat genotyping data from the legume (chickpea, groundnut and pigeonpea and cereal (sorghum and millets crops of importance in the semi-arid tropics. Conclusion A laboratory information management system is available that has been found useful in the management of microsatellite genotype data in a moderately high throughput genotyping

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.

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

[Guided and computer-assisted implant surgery and prosthetic: The continuous digital workflow].

Science.gov (United States)

Pascual, D; Vaysse, J

2016-02-01

New continuous digital workflow protocols of guided and computer-assisted implant surgery improve accuracy of implant positioning. The design of the future prosthesis is based on the available prosthetic space, gingival height and occlusal relationship with the opposing and adjacent teeth. The implant position and length depend on volume, density and bone quality, gingival height, tooth-implant and implant-implant distances, implant parallelism, axis and type of the future prosthesis. The crown modeled on the software will therefore serve as a guide to the future implant axis and not the reverse. The guide is made by 3D printing. The software determines surgical protocol with the drilling sequences. The unitary or plural prosthesis, modeled on the software and built before surgery, is loaded directly after implant placing, if needed. These protocols allow for a full continuity of the digital workflow. The software provides the surgeon and the dental technician a total freedom for the prosthetic-surgery guide design and the position of the implants. The prosthetic project, occlusal and aesthetic, taking the bony and surgical constraints into account, is optimized. The implant surgery is simplified and becomes less "stressful" for the patient and the surgeon. Guided and computer-assisted surgery with continuous digital workflow is becoming the technique of choice to improve the accuracy and quality of implant rehabilitation. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

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

Science.gov (United States)

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

2017-12-01

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

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.

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

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

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

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.

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

SU-E-T-419: Workflow and FMEA in a New Proton Therapy (PT) Facility

International Nuclear Information System (INIS)

Cheng, C; Wessels, B; Hamilton, H; Difranco, T; Mansur, D

2014-01-01

Purpose: Workflow is an important component in the operational planning of a new proton facility. By integrating the concept of failure mode and effect analysis (FMEA) and traditional QA requirements, a workflow for a proton therapy treatment course is set up. This workflow serves as the blue print for the planning of computer hardware/software requirements and network flow. A slight modification of the workflow generates a process map(PM) for FMEA and the planning of QA program in PT. Methods: A flowchart is first developed outlining the sequence of processes involved in a PT treatment course. Each process consists of a number of sub-processes to encompass a broad scope of treatment and QA procedures. For each subprocess, the personnel involved, the equipment needed and the computer hardware/software as well as network requirements are defined by a team of clinical staff, administrators and IT personnel. Results: Eleven intermediate processes with a total of 70 sub-processes involved in a PT treatment course are identified. The number of sub-processes varies, ranging from 2-12. The sub-processes within each process are used for the operational planning. For example, in the CT-Sim process, there are 12 sub-processes: three involve data entry/retrieval from a record-and-verify system, two controlled by the CT computer, two require department/hospital network, and the other five are setup procedures. IT then decides the number of computers needed and the software and network requirement. By removing the traditional QA procedures from the workflow, a PM is generated for FMEA analysis to design a QA program for PT. Conclusion: Significant efforts are involved in the development of the workflow in a PT treatment course. Our hybrid model of combining FMEA and traditional QA program serves a duo purpose of efficient operational planning and designing of a QA program in PT

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.

ESO Reflex: a graphical workflow engine for data reduction

Science.gov (United States)

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

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

FOSS geospatial libraries in scientific workflow environments: experiences and directions

CSIR Research Space (South Africa)

McFerren, G

2011-07-01

Full Text Available of experiments. In context of three sets of research (wildfire research, flood modelling and the linking of disease outbreaks to multi-scale environmental conditions), we describe our efforts to provide geospatial capability for scientific workflow software...

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.

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.

UN PATRÓN DE INTERACCIÓN ENTRE DIAGRAMAS DE ACTIVIDADES UML Y SISTEMAS WORKFLOW AN INTERACTION PATTERN BETWEEN UML ACTIVITY DIAGRAMS AND WORKFLOW SYSTEMS

Directory of Open Access Journals (Sweden)

Marta Silvia Tabares

2008-12-01

Full Text Available Actualmente en los ambientes de desarrollo de software hay un gran interés en buscar y desarrollar técnicas que puedan integrar los sistemas transaccionales con los flujos de trabajo que soportan los procesos del negocio de las organizaciones. Sin embargo, en la industria del software no es común encontrar técnicas o prácticas que faciliten el desarrollo de los modelos del sistema en función de los procesos del negocio. En este artículo se define un patrón de desarrollo que estandariza la interacción entre diagramas de actividades de UML 2.0, que representan las operaciones de un sistema, y procesos del negocio automatizados bajo tecnologías workflow. La trazabilidad de dicha interacción se mantiene por medio de modelos de trazabilidad que controlan la evolución de las operaciones del negocio y del sistema. Para mostrar la aplicación del patrón se desarrolla un caso de estudioIn software development environments there is a big interest to look and develop techniques that could integrate transactional systems with Workflow systems in order to support the business processes in organizations Nevertheless, in the software industry it is not common to find techniques or practices that facilitate the development of system models according to the business processes. In this article we define a development pattern to standardize the interaction between UML 2.0 activity diagrams, which represent the operations of a system, and the business processes automated by means of Workflow technologies. The traceability of the above mentioned interaction is supported by means of traceability models that control the evolution of both operations of the business and of the system. To show the application of the pattern a case study is developed.

SYRMEP Tomo Project: a graphical user interface for customizing CT reconstruction workflows.

Science.gov (United States)

Brun, Francesco; Massimi, Lorenzo; Fratini, Michela; Dreossi, Diego; Billé, Fulvio; Accardo, Agostino; Pugliese, Roberto; Cedola, Alessia

2017-01-01

When considering the acquisition of experimental synchrotron radiation (SR) X-ray CT data, the reconstruction workflow cannot be limited to the essential computational steps of flat fielding and filtered back projection (FBP). More refined image processing is often required, usually to compensate artifacts and enhance the quality of the reconstructed images. In principle, it would be desirable to optimize the reconstruction workflow at the facility during the experiment (beamtime). However, several practical factors affect the image reconstruction part of the experiment and users are likely to conclude the beamtime with sub-optimal reconstructed images. Through an example of application, this article presents SYRMEP Tomo Project (STP), an open-source software tool conceived to let users design custom CT reconstruction workflows. STP has been designed for post-beamtime (off-line use) and for a new reconstruction of past archived data at user's home institution where simple computing resources are available. Releases of the software can be downloaded at the Elettra Scientific Computing group GitHub repository https://github.com/ElettraSciComp/STP-Gui.

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

Directory of Open Access Journals (Sweden)

David Bruce Stockton

2015-10-01

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

Competence Centered Specialization in Web Engineering Topics in a Software Engineering Masters Degree Programme

DEFF Research Database (Denmark)

Dolog, Peter; Thomsen, Lone Leth; Thomsen, Bent

2010-01-01

Web applications and Web-based systems are becoming increasingly complex as a result of either customer requests or technology evolution which has eased other aspects of software engineering. Therefore, there is an increasing demand for highly skilled software engineers able to build and also...... advance the systems on the one hand as well as professionals who are able to evaluate their eectiveness on the other hand. With this idea in mind, the computer science department at Aalborg University is continuously working on improvements in its specialization in web engineering topics as well...... as on general competence based web engineering proles oered also for those who specialize in other areas of software engineering. We describe the current state of the art and our experience with a web engineering curriculum within the software engineering masters degree programme. We also discuss an evolution...

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.

Reproducibility and Practical Adoption of GEOBIA with Open-Source Software in Docker Containers

Directory of Open Access Journals (Sweden)

Christian Knoth

2017-03-01

Full Text Available Geographic Object-Based Image Analysis (GEOBIA mostly uses proprietary software,but the interest in Free and Open-Source Software (FOSS for GEOBIA is growing. This interest stems not only from cost savings, but also from benefits concerning reproducibility and collaboration. Technical challenges hamper practical reproducibility, especially when multiple software packages are required to conduct an analysis. In this study, we use containerization to package a GEOBIA workflow in a well-defined FOSS environment. We explore the approach using two software stacks to perform an exemplary analysis detecting destruction of buildings in bi-temporal images of a conflict area. The analysis combines feature extraction techniques with segmentation and object-based analysis to detect changes using automatically-defined local reference values and to distinguish disappeared buildings from non-target structures. The resulting workflow is published as FOSS comprising both the model and data in a ready to use Docker image and a user interface for interaction with the containerized workflow. The presented solution advances GEOBIA in the following aspects: higher transparency of methodology; easier reuse and adaption of workflows; better transferability between operating systems; complete description of the software environment; and easy application of workflows by image analysis experts and non-experts. As a result, it promotes not only the reproducibility of GEOBIA, but also its practical adoption.

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.

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

a Standardized Approach to Topographic Data Processing and Workflow Management

Science.gov (United States)

Wheaton, J. M.; Bailey, P.; Glenn, N. F.; Hensleigh, J.; Hudak, A. T.; Shrestha, R.; Spaete, L.

2013-12-01

An ever-increasing list of options exist for collecting high resolution topographic data, including airborne LIDAR, terrestrial laser scanners, bathymetric SONAR and structure-from-motion. An equally rich, arguably overwhelming, variety of tools exists with which to organize, quality control, filter, analyze and summarize these data. However, scientists are often left to cobble together their analysis as a series of ad hoc steps, often using custom scripts and one-time processes that are poorly documented and rarely shared with the community. Even when literature-cited software tools are used, the input and output parameters differ from tool to tool. These parameters are rarely archived and the steps performed lost, making the analysis virtually impossible to replicate precisely. What is missing is a coherent, robust, framework for combining reliable, well-documented topographic data-processing steps into a workflow that can be repeated and even shared with others. We have taken several popular topographic data processing tools - including point cloud filtering and decimation as well as DEM differencing - and defined a common protocol for passing inputs and outputs between them. This presentation describes a free, public online portal that enables scientists to create custom workflows for processing topographic data using a number of popular topographic processing tools. Users provide the inputs required for each tool and in what sequence they want to combine them. This information is then stored for future reuse (and optionally sharing with others) before the user then downloads a single package that contains all the input and output specifications together with the software tools themselves. The user then launches the included batch file that executes the workflow on their local computer against their topographic data. This ZCloudTools architecture helps standardize, automate and archive topographic data processing. It also represents a forum for discovering and

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.

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.

iLAP: a workflow-driven software for experimental protocol development, data acquisition and analysis

Directory of Open Access Journals (Sweden)

McNally James

2009-01-01

Full Text Available Abstract Background In recent years, the genome biology community has expended considerable effort to confront the challenges of managing heterogeneous data in a structured and organized way and developed laboratory information management systems (LIMS for both raw and processed data. On the other hand, electronic notebooks were developed to record and manage scientific data, and facilitate data-sharing. Software which enables both, management of large datasets and digital recording of laboratory procedures would serve a real need in laboratories using medium and high-throughput techniques. Results We have developed iLAP (Laboratory data management, Analysis, and Protocol development, a workflow-driven information management system specifically designed to create and manage experimental protocols, and to analyze and share laboratory data. The system combines experimental protocol development, wizard-based data acquisition, and high-throughput data analysis into a single, integrated system. We demonstrate the power and the flexibility of the platform using a microscopy case study based on a combinatorial multiple fluorescence in situ hybridization (m-FISH protocol and 3D-image reconstruction. iLAP is freely available under the open source license AGPL from http://genome.tugraz.at/iLAP/. Conclusion iLAP is a flexible and versatile information management system, which has the potential to close the gap between electronic notebooks and LIMS and can therefore be of great value for a broad scientific community.

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

Towards a New Paradigm of Software Development: an Ambassador Driven Process in Distributed Software Companies

Science.gov (United States)

Kumlander, Deniss

The globalization of companies operations and competitor between software vendors demand improving quality of delivered software and decreasing the overall cost. The same in fact introduce a lot of problem into software development process as produce distributed organization breaking the co-location rule of modern software development methodologies. Here we propose a reformulation of the ambassador position increasing its productivity in order to bridge communication and workflow gap by managing the entire communication process rather than concentrating purely on the communication result.

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

Translating Colored Control Flow Nets into Readable Java via Annotated Java Workflow Nets

DEFF Research Database (Denmark)

Lassen, Kristian Bisgaard; Tjell, Simon

2007-01-01

In this paper, we present a method for developing Java applications from Colored Control Flow Nets (CCFNs), which is a special kind of Colored Petri Nets (CPNs) that we introduce. CCFN makes an explicit distinction between the representation of: The system, the environment of the system, and the ......In this paper, we present a method for developing Java applications from Colored Control Flow Nets (CCFNs), which is a special kind of Colored Petri Nets (CPNs) that we introduce. CCFN makes an explicit distinction between the representation of: The system, the environment of the system......, and the interface between the system and the environment. Our translation maps CCFNs into Anno- tated Java Workflow Nets (AJWNs) as an intermediate step, and these AJWNs are finally mapped to Java. CCFN is intended to enforce the modeler to describe the system in an imperative manner which makes the subsequent...... translation to Java easier to define. The translation to Java preserves data dependencies and control-flow aspects of the source CCFN. This paper contributes to the model-driven software development paradigm, by showing how to model a system, environment, and their interface, as a CCFN and presenting a fully...

The development and implementation of MOSAIQ Integration Platform (MIP) based on the radiotherapy workflow

Science.gov (United States)

Yang, Xin; He, Zhen-yu; Jiang, Xiao-bo; Lin, Mao-sheng; Zhong, Ning-shan; Hu, Jiang; Qi, Zhen-yu; Bao, Yong; Li, Qiao-qiao; Li, Bao-yue; Hu, Lian-ying; Lin, Cheng-guang; Gao, Yuan-hong; Liu, Hui; Huang, Xiao-yan; Deng, Xiao-wu; Xia, Yun-fei; Liu, Meng-zhong; Sun, Ying

2017-03-01

To meet the special demands in China and the particular needs for the radiotherapy department, a MOSAIQ Integration Platform CHN (MIP) based on the workflow of radiation therapy (RT) has been developed, as a supplement system to the Elekta MOSAIQ. The MIP adopts C/S (client-server) structure mode, and its database is based on the Treatment Planning System (TPS) and MOSAIQ SQL Server 2008, running on the hospital local network. Five network servers, as a core hardware, supply data storage and network service based on the cloud services. The core software, using C# programming language, is developed based on Microsoft Visual Studio Platform. The MIP server could offer network service, including entry, query, statistics and print information for about 200 workstations at the same time. The MIP was implemented in the past one and a half years, and some practical patient-oriented functions were developed. And now the MIP is almost covering the whole workflow of radiation therapy. There are 15 function modules, such as: Notice, Appointment, Billing, Document Management (application/execution), System Management, and so on. By June of 2016, recorded data in the MIP are as following: 13546 patients, 13533 plan application, 15475 RT records, 14656 RT summaries, 567048 billing records and 506612 workload records, etc. The MIP based on the RT workflow has been successfully developed and clinically implemented with real-time performance, data security, stable operation. And it is demonstrated to be user-friendly and is proven to significantly improve the efficiency of the department. It is a key to facilitate the information sharing and department management. More functions can be added or modified for further enhancement its potentials in research and clinical practice.

ESO Reflex: A Graphical Workflow Engine for Data Reduction

Science.gov (United States)

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

2008-08-01

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

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

Special issue on new ideas and emerging results in understanding software

NARCIS (Netherlands)

Vinju, J.J.

2015-01-01

Welcome to the special issue on new ideas and emerging results in understanding software. It is a present to Prof. Dr. Paul Klint on the occasion of his 65th birthday. His colleagues and friends who share similar research interests have written the papers, wanting to present Paul with a worthy gift.

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.

Specialized software for optimization of the quality control of the mammography units

International Nuclear Information System (INIS)

Stoeva, M.; Vassileva, J.

2004-01-01

Quality control is essential to ensure the equipment used is reliable and consistent in order to maintain radiation does as low as reasonably achievable whilst optimizing image quality and performance in mammography. The effectiveness of mammographic screening is highly dependent on the consistent production of high quality diagnostic images. Mammography is highly dependent on the equipment status, which requires an effective Quality Control (QC) program to provide tools for continuous assessment of the equipment performance and also data storage and analysis of the protocols' data. The objective of this paper is to present the specialized software for Quality Control of the Mammography Units, as tool providing additional functionality for optimizations of the Mammography QC data storage and management. The PC program was developed according to the requirements stated in the European protocol for Quality Control of the Mammography Screening and the data collected as a result of its application in several Bulgarian hospitals. The Structured Analysis method was used in order to perform a case, which resulted in the development of the specialized software with a database module, providing the following functionality: Data Storage, Preliminary Data Processing and Post-Processing, Manual Data Entry, Data Import from XLS format, Data Export to XLS format, Printing, Data Filters, Automated Calculation, Automated Graphical Representation, Archiving The development of specialized QC software with a database for mammography units facilitates the process of QC data storage and handling and minimizes the errors. The electronic format for data storage is especially useful in case of long-term storage and periodical data analysis/access. The integrated data processing functionality and the automated import/export features based on standard platform increase the compatibility of the data. (authors)

Software Prototyping

Science.gov (United States)

Del Fiol, Guilherme; Hanseler, Haley; Crouch, Barbara Insley; Cummins, Mollie R.

2016-01-01

Summary Background Health information exchange (HIE) between Poison Control Centers (PCCs) and Emergency Departments (EDs) could improve care of poisoned patients. However, PCC information systems are not designed to facilitate HIE with EDs; therefore, we are developing specialized software to support HIE within the normal workflow of the PCC using user-centered design and rapid prototyping. Objective To describe the design of an HIE dashboard and the refinement of user requirements through rapid prototyping. Methods Using previously elicited user requirements, we designed low-fidelity sketches of designs on paper with iterative refinement. Next, we designed an interactive high-fidelity prototype and conducted scenario-based usability tests with end users. Users were asked to think aloud while accomplishing tasks related to a case vignette. After testing, the users provided feedback and evaluated the prototype using the System Usability Scale (SUS). Results Survey results from three users provided useful feedback that was then incorporated into the design. After achieving a stable design, we used the prototype itself as the specification for development of the actual software. Benefits of prototyping included having 1) subject-matter experts heavily involved with the design; 2) flexibility to make rapid changes, 3) the ability to minimize software development efforts early in the design stage; 4) rapid finalization of requirements; 5) early visualization of designs; 6) and a powerful vehicle for communication of the design to the programmers. Challenges included 1) time and effort to develop the prototypes and case scenarios; 2) no simulation of system performance; 3) not having all proposed functionality available in the final product; and 4) missing needed data elements in the PCC information system. PMID:27081404

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.

3D Printing of CT Dataset: Validation of an Open Source and Consumer-Available Workflow.

Science.gov (United States)

Bortolotto, Chandra; Eshja, Esmeralda; Peroni, Caterina; Orlandi, Matteo A; Bizzotto, Nicola; Poggi, Paolo

2016-02-01

The broad availability of cheap three-dimensional (3D) printing equipment has raised the need for a thorough analysis on its effects on clinical accuracy. Our aim is to determine whether the accuracy of 3D printing process is affected by the use of a low-budget workflow based on open source software and consumer's commercially available 3D printers. A group of test objects was scanned with a 64-slice computed tomography (CT) in order to build their 3D copies. CT datasets were elaborated using a software chain based on three free and open source software. Objects were printed out with a commercially available 3D printer. Both the 3D copies and the test objects were measured using a digital professional caliper. Overall, the objects' mean absolute difference between test objects and 3D copies is 0.23 mm and the mean relative difference amounts to 0.55 %. Our results demonstrate that the accuracy of 3D printing process remains high despite the use of a low-budget workflow.

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.

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.

Development of 'Enhance reconstruction package' software for whole-body PET

International Nuclear Information System (INIS)

Mizuta, Tetsuro; Imanishi, Tatsuru; Ishikawa, Akihiro

2011-01-01

We have developed 'Enhance Reconstruction Package' Software for our whole-body positron emission tomography (PET) Eminence series. This package improves image quality and streamlines the workflow in clinical PET and PET/CT studies. The present paper describes an outline of the applications for data collection, normalization, etc. and also reports some PET images obtained by the software. The signal to noise ratio was optimized in the phantom study, leading to the improvement in image quality. The real time display tool and the remote control tool would make a contribution to enhancement in operability in the routine workflow. (author)

Software Project Management and Measurement on the World-Wide-Web (WWW)

Science.gov (United States)

Callahan, John; Ramakrishnan, Sudhaka

1996-01-01

We briefly describe a system for forms-based, work-flow management that helps members of a software development team overcome geographical barriers to collaboration. Our system, called the Web Integrated Software Environment (WISE), is implemented as a World-Wide-Web service that allows for management and measurement of software development projects based on dynamic analysis of change activity in the workflow. WISE tracks issues in a software development process, provides informal communication between the users with different roles, supports to-do lists, and helps in software process improvement. WISE minimizes the time devoted to metrics collection and analysis by providing implicit delivery of messages between users based on the content of project documents. The use of a database in WISE is hidden from the users who view WISE as maintaining a personal 'to-do list' of tasks related to the many projects on which they may play different roles.

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

Parametric Room Acoustic Workflows

DEFF Research Database (Denmark)

Parigi, Dario; Svidt, Kjeld; Molin, Erik

2017-01-01

The paper investigates and assesses different room acoustics software and the opportunities they offer to engage in parametric acoustics workflow and to influence architectural designs. The first step consists in the testing and benchmarking of different tools on the basis of accuracy, speed...... and interoperability with Grasshopper 3d. The focus will be placed to the benchmarking of three different acoustic analysis tools based on raytracing. To compare the accuracy and speed of the acoustic evaluation across different tools, a homogeneous set of acoustic parameters is chosen. The room acoustics parameters...... included in the set are reverberation time (EDT, RT30), clarity (C50), loudness (G), and definition (D50). Scenarios are discussed for determining at different design stages the most suitable acoustic tool. Those scenarios are characterized, by the use of less accurate but fast evaluation tools to be used...

Soarian--workflow management applied for health care.

Science.gov (United States)

Haux, R; Seggewies, C; Baldauf-Sobez, W; Kullmann, P; Reichert, H; Luedecke, L; Seibold, H

2003-01-01

To describe and comment on functionality and architecture of the software product Soarian developed by Siemens, to identify key differentiators to related products, and to comment on predecessor systems and beta versions. This has been done in the framework of a conference on health information systems of the IMIA. Analyzing existing literature. Site visit of a predecessor system at Haukeland Sykehus, Bergen. Pilot of a beta version at the Erlangen University Medical Center, elaborating on major characteristics in discussion rounds. Soarian is a functional comprehensive, clinically oriented software product to support health care processes and to be used for health care professional workstations. It is a software product, designed and written completely new. Three major key differentiators were identified in comparison to related software products: Soarian's workflow engine, its embedded analytics, and its 'smart' user interface. The targeted reduced installation time is stated to be 12 months or less. Soarian has good chances to become one of the major software products for health care professional workstations in the international market to support patient-centered, shared care. Its global design may help to better support and maintain national or language specific versions. The first installations of Soarian will be critical, as they will show how the system will be accepted. To use such software products efficiently, organizational aspects within hospitals as well as between health care institutions have to be considered, e.g. strategic IT planning.

APPLICATION OF THE SPECTRUM ANALYSIS WITH USING BERG METHOD TO DEVELOPED SPECIAL SOFTWARE TOOLS FOR OPTICAL VIBRATION DIAGNOSTICS SYSTEM

Directory of Open Access Journals (Sweden)

E. O. Zaitsev

2016-01-01

Full Text Available The objective of this paper is development and experimental verification special software of spectral analysis. Spectral analysis use of controlled vibrations objects. Spectral analysis of vibration based on use maximum-entropy autoregressive method of spectral analysis by the Berg algorithm. For measured signals use preliminary analysis based on regression analysis. This analysis of the signal enables to eliminate uninformative parameters such as – the noise and the trend. For preliminary analysis developed special software tools. Non-contact measurement of mechanical vibrations parameters rotating diffusely-reflecting surfaces used in circumstances where the use of contact sensors difficult or impossible for a number of reasons, including lack of access to the object, the small size of the controlled area controlled portion has a high temperature or is affected by strong electromagnetic fields. For control use offered laser measuring system. This measuring system overcomes the shortcomings interference or Doppler optical measuring systems. Such as measure the large amplitude and inharmonious vibration. On the basis of the proposed methods developed special software tools for use measuring laser system. LabVIEW using for developed special software. Experimental research of the proposed method of vibration signals processing is checked in the analysis of the diagnostic information obtained by measuring the vibration system grinding diamond wheel cold solid tungsten-containing alloy TK8. A result of work special software tools was complex spectrum obtained «purified» from non-informative parameters. Spectrum of the signal corresponding to the vibration process observed object. 

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

International Nuclear Information System (INIS)

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

2009-01-01

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

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

Energy Technology Data Exchange (ETDEWEB)

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

2009-07-15

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

Challenges and benefits of digital workflow implementation in aerospace manufacturing engineering

OpenAIRE

Rojo Abollado, Jaime; Shehab, Essam; Bamforth, P.

2017-01-01

Companies who operate in highly regulated industries have further challenges to the usual competition, continuous cost reduction and product development challenges. To address these requirements companies optimise their business processes and change their applications and information systems to support their evolving way of doing business. Workflow management technology eases the achievement of these necessities by providing methodologies, software and tools to support business process mo...

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

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.

SOFTWARE SUPPORT FOR RICH PICTURES

DEFF Research Database (Denmark)

Valente, Andrea; Marchetti, Emanuela

2010-01-01

Rich pictures (RP) are common in object-oriented analysis and design courses, but students seem to have problems in integrating them in their projects' workflow. A new software tool is being developed, specific for RP authoring. To better understand students' issues and working practice with RP...

Software and the Scientist: Coding and Citation Practices in Geodynamics

Science.gov (United States)

Hwang, Lorraine; Fish, Allison; Soito, Laura; Smith, MacKenzie; Kellogg, Louise H.

2017-11-01

In geodynamics as in other scientific areas, computation has become a core component of research, complementing field observation, laboratory analysis, experiment, and theory. Computational tools for data analysis, mapping, visualization, modeling, and simulation are essential for all aspects of the scientific workflow. Specialized scientific software is often developed by geodynamicists for their own use, and this effort represents a distinctive intellectual contribution. Drawing on a geodynamics community that focuses on developing and disseminating scientific software, we assess the current practices of software development and attribution, as well as attitudes about the need and best practices for software citation. We analyzed publications by participants in the Computational Infrastructure for Geodynamics and conducted mixed method surveys of the solid earth geophysics community. From this we learned that coding skills are typically learned informally. Participants considered good code as trusted, reusable, readable, and not overly complex and considered a good coder as one that participates in the community in an open and reasonable manor contributing to both long- and short-term community projects. Participants strongly supported citing software reflected by the high rate a software package was named in the literature and the high rate of citations in the references. However, lacking are clear instructions from developers on how to cite and education of users on what to cite. In addition, citations did not always lead to discoverability of the resource. A unique identifier to the software package itself, community education, and citation tools would contribute to better attribution practices.

Randomized controlled within-subject evaluation of digital and conventional workflows for the fabrication of lithium disilicate single crowns. Part II: CAD-CAM versus conventional laboratory procedures.

Science.gov (United States)

Sailer, Irena; Benic, Goran I; Fehmer, Vincent; Hämmerle, Christoph H F; Mühlemann, Sven

2017-07-01

Clinical studies are needed to evaluate the entire digital and conventional workflows in prosthetic dentistry. The purpose of the second part of this clinical study was to compare the laboratory production time for tooth-supported single crowns made with 4 different digital workflows and 1 conventional workflow and to compare these crowns clinically. For each of 10 participants, a monolithic crown was fabricated in lithium disilicate-reinforced glass ceramic (IPS e.max CAD). The computer-aided design and computer-aided manufacturing (CAD-CAM) systems were Lava C.O.S. CAD software and centralized CAM (group L), Cares CAD software and centralized CAM (group iT), Cerec Connect CAD software and lab side CAM (group CiL), and Cerec Connect CAD software with centralized CAM (group CiD). The conventional fabrication (group K) included a wax pattern of the crown and heat pressing according to the lost-wax technique (IPS e.max Press). The time for the fabrication of the casts and the crowns was recorded. Subsequently, the crowns were clinically evaluated and the corresponding treatment times were recorded. The Paired Wilcoxon test with the Bonferroni correction was applied to detect differences among treatment groups (α=.05). The total mean (±standard deviation) active working time for the dental technician was 88 ±6 minutes in group L, 74 ±12 minutes in group iT, 74 ±5 minutes in group CiL, 92 ±8 minutes in group CiD, and 148 ±11 minutes in group K. The dental technician spent significantly more working time for the conventional workflow than for the digital workflows (P.05). Irrespective of the CAD-CAM system, the overall laboratory working time for a digital workflow was significantly shorter than for the conventional workflow, since the dental technician needed less active working time. Copyright © 2016 Editorial Council for the Journal of Prosthetic Dentistry. Published by Elsevier Inc. All rights reserved.

Separating Business Logic from Medical Knowledge in Digital Clinical Workflows Using Business Process Model and Notation and Arden Syntax.

Science.gov (United States)

de Bruin, Jeroen S; Adlassnig, Klaus-Peter; Leitich, Harald; Rappelsberger, Andrea

2018-01-01

Evidence-based clinical guidelines have a major positive effect on the physician's decision-making process. Computer-executable clinical guidelines allow for automated guideline marshalling during a clinical diagnostic process, thus improving the decision-making process. Implementation of a digital clinical guideline for the prevention of mother-to-child transmission of hepatitis B as a computerized workflow, thereby separating business logic from medical knowledge and decision-making. We used the Business Process Model and Notation language system Activiti for business logic and workflow modeling. Medical decision-making was performed by an Arden-Syntax-based medical rule engine, which is part of the ARDENSUITE software. We succeeded in creating an electronic clinical workflow for the prevention of mother-to-child transmission of hepatitis B, where institution-specific medical decision-making processes could be adapted without modifying the workflow business logic. Separation of business logic and medical decision-making results in more easily reusable electronic clinical workflows.

Software development minimum guidance system. Algorithm and specifications of realizing special hardware processor data prefilter program

International Nuclear Information System (INIS)

Baginyan, S.A.; Govorun, N.N.; Tkhang, T.L.; Shigaev, V.N.

1982-01-01

Software development minimum guidance system for measuring pictures of bubble chamber on the base of a scanner (HPD) and special hardware processor (SHP) is described. The algorithm of selective filter is proposed. The local software structure and functional specifications of its major parts are described. Some examples of processing picture from HBC-1 (JINR) are also presented

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

Temporary Shell Proof-of-Concept Technique: Digital-Assisted Workflow to Enable Customized Immediate Function in Two Visits in Partially Edentulous Patients

Science.gov (United States)

Pozzi, Alessandro; Arcuri, Lorenzo; Moy, Peter K

2018-03-01

The growing interest in minimally invasive implant placement and delivery of a prefabricated provisional prosthesis immediately, thus minimizing "time to teeth," has led to the development of numerous 3-dimensional (3D) planning software programs. Given the enhancements associated with fully digital workflows, such as better 3D soft-tissue visualization and virtual tooth rendering, computer-guided implant surgery and immediate function has become an effective and reliable procedure. This article describes how modern implant planning software programs provide a comprehensive digital platform that enables efficient interplay between the surgical and restorative aspects of implant treatment. These new technologies that streamline the overall digital workflow allow transformation of the digital wax-up into a personalized, CAD/CAM-milled provisional restoration. Thus, collaborative digital workflows provide a novel approach for time-efficient delivery of a customized, screw-retained provisional restoration on the day of implant surgery, resulting in improved predictability for immediate function in the partially edentate patient.

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

Science.gov (United States)

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

2016-10-25

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

Computational workflow for the fine-grained analysis of metagenomic samples

Directory of Open Access Journals (Sweden)

Esteban Pérez-Wohlfeil

2016-10-01

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

A specialized plug-in software module for computer-aided quantitative measurement of medical images.

Science.gov (United States)

Wang, Q; Zeng, Y J; Huo, P; Hu, J L; Zhang, J H

2003-12-01

This paper presents a specialized system for quantitative measurement of medical images. Using Visual C++, we developed a computer-aided software based on Image-Pro Plus (IPP), a software development platform. When transferred to the hard disk of a computer by an MVPCI-V3A frame grabber, medical images can be automatically processed by our own IPP plug-in for immunohistochemical analysis, cytomorphological measurement and blood vessel segmentation. In 34 clinical studies, the system has shown its high stability, reliability and ease of utility.

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.

A workflow for peptide-based proteomics in a poorly sequenced plant: A case study on the plasma membrane proteome of banana

DEFF Research Database (Denmark)

Vertommen, A.; Laurell Blom Møller, Anders; Cordewener, J. H. G.

2011-01-01

for membrane proteomics. However, their application in non-model plants demands special precautions to prevent false positive identification of proteins.In the current paper, a workflow for membrane proteomics in banana, a poorly sequenced plant, is proposed. The main steps of this workflow are (i......) optimization of the peptide separation, (ii) performing de novo sequencing to allow a sequence homology search and (iii) visualization of identified peptide–protein associations using Cytoscape to remove redundancy and wrongly assigned peptides, based on species-specific information. By applying this workflow...

TU-E-BRB-01: Overview of DIR Advantages/Challenges and Workflow

International Nuclear Information System (INIS)

Geneser, S.

2015-01-01

Deformable image registration (DIR) is developing rapidly and is poised to substantially improve dose fusion accuracy for adaptive and retreatment planning and motion management and PET fusion to enhance contour delineation for treatment planning. However, DIR dose warping accuracy is difficult to quantify, in general, and particularly difficult to do so on a patient-specific basis. As clinical DIR options become more widely available, there is an increased need to understand the implications of incorporating DIR into clinical workflow. Several groups have assessed DIR accuracy in clinically relevant scenarios, but no comprehensive review material is yet available. This session will also discuss aspects of the AAPM Task Group 132 on the Use of Image Registration and Data Fusion Algorithms and Techniques in Radiotherapy Treatment Planning official report, which provides recommendations for DIR clinical use. We will summarize and compare various commercial DIR software options, outline successful clinical techniques, show specific examples with discussion of appropriate and inappropriate applications of DIR, discuss the clinical implications of DIR, provide an overview of current DIR error analysis research, review QA options and research phantom development and present TG-132 recommendations. Learning Objectives: Compare/contrast commercial DIR software and QA options Overview clinical DIR workflow for retreatment To understand uncertainties introduced by DIR Review TG-132 proposed recommendations

TU-E-BRB-01: Overview of DIR Advantages/Challenges and Workflow

Energy Technology Data Exchange (ETDEWEB)

Geneser, S. [University of California San Francisco (United States)

2015-06-15

Deformable image registration (DIR) is developing rapidly and is poised to substantially improve dose fusion accuracy for adaptive and retreatment planning and motion management and PET fusion to enhance contour delineation for treatment planning. However, DIR dose warping accuracy is difficult to quantify, in general, and particularly difficult to do so on a patient-specific basis. As clinical DIR options become more widely available, there is an increased need to understand the implications of incorporating DIR into clinical workflow. Several groups have assessed DIR accuracy in clinically relevant scenarios, but no comprehensive review material is yet available. This session will also discuss aspects of the AAPM Task Group 132 on the Use of Image Registration and Data Fusion Algorithms and Techniques in Radiotherapy Treatment Planning official report, which provides recommendations for DIR clinical use. We will summarize and compare various commercial DIR software options, outline successful clinical techniques, show specific examples with discussion of appropriate and inappropriate applications of DIR, discuss the clinical implications of DIR, provide an overview of current DIR error analysis research, review QA options and research phantom development and present TG-132 recommendations. Learning Objectives: Compare/contrast commercial DIR software and QA options Overview clinical DIR workflow for retreatment To understand uncertainties introduced by DIR Review TG-132 proposed recommendations.

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...

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

Science.gov (United States)

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

2014-01-01

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

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

Software bots -The next frontier for shared services and functional excellence

NARCIS (Netherlands)

Suri, Vipin K.; Elia, Marianne; van Hillegersberg, Jos

2017-01-01

A Software Bot is a fundamental element of Robotics Process Automation (RPA). RPA can be deployed to automate repeatable, mundane, rules-based work-flowed process tasks across multiple functions in an organization, including Shared Services. While RPA holds high promise, using Software Bots for

Recommendation systems in software engineering

CERN Document Server

Robillard, Martin P; Walker, Robert J; Zimmermann, Thomas

2014-01-01

With the growth of public and private data stores and the emergence of off-the-shelf data-mining technology, recommendation systems have emerged that specifically address the unique challenges of navigating and interpreting software engineering data.This book collects, structures and formalizes knowledge on recommendation systems in software engineering. It adopts a pragmatic approach with an explicit focus on system design, implementation, and evaluation. The book is divided into three parts: "Part I - Techniques" introduces basics for building recommenders in software engineering, including techniques for collecting and processing software engineering data, but also for presenting recommendations to users as part of their workflow.?"Part II - Evaluation" summarizes methods and experimental designs for evaluating recommendations in software engineering.?"Part III - Applications" describes needs, issues and solution concepts involved in entire recommendation systems for specific software engineering tasks, fo...

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.

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.

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

display massive datasets. As large parts of the workflow are embarrassingly parallel, we also investigate the possibility of automating the imaging process with the integration of scientific workflow management software, such as Pegasus, Kepler, or Swift.

Pegasys: software for executing and integrating analyses of biological sequences

Directory of Open Access Journals (Sweden)

Lett Drew

2004-04-01

Full Text Available Abstract Background We present Pegasys – a flexible, modular and customizable software system that facilitates the execution and data integration from heterogeneous biological sequence analysis tools. Results The Pegasys system includes numerous tools for pair-wise and multiple sequence alignment, ab initio gene prediction, RNA gene detection, masking repetitive sequences in genomic DNA as well as filters for database formatting and processing raw output from various analysis tools. We introduce a novel data structure for creating workflows of sequence analyses and a unified data model to store its results. The software allows users to dynamically create analysis workflows at run-time by manipulating a graphical user interface. All non-serial dependent analyses are executed in parallel on a compute cluster for efficiency of data generation. The uniform data model and backend relational database management system of Pegasys allow for results of heterogeneous programs included in the workflow to be integrated and exported into General Feature Format for further analyses in GFF-dependent tools, or GAME XML for import into the Apollo genome editor. The modularity of the design allows for new tools to be added to the system with little programmer overhead. The database application programming interface allows programmatic access to the data stored in the backend through SQL queries. Conclusions The Pegasys system enables biologists and bioinformaticians to create and manage sequence analysis workflows. The software is released under the Open Source GNU General Public License. All source code and documentation is available for download at http://bioinformatics.ubc.ca/pegasys/.

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.)

PyDBS: an automated image processing workflow for deep brain stimulation surgery.

Science.gov (United States)

D'Albis, Tiziano; Haegelen, Claire; Essert, Caroline; Fernández-Vidal, Sara; Lalys, Florent; Jannin, Pierre

2015-02-01

Deep brain stimulation (DBS) is a surgical procedure for treating motor-related neurological disorders. DBS clinical efficacy hinges on precise surgical planning and accurate electrode placement, which in turn call upon several image processing and visualization tasks, such as image registration, image segmentation, image fusion, and 3D visualization. These tasks are often performed by a heterogeneous set of software tools, which adopt differing formats and geometrical conventions and require patient-specific parameterization or interactive tuning. To overcome these issues, we introduce in this article PyDBS, a fully integrated and automated image processing workflow for DBS surgery. PyDBS consists of three image processing pipelines and three visualization modules assisting clinicians through the entire DBS surgical workflow, from the preoperative planning of electrode trajectories to the postoperative assessment of electrode placement. The system's robustness, speed, and accuracy were assessed by means of a retrospective validation, based on 92 clinical cases. The complete PyDBS workflow achieved satisfactory results in 92 % of tested cases, with a median processing time of 28 min per patient. The results obtained are compatible with the adoption of PyDBS in clinical practice.

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...

DERIVING 3D POINT CLOUDS FROM TERRESTRIAL PHOTOGRAPHS - COMPARISON OF DIFFERENT SENSORS AND SOFTWARE

Directory of Open Access Journals (Sweden)

R. Niederheiser

2016-06-01

Full Text Available Terrestrial photogrammetry nowadays offers a reasonably cheap, intuitive and effective approach to 3D-modelling. However, the important choice, which sensor and which software to use is not straight forward and needs consideration as the choice will have effects on the resulting 3D point cloud and its derivatives. We compare five different sensors as well as four different state-of-the-art software packages for a single application, the modelling of a vegetated rock face. The five sensors represent different resolutions, sensor sizes and price segments of the cameras. The software packages used are: (1 Agisoft PhotoScan Pro (1.16, (2 Pix4D (2.0.89, (3 a combination of Visual SFM (V0.5.22 and SURE (1.2.0.286, and (4 MicMac (1.0. We took photos of a vegetated rock face from identical positions with all sensors. Then we compared the results of the different software packages regarding the ease of the workflow, visual appeal, similarity and quality of the point cloud. While PhotoScan and Pix4D offer the user-friendliest workflows, they are also “black-box” programmes giving only little insight into their processing. Unsatisfying results may only be changed by modifying settings within a module. The combined workflow of Visual SFM, SURE and CloudCompare is just as simple but requires more user interaction. MicMac turned out to be the most challenging software as it is less user-friendly. However, MicMac offers the most possibilities to influence the processing workflow. The resulting point-clouds of PhotoScan and MicMac are the most appealing.

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).

Pathology economic model tool: a novel approach to workflow and budget cost analysis in an anatomic pathology laboratory.

Science.gov (United States)

Muirhead, David; Aoun, Patricia; Powell, Michael; Juncker, Flemming; Mollerup, Jens

2010-08-01

The need for higher efficiency, maximum quality, and faster turnaround time is a continuous focus for anatomic pathology laboratories and drives changes in work scheduling, instrumentation, and management control systems. To determine the costs of generating routine, special, and immunohistochemical microscopic slides in a large, academic anatomic pathology laboratory using a top-down approach. The Pathology Economic Model Tool was used to analyze workflow processes at The Nebraska Medical Center's anatomic pathology laboratory. Data from the analysis were used to generate complete cost estimates, which included not only materials, consumables, and instrumentation but also specific labor and overhead components for each of the laboratory's subareas. The cost data generated by the Pathology Economic Model Tool were compared with the cost estimates generated using relative value units. Despite the use of automated systems for different processes, the workflow in the laboratory was found to be relatively labor intensive. The effect of labor and overhead on per-slide costs was significantly underestimated by traditional relative-value unit calculations when compared with the Pathology Economic Model Tool. Specific workflow defects with significant contributions to the cost per slide were identified. The cost of providing routine, special, and immunohistochemical slides may be significantly underestimated by traditional methods that rely on relative value units. Furthermore, a comprehensive analysis may identify specific workflow processes requiring improvement.

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

International Nuclear Information System (INIS)

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

2002-01-01

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

Managing Library IT Workflow with Bugzilla

Directory of Open Access Journals (Sweden)

Nina McHale

2010-09-01

Full Text Available Prior to September 2008, all technology issues at the University of Colorado Denver's Auraria Library were reported to a dedicated departmental phone line. A variety of staff changes necessitated a more formal means of tracking, delegating, and resolving reported issues, and the department turned to Bugzilla, an open source bug tracking application designed by Mozilla.org developers. While designed with software development bug tracking in mind, Bugzilla can be easily customized and modified to serve as an IT ticketing system. Twenty-three months and over 2300 trouble tickets later, Auraria's IT department workflow is much smoother and more efficient. This article includes two Perl Template Toolkit code samples for customized Bugzilla screens for its use in a library environment; readers will be able to easily replicate the project in their own environments.

Earth Observing System (EOS)/ Advanced Microwave Sounding Unit-A (AMSU-A): Special Test Equipment. Software Requirements

Science.gov (United States)

Schwantje, Robert

1995-01-01

This document defines the functional, performance, and interface requirements for the Earth Observing System/Advanced Microwave Sounding Unit-A (EOS/AMSU-A) Special Test Equipment (STE) software used in the test and integration of the instruments.

The use of a special software for induction motor diagnostics in the diamond industry

Directory of Open Access Journals (Sweden)

Shevchuk Vladislav A.

2017-01-01

Full Text Available The field of induction motor application in the diamond industry has considerably increased due to the transition to the underground mining method. This article is devoted to the research the induction motor diagnostic technique in the diamond industry using special software. The practice shows that unreliability of induction motors causes some serious economic losses related to the expenses on premature maintenance and idle time. This article is devoted to the research of diagnostic technique of induction motors in the diamond industry using a special software. The article presents some data obtained in the course of the research conducted at an industrial site of the diamond company “ALROSA” in Mirny using the vibration-based diagnostics. Thus, based on the analysis of the findings some recommendations concerning the improvement of maintenance and servicing system have been given. The use of these recommendations allows assessing the operational reliability of induction motors in the diamond industry, minimizing the risk of sudden failures and reducing the maintenance and repair expenses.

Advantages and Disadvantages of 1-Incision, 2-Incision, 3-Incision, and 4-Incision Laparoscopic Cholecystectomy: A Workflow Comparison Study.

Science.gov (United States)

Bartnicka, Joanna; Zietkiewicz, Agnieszka A; Kowalski, Grzegorz J

2016-08-01

A comparison of 1-port, 2-port, 3-port, and 4-port laparoscopic cholecystectomy techniques from the point of view of workflow criteria was made to both identify specific workflow components that can cause surgical disturbances and indicate good and bad practices. As a case study, laparoscopic cholecystectomies, including manual tasks and interactions within teamwork members, were video-recorded and analyzed on the basis of specially encoded workflow information. The parameters for comparison were defined as follows: surgery time, tool and hand activeness, operator's passive work, collisions, and operator interventions. It was found that 1-port cholecystectomy is the worst technique because of nonergonomic body position, technical complexity, organizational anomalies, and operational dynamism. The differences between laparoscopic techniques are closely linked to the costs of the medical procedures. Hence, knowledge about the surgical workflow can be used for both planning surgical procedures and balancing the expenses associated with surgery.

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.

The MPO API: A tool for recording scientific workflows

Energy Technology Data Exchange (ETDEWEB)

Wright, John C., E-mail: jcwright@mit.edu [MIT Plasma Science and Fusion Center, Cambridge, MA (United States); Greenwald, Martin; Stillerman, Joshua [MIT Plasma Science and Fusion Center, Cambridge, MA (United States); Abla, Gheni; Chanthavong, Bobby; Flanagan, Sean; Schissel, David; Lee, Xia [General Atomics, San Diego, CA (United States); Romosan, Alex; Shoshani, Arie [Lawrence Berkeley Laboratory, Berkeley, CA (United States)

2014-05-15

Highlights: • A description of a new framework and tool for recording scientific workflows, especially those resulting from simulation and analysis. • An explanation of the underlying technologies used to implement this web based tool. • Several examples of using the tool. - Abstract: Data from large-scale experiments and extreme-scale computing is expensive to produce and may be used for high-consequence applications. The Metadata, Provenance and Ontology (MPO) project builds on previous work [M. Greenwald, Fusion Eng. Des. 87 (2012) 2205–2208] and is focused on providing documentation of workflows, data provenance and the ability to data-mine large sets of results. While there are important design and development aspects to the data structures and user interfaces, we concern ourselves in this paper with the application programming interface (API) – the set of functions that interface with the data server. Our approach for the data server is to follow the Representational State Transfer (RESTful) software architecture style for client–server communication. At its core, the API uses the POST and GET methods of the HTTP protocol to transfer workflow information in message bodies to targets specified in the URL to and from the database via a web server. Higher level API calls are built upon this core API. This design facilitates implementation on different platforms and in different languages and is robust to changes in the underlying technologies used. The command line client implementation can communicate with the data server from any machine with HTTP access.

The MPO API: A tool for recording scientific workflows

International Nuclear Information System (INIS)

Wright, John C.; Greenwald, Martin; Stillerman, Joshua; Abla, Gheni; Chanthavong, Bobby; Flanagan, Sean; Schissel, David; Lee, Xia; Romosan, Alex; Shoshani, Arie

2014-01-01

Highlights: • A description of a new framework and tool for recording scientific workflows, especially those resulting from simulation and analysis. • An explanation of the underlying technologies used to implement this web based tool. • Several examples of using the tool. - Abstract: Data from large-scale experiments and extreme-scale computing is expensive to produce and may be used for high-consequence applications. The Metadata, Provenance and Ontology (MPO) project builds on previous work [M. Greenwald, Fusion Eng. Des. 87 (2012) 2205–2208] and is focused on providing documentation of workflows, data provenance and the ability to data-mine large sets of results. While there are important design and development aspects to the data structures and user interfaces, we concern ourselves in this paper with the application programming interface (API) – the set of functions that interface with the data server. Our approach for the data server is to follow the Representational State Transfer (RESTful) software architecture style for client–server communication. At its core, the API uses the POST and GET methods of the HTTP protocol to transfer workflow information in message bodies to targets specified in the URL to and from the database via a web server. Higher level API calls are built upon this core API. This design facilitates implementation on different platforms and in different languages and is robust to changes in the underlying technologies used. The command line client implementation can communicate with the data server from any machine with HTTP access

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

Software for rapid prototyping in the pharmaceutical and biotechnology industries.

Science.gov (United States)

Kappler, Michael A

2008-05-01

The automation of drug discovery methods continues to develop, especially techniques that process information, represent workflow and facilitate decision-making. The magnitude of data and the plethora of questions in pharmaceutical and biotechnology research give rise to the need for rapid prototyping software. This review describes the advantages and disadvantages of three solutions: Competitive Workflow, Taverna and Pipeline Pilot. Each of these systems processes large amounts of data, integrates diverse systems and assists novice programmers and human experts in critical decision-making steps.

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...

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

Energy Technology Data Exchange (ETDEWEB)

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

2009-04-20

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

The Prosthetic Workflow in the Digital Era

Directory of Open Access Journals (Sweden)

Lidia Tordiglione

2016-01-01

Full Text Available The purpose of this retrospective study was to clinically evaluate the benefits of adopting a full digital workflow for the implementation of fixed prosthetic restorations on natural teeth. To evaluate the effectiveness of these protocols, treatment plans were drawn up for 15 patients requiring rehabilitation of one or more natural teeth. All the dental impressions were taken using a Planmeca PlanScan® (Planmeca OY, Helsinki, Finland intraoral scanner, which provided digital casts on which the restorations were digitally designed using Exocad® (Exocad GmbH, Germany, 2010 software and fabricated by CAM processing on 5-axis milling machines. A total of 28 single crowns were made from monolithic zirconia, 12 vestibular veneers from lithium disilicate, and 4 three-quarter vestibular veneers with palatal extension. While the restorations were applied, the authors could clinically appreciate the excellent match between the digitally produced prosthetic design and the cemented prostheses, which never required any occlusal or proximal adjustment. Out of all the restorations applied, only one exhibited premature failure and was replaced with no other complications or need for further scanning. From the clinical experience gained using a full digital workflow, the authors can confirm that these work processes enable the fabrication of clinically reliable restorations, with all the benefits that digital methods bring to the dentist, the dental laboratory, and the patient.

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.

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...

Multilevel Workflow System in the ATLAS Experiment

CERN Document Server

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

2015-01-01

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

CMS Distributed Computing Workflow Experience

CERN Document Server

Haas, Jeffrey David

2010-01-01

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

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

DEFF Research Database (Denmark)

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

2007-01-01

Care organizations, such as hospitals, need to support complex and dynamic workflows. More- over, many disciplines are involved. This makes it important to avoid the typical disconnect between requirements and the actual implementation of the system. This paper proposes an approach where an Execu......Care organizations, such as hospitals, need to support complex and dynamic workflows. More- over, many disciplines are involved. This makes it important to avoid the typical disconnect between requirements and the actual implementation of the system. This paper proposes an approach where...... an Executable Use Case (EUC) and Colored Care organizations, such as hospitals, need to support complex and dynamic workflows. Moreover, many disciplines are involved. This makes it important to avoid the typical disconnect between requirements and the actual implementation of the system. This paper proposes...

Monitoring of computing resource use of active software releases at ATLAS

Science.gov (United States)

Limosani, Antonio; ATLAS Collaboration

2017-10-01

The LHC is the world’s most powerful particle accelerator, colliding protons at centre of mass energy of 13 TeV. As the energy and frequency of collisions has grown in the search for new physics, so too has demand for computing resources needed for event reconstruction. We will report on the evolution of resource usage in terms of CPU and RAM in key ATLAS offline reconstruction workflows at the TierO at CERN and on the WLCG. Monitoring of workflows is achieved using the ATLAS PerfMon package, which is the standard ATLAS performance monitoring system running inside Athena jobs. Systematic daily monitoring has recently been expanded to include all workflows beginning at Monte Carlo generation through to end-user physics analysis, beyond that of event reconstruction. Moreover, the move to a multiprocessor mode in production jobs has facilitated the use of tools, such as “MemoryMonitor”, to measure the memory shared across processors in jobs. Resource consumption is broken down into software domains and displayed in plots generated using Python visualization libraries and collected into pre-formatted auto-generated Web pages, which allow the ATLAS developer community to track the performance of their algorithms. This information is however preferentially filtered to domain leaders and developers through the use of JIRA and via reports given at ATLAS software meetings. Finally, we take a glimpse of the future by reporting on the expected CPU and RAM usage in benchmark workflows associated with the High Luminosity LHC and anticipate the ways performance monitoring will evolve to understand and benchmark future workflows.

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.

Geometric processing workflow for vertical and oblique hyperspectral frame images collected using UAV

Science.gov (United States)

Markelin, L.; Honkavaara, E.; Näsi, R.; Nurminen, K.; Hakala, T.

2014-08-01

Remote sensing based on unmanned airborne vehicles (UAVs) is a rapidly developing field of technology. UAVs enable accurate, flexible, low-cost and multiangular measurements of 3D geometric, radiometric, and temporal properties of land and vegetation using various sensors. In this paper we present a geometric processing chain for multiangular measurement system that is designed for measuring object directional reflectance characteristics in a wavelength range of 400-900 nm. The technique is based on a novel, lightweight spectral camera designed for UAV use. The multiangular measurement is conducted by collecting vertical and oblique area-format spectral images. End products of the geometric processing are image exterior orientations, 3D point clouds and digital surface models (DSM). This data is needed for the radiometric processing chain that produces reflectance image mosaics and multiangular bidirectional reflectance factor (BRF) observations. The geometric processing workflow consists of the following three steps: (1) determining approximate image orientations using Visual Structure from Motion (VisualSFM) software, (2) calculating improved orientations and sensor calibration using a method based on self-calibrating bundle block adjustment (standard photogrammetric software) (this step is optional), and finally (3) creating dense 3D point clouds and DSMs using Photogrammetric Surface Reconstruction from Imagery (SURE) software that is based on semi-global-matching algorithm and it is capable of providing a point density corresponding to the pixel size of the image. We have tested the geometric processing workflow over various targets, including test fields, agricultural fields, lakes and complex 3D structures like forests.

Next-generation sequencing meets genetic diagnostics: development of a comprehensive workflow for the analysis of BRCA1 and BRCA2 genes

Science.gov (United States)

Feliubadaló, Lídia; Lopez-Doriga, Adriana; Castellsagué, Ester; del Valle, Jesús; Menéndez, Mireia; Tornero, Eva; Montes, Eva; Cuesta, Raquel; Gómez, Carolina; Campos, Olga; Pineda, Marta; González, Sara; Moreno, Victor; Brunet, Joan; Blanco, Ignacio; Serra, Eduard; Capellá, Gabriel; Lázaro, Conxi

2013-01-01

Next-generation sequencing (NGS) is changing genetic diagnosis due to its huge sequencing capacity and cost-effectiveness. The aim of this study was to develop an NGS-based workflow for routine diagnostics for hereditary breast and ovarian cancer syndrome (HBOCS), to improve genetic testing for BRCA1 and BRCA2. A NGS-based workflow was designed using BRCA MASTR kit amplicon libraries followed by GS Junior pyrosequencing. Data analysis combined Variant Identification Pipeline freely available software and ad hoc R scripts, including a cascade of filters to generate coverage and variant calling reports. A BRCA homopolymer assay was performed in parallel. A research scheme was designed in two parts. A Training Set of 28 DNA samples containing 23 unique pathogenic mutations and 213 other variants (33 unique) was used. The workflow was validated in a set of 14 samples from HBOCS families in parallel with the current diagnostic workflow (Validation Set). The NGS-based workflow developed permitted the identification of all pathogenic mutations and genetic variants, including those located in or close to homopolymers. The use of NGS for detecting copy-number alterations was also investigated. The workflow meets the sensitivity and specificity requirements for the genetic diagnosis of HBOCS and improves on the cost-effectiveness of current approaches. PMID:23249957

Handling of Multimedia Files in the Invenio Software

CERN Document Server

Oltmanns, Björn; Schiefer, Bernhard

‘Handling of multimedia files in the Invenio Software’ is motivated by the need for integration of multimedia files in the open-source, large-scale digital library software Invenio, developed and used at CERN, the European Organisation for Nuclear Research. In the last years, digital assets like pictures, presentations podcasts and videos became abundant in these systems and digital libraries have grown out of their classic role of only storing bibliographical metadata. The thesis focuses on digital video as a type of multimedia and covers the complete workflow of handling video material in the Invenio software: from the ingestion of digital video material to its processing on to the storage and preservation and finally the streaming and presentation of videos to the user. The potential technologies to realise a video submission workflow are discussed in-depth and evaluated towards system integration with Invenio. The focus is set on open and free technologies, which can be redistributed with the Inve...

Incorporating Geoscience, Field Data Collection Workflows into Software Developed for Mobile Devices

Science.gov (United States)

Vieira, D. A.; Mookerjee, M.; Matsa, S.

2014-12-01

Modern geological sciences depend heavily on investigating the natural world in situ, i.e., within "the field," as well as managing data collections in the light of evolving advances in technology and cyberinfrastructure. To accelerate the rate of scientific discovery, we need to expedite data collection and management in such a way so as to not interfere with the typical geoscience, field workflow. To this end, we suggest replacing traditional analog methods of data collection, such as the standard field notebook and compass, with primary digital data collection applications. While some field data collecting apps exist for both the iOS and android operating systems, they do not communicate with each other in an organized data collection effort. We propose the development of a mobile app that coordinates the collection of GPS, photographic, and orientation data, along with field observations. Additionally, this application should be able to pair with other devices in order to incorporate other sensor data. In this way, the app can generate a single file that includes all field data elements and can be synced to the appropriate database with ease and efficiency. We present here a prototype application that attempts to illustrate how digital collection can be integrated into a "typical" geoscience, field workflow. The purpose of our app is to get field scientists to think about specific requirements for the development of a unified field data collection application. One fundamental step in the development of such an app is the community-based, decision-making process of adopting certain data/metadata standards and conventions. In August of 2014, on a four-day field trip to Yosemite National Park and Owens Valley, we engaged a group of field-based geologists and computer/cognitive scientists to start building a community consensus on these cyberinfrastructure-related issues. Discussing the unique problems of field data recording, conventions, storage, representation

Intellectual Property Protection of Software – At the Crossroads of Software Patents and Open Source Software

OpenAIRE

Tantarimäki, Maria

2018-01-01

The thesis considers the intellectual property protection of software in Europe and in the US, which is increasingly important subject as the world is globalizing and digitalizing. The special nature of software has challenges the intellectual property rights. The current protection of software is based on copyright protection but in this thesis, two other options are considered: software patents and open source software. Software patents provide strong protection for software whereas the pur...

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

Clinical, information and business process modeling to promote development of safe and flexible software.

Science.gov (United States)

Liaw, Siaw-Teng; Deveny, Elizabeth; Morrison, Iain; Lewis, Bryn

2006-09-01

Using a factorial vignette survey and modeling methodology, we developed clinical and information models - incorporating evidence base, key concepts, relevant terms, decision-making and workflow needed to practice safely and effectively - to guide the development of an integrated rule-based knowledge module to support prescribing decisions in asthma. We identified workflows, decision-making factors, factor use, and clinician information requirements. The Unified Modeling Language (UML) and public domain software and knowledge engineering tools (e.g. Protégé) were used, with the Australian GP Data Model as the starting point for expressing information needs. A Web Services service-oriented architecture approach was adopted within which to express functional needs, and clinical processes and workflows were expressed in the Business Process Execution Language (BPEL). This formal analysis and modeling methodology to define and capture the process and logic of prescribing best practice in a reference implementation is fundamental to tackling deficiencies in prescribing decision support software.

Responsive web design workflow

OpenAIRE

LAAK, TIMO

2013-01-01

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

Pro WF Windows Workflow in NET 40

CERN Document Server

Bukovics, Bruce

2010-01-01

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

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

Science.gov (United States)

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

2013-06-01

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

Using Mobile Agents to Implement Workflow System

Institute of Scientific and Technical Information of China (English)

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

2004-01-01

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

DNAseq Workflow in a Diagnostic Context and an Example of a User Friendly Implementation

Directory of Open Access Journals (Sweden)

Beat Wolf

2015-01-01

Full Text Available Over recent years next generation sequencing (NGS technologies evolved from costly tools used by very few, to a much more accessible and economically viable technology. Through this recently gained popularity, its use-cases expanded from research environments into clinical settings. But the technical know-how and infrastructure required to analyze the data remain an obstacle for a wider adoption of this technology, especially in smaller laboratories. We present GensearchNGS, a commercial DNAseq software suite distributed by Phenosystems SA. The focus of GensearchNGS is the optimal usage of already existing infrastructure, while keeping its use simple. This is achieved through the integration of existing tools in a comprehensive software environment, as well as custom algorithms developed with the restrictions of limited infrastructures in mind. This includes the possibility to connect multiple computers to speed up computing intensive parts of the analysis such as sequence alignments. We present a typical DNAseq workflow for NGS data analysis and the approach GensearchNGS takes to implement it. The presented workflow goes from raw data quality control to the final variant report. This includes features such as gene panels and the integration of online databases, like Ensembl for annotations or Cafe Variome for variant sharing.

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

Trustworthiness Measurement Algorithm for TWfMS Based on Software Behaviour Entropy

Directory of Open Access Journals (Sweden)

Qiang Han

2018-03-01

Full Text Available As the virtual mirror of complex real-time business processes of organisations’ underlying information systems, the workflow management system (WfMS has emerged in recent decades as a new self-autonomous paradigm in the open, dynamic, distributed computing environment. In order to construct a trustworthy workflow management system (TWfMS, the design of a software behaviour trustworthiness measurement algorithm is an urgent task for researchers. Accompanying the trustworthiness mechanism, the measurement algorithm, with uncertain software behaviour trustworthiness information of the WfMS, should be resolved as an infrastructure. Based on the framework presented in our research prior to this paper, we firstly introduce a formal model for the WfMS trustworthiness measurement, with the main property reasoning based on calculus operators. Secondly, this paper proposes a novel measurement algorithm from the software behaviour entropy of calculus operators through the principle of maximum entropy (POME and the data mining method. Thirdly, the trustworthiness measurement algorithm for incomplete software behaviour tests and runtime information is discussed and compared by means of a detailed explanation. Finally, we provide conclusions and discuss certain future research areas of the TWfMS.

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...

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.

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

The Event Coordination Notation: Behaviour Modelling Beyond Mickey Mouse

DEFF Research Database (Denmark)

Jepsen, Jesper; Kindler, Ekkart

2015-01-01

The Event Coordination Notation (ECNO) allows modelling the desired behaviour of a software system on top of any object-oriented software. Together with existing technologies from Model-based Software Engineering (MBSE) for automatically generating the software for the structural parts, ECNO allows...... special aspect of ECNO or another; and it would be fair to call them “Mickey Mouse examples”. In this paper, we give a concise overview of the motivation, ideas, and concepts of ECNO. More importantly, we discuss a larger system, which was completely generated from the underlying models: a workflow...... management system. This way, we demonstrate that ECNO can be used for modelling software beyond the typical Mickey Mouse examples. This example demonstrates that the essence of workflow management – including its behaviour – can be captured in ECNO: in a sense, it is a domain model of workflow management...

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

Methodology for the design of the method of siliceous sandstones operation using special software

Directory of Open Access Journals (Sweden)

Luis Ángel Lara-González

2014-12-01

Full Text Available The methodologies used for the design of the method of sandstones explotation by descending staggered banks using specialized software tools are reported. The data analyzed were collected in the field for the operating license 14816 in Melgar, Tolima. The characterization of the rock mass was held from physical and mechanical tests, performed on cylindrical test tubes in order to obtain the value of the maximum strenght and elastic modulus of the rock. The direction and dip of the sandstone package was rock. The direction and dip of the sandstone package was determined by using the stereographic projection whit DIPS®  software, and the safety factor of the slope was obtained with established banks whit SLIDE® . The slops are 8 meters high and 8 meters wide whit a tilt angle 60°, which generated a safety factor  of 2.1. The design  of the mining method was carried out with GEOVIA SURPAC® , at an early stage of development ascending to the level 11 of the exploitation, to then start mining in descending order to control the stabiLity of slopes. The results obtained allow a general methodology for the development of projects to optimize the process of evaluation and selection of mining method by using specialized design tools.

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...

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

The CMS Data Quality Monitoring software experience and future improvements

CERN Document Server

Batinkov, Atanas Ivanov

2013-01-01

The Data Quality Monitoring Software proved to be a central tool in the Compact Muon Solenoid experiment. Its flexibility allowed its integration in several environments: online, for real-time detector monitoring; offline, for the final, fine-grained data certification. The usage of the Data Quality Monitoring software in the different environments and its integration in the Compact Muon Solenoid reconstruction software framework and in all production workflows are presented. The main technical challenges and the adopted solutions to them will be also discussed with emphasis on functionality, long-term robustness and performance.

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.

IBEX: an open infrastructure software platform to facilitate collaborative work in radiomics.

Science.gov (United States)

Zhang, Lifei; Fried, David V; Fave, Xenia J; Hunter, Luke A; Yang, Jinzhong; Court, Laurence E

2015-03-01

Radiomics, which is the high-throughput extraction and analysis of quantitative image features, has been shown to have considerable potential to quantify the tumor phenotype. However, at present, a lack of software infrastructure has impeded the development of radiomics and its applications. Therefore, the authors developed the imaging biomarker explorer (IBEX), an open infrastructure software platform that flexibly supports common radiomics workflow tasks such as multimodality image data import and review, development of feature extraction algorithms, model validation, and consistent data sharing among multiple institutions. The IBEX software package was developed using the MATLAB and c/c++ programming languages. The software architecture deploys the modern model-view-controller, unit testing, and function handle programming concepts to isolate each quantitative imaging analysis task, to validate if their relevant data and algorithms are fit for use, and to plug in new modules. On one hand, IBEX is self-contained and ready to use: it has implemented common data importers, common image filters, and common feature extraction algorithms. On the other hand, IBEX provides an integrated development environment on top of MATLAB and c/c++, so users are not limited to its built-in functions. In the IBEX developer studio, users can plug in, debug, and test new algorithms, extending IBEX's functionality. IBEX also supports quality assurance for data and feature algorithms: image data, regions of interest, and feature algorithm-related data can be reviewed, validated, and/or modified. More importantly, two key elements in collaborative workflows, the consistency of data sharing and the reproducibility of calculation result, are embedded in the IBEX workflow: image data, feature algorithms, and model validation including newly developed ones from different users can be easily and consistently shared so that results can be more easily reproduced between institutions

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

Science.gov (United States)

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

2015-01-01

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

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.

Interactive reconstructions of cranial 3D implants under MeVisLab as an alternative to commercial planning software.

Directory of Open Access Journals (Sweden)

Jan Egger

Full Text Available In this publication, the interactive planning and reconstruction of cranial 3D Implants under the medical prototyping platform MeVisLab as alternative to commercial planning software is introduced. In doing so, a MeVisLab prototype consisting of a customized data-flow network and an own C++ module was set up. As a result, the Computer-Aided Design (CAD software prototype guides a user through the whole workflow to generate an implant. Therefore, the workflow begins with loading and mirroring the patients head for an initial curvature of the implant. Then, the user can perform an additional Laplacian smoothing, followed by a Delaunay triangulation. The result is an aesthetic looking and well-fitting 3D implant, which can be stored in a CAD file format, e.g. STereoLithography (STL, for 3D printing. The 3D printed implant can finally be used for an in-depth pre-surgical evaluation or even as a real implant for the patient. In a nutshell, our research and development shows that a customized MeVisLab software prototype can be used as an alternative to complex commercial planning software, which may also not be available in every clinic. Finally, not to conform ourselves directly to available commercial software and look for other options that might improve the workflow.

Interactive reconstructions of cranial 3D implants under MeVisLab as an alternative to commercial planning software

Science.gov (United States)

Egger, Jan; Gall, Markus; Tax, Alois; Ücal, Muammer; Zefferer, Ulrike; Li, Xing; von Campe, Gord; Schäfer, Ute; Schmalstieg, Dieter; Chen, Xiaojun

2017-01-01

In this publication, the interactive planning and reconstruction of cranial 3D Implants under the medical prototyping platform MeVisLab as alternative to commercial planning software is introduced. In doing so, a MeVisLab prototype consisting of a customized data-flow network and an own C++ module was set up. As a result, the Computer-Aided Design (CAD) software prototype guides a user through the whole workflow to generate an implant. Therefore, the workflow begins with loading and mirroring the patients head for an initial curvature of the implant. Then, the user can perform an additional Laplacian smoothing, followed by a Delaunay triangulation. The result is an aesthetic looking and well-fitting 3D implant, which can be stored in a CAD file format, e.g. STereoLithography (STL), for 3D printing. The 3D printed implant can finally be used for an in-depth pre-surgical evaluation or even as a real implant for the patient. In a nutshell, our research and development shows that a customized MeVisLab software prototype can be used as an alternative to complex commercial planning software, which may also not be available in every clinic. Finally, not to conform ourselves directly to available commercial software and look for other options that might improve the workflow. PMID:28264062

Multilevel Workflow System in the ATLAS Experiment

International Nuclear Information System (INIS)

Borodin, M; De, K; Navarro, J Garcia; Golubkov, D; Klimentov, A; Maeno, T; Vaniachine, A

2015-01-01

The ATLAS experiment is scaling up Big Data processing for the next LHC run using a multilevel workflow system comprised of many layers. In Big Data processing ATLAS deals with datasets, not individual files. Similarly a task (comprised of many jobs) has become a unit of the ATLAS workflow in distributed computing, with about 0.8M tasks processed per year. In order to manage the diversity of LHC physics (exceeding 35K physics samples per year), the individual data processing tasks are organized into workflows. For example, the Monte Carlo workflow is composed of many steps: generate or configure hard-processes, hadronize signal and minimum-bias (pileup) events, simulate energy deposition in the ATLAS detector, digitize electronics response, simulate triggers, reconstruct data, convert the reconstructed data into ROOT ntuples for physics analysis, etc. Outputs are merged and/or filtered as necessary to optimize the chain. The bi-level workflow manager - ProdSys2 - generates actual workflow tasks and their jobs are executed across more than a hundred distributed computing sites by PanDA - the ATLAS job-level workload management system. On the outer level, the Database Engine for Tasks (DEfT) empowers production managers with templated workflow definitions. On the next level, the Job Execution and Definition Interface (JEDI) is integrated with PanDA to provide dynamic job definition tailored to the sites capabilities. We report on scaling up the production system to accommodate a growing number of requirements from main ATLAS areas: Trigger, Physics and Data Preparation. (paper)

Workflow User Interfaces Patterns

Directory of Open Access Journals (Sweden)

Jean Vanderdonckt

2012-03-01

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

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.

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

Science.gov (United States)

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

2016-12-01

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

Resilient workflows for computational mechanics platforms

International Nuclear Information System (INIS)

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

2010-01-01

Workflow management systems have recently been the focus of much interest and many research and deployment for scientific applications worldwide. Their ability to abstract the applications by wrapping application codes have also stressed the usefulness of such systems for multidiscipline applications. When complex applications need to provide seamless interfaces hiding the technicalities of the computing infrastructures, their high-level modeling, monitoring and execution functionalities help giving production teams seamless and effective facilities. Software integration infrastructures based on programming paradigms such as Python, Mathlab and Scilab have also provided evidence of the usefulness of such approaches for the tight coupling of multidisciplne application codes. Also high-performance computing based on multi-core multi-cluster infrastructures open new opportunities for more accurate, more extensive and effective robust multi-discipline simulations for the decades to come. This supports the goal of full flight dynamics simulation for 3D aircraft models within the next decade, opening the way to virtual flight-tests and certification of aircraft in the future.

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

The CMS Data Quality Monitoring software experience and future improvements

CERN Document Server

De Guio, Federico

2013-01-01

The Data Quality Monitoring (DQM) Software proved to be a central tool in the CMS experiment. Its flexibility allowed its integration in several environments Online, for real-time detector monitoring; Offline, for the final, fine-grained Data Certification; Release Validation, to constantly validate the functionality and the performance of the reconstruction software; in Monte Carlo productions. The central tool to deliver Data Quality information is a web site for browsing data quality histograms (DQM GUI). In this contribution the usage of the DQM Software in the different environments and its integration in the CMS Reconstruction Software Framework and in all production workflows are presented.

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...

The CASA Software Package

Science.gov (United States)

Petry, Dirk

2018-03-01

CASA is the standard science data analysis package for ALMA and VLA but it can also be used for the analysis of data from other observatories. In this talk, I will give an overview of the structure and features of CASA, who develops it, and the present status and plans, and then show typical analysis workflows for ALMA data with special emphasis on the handling of single dish data and its combination with interferometric data.

Full 3-dimensional digital workflow for multicomponent dental appliances: A proof of concept.

Science.gov (United States)

van der Meer, W Joerd; Vissink, Arjan; Ren, Yijin

2016-04-01

The authors used a 3-dimensional (3D) printer and a bending robot to produce a multicomponent dental appliance to assess whether 3D digital models of the dentition are applicable for a full digital workflow. The authors scanned a volunteer's dentition with an intraoral scanner (Lava Chairside Oral Scanner C.O.S., 3M). A digital impression was used to design 2 multicomponent orthodontic appliances. Biocompatible acrylic baseplates were produced with the aid of a 3D printer. The metal springs and clasps were produced by a bending robot. The fit of the 2 appliances was assessed by 2 experienced orthodontists. The authors assessed both orthodontic appliances with the volunteer's dentition and found the fit to be excellent. Clinicians can fully produce a multicomponent dental appliance consisting of both an acrylic baseplate and other parts, such as clasps, springs, or screws, using a digital workflow process without the need for a physical model of the patient's dentition. Plaster models can be superfluous for orthodontic treatment as digital models can be used in all phases of a full digital workflow in orthodontics. The arduous task of making a multicomponent dental appliance that involves bending wires can possibly be replaced by a computer, design software, a 3D printer, and a bending robot. Copyright © 2016 American Dental Association. Published by Elsevier Inc. All rights reserved.

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

Science.gov (United States)

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

2014-12-01

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

CMS distributed computing workflow experience

Science.gov (United States)

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

2011-12-01

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

CMS distributed computing workflow experience

International Nuclear Information System (INIS)

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

2011-01-01

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

Verifying generalized soundness for workflow nets

NARCIS (Netherlands)

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

2007-01-01

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

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.

JMS: An Open Source Workflow Management System and Web-Based Cluster Front-End for High Performance Computing.

Science.gov (United States)

Brown, David K; Penkler, David L; Musyoka, Thommas M; Bishop, Özlem Tastan

2015-01-01

Complex computational pipelines are becoming a staple of modern scientific research. Often these pipelines are resource intensive and require days of computing time. In such cases, it makes sense to run them over high performance computing (HPC) clusters where they can take advantage of the aggregated resources of many powerful computers. In addition to this, researchers often want to integrate their workflows into their own web servers. In these cases, software is needed to manage the submission of jobs from the web interface to the cluster and then return the results once the job has finished executing. We have developed the Job Management System (JMS), a workflow management system and web interface for high performance computing (HPC). JMS provides users with a user-friendly web interface for creating complex workflows with multiple stages. It integrates this workflow functionality with the resource manager, a tool that is used to control and manage batch jobs on HPC clusters. As such, JMS combines workflow management functionality with cluster administration functionality. In addition, JMS provides developer tools including a code editor and the ability to version tools and scripts. JMS can be used by researchers from any field to build and run complex computational pipelines and provides functionality to include these pipelines in external interfaces. JMS is currently being used to house a number of bioinformatics pipelines at the Research Unit in Bioinformatics (RUBi) at Rhodes University. JMS is an open-source project and is freely available at https://github.com/RUBi-ZA/JMS.

JMS: An Open Source Workflow Management System and Web-Based Cluster Front-End for High Performance Computing.

Directory of Open Access Journals (Sweden)

David K Brown

Full Text Available Complex computational pipelines are becoming a staple of modern scientific research. Often these pipelines are resource intensive and require days of computing time. In such cases, it makes sense to run them over high performance computing (HPC clusters where they can take advantage of the aggregated resources of many powerful computers. In addition to this, researchers often want to integrate their workflows into their own web servers. In these cases, software is needed to manage the submission of jobs from the web interface to the cluster and then return the results once the job has finished executing. We have developed the Job Management System (JMS, a workflow management system and web interface for high performance computing (HPC. JMS provides users with a user-friendly web interface for creating complex workflows with multiple stages. It integrates this workflow functionality with the resource manager, a tool that is used to control and manage batch jobs on HPC clusters. As such, JMS combines workflow management functionality with cluster administration functionality. In addition, JMS provides developer tools including a code editor and the ability to version tools and scripts. JMS can be used by researchers from any field to build and run complex computational pipelines and provides functionality to include these pipelines in external interfaces. JMS is currently being used to house a number of bioinformatics pipelines at the Research Unit in Bioinformatics (RUBi at Rhodes University. JMS is an open-source project and is freely available at https://github.com/RUBi-ZA/JMS.

JMS: An Open Source Workflow Management System and Web-Based Cluster Front-End for High Performance Computing

Science.gov (United States)

Brown, David K.; Penkler, David L.; Musyoka, Thommas M.; Bishop, Özlem Tastan

2015-01-01

Complex computational pipelines are becoming a staple of modern scientific research. Often these pipelines are resource intensive and require days of computing time. In such cases, it makes sense to run them over high performance computing (HPC) clusters where they can take advantage of the aggregated resources of many powerful computers. In addition to this, researchers often want to integrate their workflows into their own web servers. In these cases, software is needed to manage the submission of jobs from the web interface to the cluster and then return the results once the job has finished executing. We have developed the Job Management System (JMS), a workflow management system and web interface for high performance computing (HPC). JMS provides users with a user-friendly web interface for creating complex workflows with multiple stages. It integrates this workflow functionality with the resource manager, a tool that is used to control and manage batch jobs on HPC clusters. As such, JMS combines workflow management functionality with cluster administration functionality. In addition, JMS provides developer tools including a code editor and the ability to version tools and scripts. JMS can be used by researchers from any field to build and run complex computational pipelines and provides functionality to include these pipelines in external interfaces. JMS is currently being used to house a number of bioinformatics pipelines at the Research Unit in Bioinformatics (RUBi) at Rhodes University. JMS is an open-source project and is freely available at https://github.com/RUBi-ZA/JMS. PMID:26280450

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...

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.

Surgical Workflow Analysis: Ideal Application of Navigated Linear Array Ultrasound in Low-Grade Glioma Surgery.

Science.gov (United States)

Lothes, Thomas Ernst; Siekmann, Max; König, Ralph Werner; Wirtz, Christian Rainer; Coburger, Jan

2016-11-01

Background  Intraoperative imaging in low-grade glioma (LGG) surgery can facilitate residual tumor control and improve surgical outcome. The aim of the study was to evaluate the ideal application and typical interactions of intraoperative MRI (iMRI), conventional low-frequency intraoperative ultrasound (cioUS), and high-frequency linear array intraoperative ultrasound (lioUS) to optimize surgical workflow. Methods  Prospectively, we included 11 patients with an LGG. Typical procedural workflow in the iMRI suite was recorded with a compatible software. We took notes of duration, frequency of application, the surgeon's evaluation of image quality, and the respective benefit of lioUS (15 MHz), cioUS (7 MHz), and iMRI (1.5 T). With the help of the workflow software, we meticulously analyzed ∼ 55 hours of surgery. Results  During the interventions, lioUS was used more often (76.3%) than cioUS (23.7%) and showed a better mean image quality (1 = best to 6 = worst) of 2.08 versus 3.26 with cioUS. The benefit of the lioUS application was rated with an average of 2.27, whereas the cioUS probe only reached a mean value of 3.83. The most common application of lioUS was resection control (42.6%); cioUS was used mainly for orientation (63.2%). Overall, lioUS was used more often and was rated better for both the purposes just described regarding image quality and benefit. Estimated residual tumor based on lioUS alone was lower than the final residual tumor detected with iMRI (7.5% versus 14.5%). The latter technique was rated as the best imaging modality for resection control in all cases followed by lioUS. Conclusion  We provide proof of principle for workflow assessment in cranial neurosurgery. Although iMRI remains the imaging method of choice, lioUS has shown to be beneficial in a combined setup. Evaluation of lioUS was significantly superior to cioUS in most indications except for subcortical lesions. Georg Thieme Verlag KG Stuttgart · New York.

Workflow of CAD / CAM Scoliosis Brace Adjustment in Preparation Using 3D Printing.

Science.gov (United States)

Weiss, Hans-Rudolf; Tournavitis, Nicos; Nan, Xiaofeng; Borysov, Maksym; Paul, Lothar

2017-01-01

High correction bracing is the most effective conservative treatment for patients with scoliosis during growth. Still today braces for the treatment of scoliosis are made by casting patients while computer aided design (CAD) and computer aided manufacturing (CAM) is available with all possibilities to standardize pattern specific brace treatment and improve wearing comfort. CAD / CAM brace production mainly relies on carving a polyurethane foam model which is the basis for vacuuming a polyethylene (PE) or polypropylene (PP) brace. Purpose of this short communication is to describe the workflow currently used and to outline future requirements with respect to 3D printing technology. Description of the steps of virtual brace adjustment as available today are content of this paper as well as an outline of the great potential there is for the future 3D printing technology. For 3D printing of scoliosis braces it is necessary to establish easy to use software plug-ins in order to allow adding 3D printing technology to the current workflow of virtual CAD / CAM brace adjustment. Textures and structures can be added to the brace models at certain well defined locations offering the potential of more wearing comfort without losing in-brace correction. Advances have to be made in the field of CAD / CAM software tools with respect to design and generation of individually structured brace models based on currently well established and standardized scoliosis brace libraries.

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....

GO2OGS 1.0: a versatile workflow to integrate complex geological information with fault data into numerical simulation models

Science.gov (United States)

Fischer, T.; Naumov, D.; Sattler, S.; Kolditz, O.; Walther, M.

2015-11-01

We offer a versatile workflow to convert geological models built with the ParadigmTM GOCAD© (Geological Object Computer Aided Design) software into the open-source VTU (Visualization Toolkit unstructured grid) format for usage in numerical simulation models. Tackling relevant scientific questions or engineering tasks often involves multidisciplinary approaches. Conversion workflows are needed as a way of communication between the diverse tools of the various disciplines. Our approach offers an open-source, platform-independent, robust, and comprehensible method that is potentially useful for a multitude of environmental studies. With two application examples in the Thuringian Syncline, we show how a heterogeneous geological GOCAD model including multiple layers and faults can be used for numerical groundwater flow modeling, in our case employing the OpenGeoSys open-source numerical toolbox for groundwater flow simulations. The presented workflow offers the chance to incorporate increasingly detailed data, utilizing the growing availability of computational power to simulate numerical models.

LabelFlow Framework for Annotating Workflow Provenance

Directory of Open Access Journals (Sweden)

Pinar Alper

2018-02-01

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

Provenance-based refresh in data-oriented workflows

KAUST Repository

Ikeda, Robert; Salihoglu, Semih; Widom, Jennifer

2011-01-01

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

Towards seamless workflows in agile data science

Science.gov (United States)

Klump, J. F.; Robertson, J.

2017-12-01

Agile workflows are a response to projects with requirements that may change over time. They prioritise rapid and flexible responses to change, preferring to adapt to changes in requirements rather than predict them before a project starts. This suits the needs of research very well because research is inherently agile in its methodology. The adoption of agile methods has made collaborative data analysis much easier in a research environment fragmented across institutional data stores, HPC, personal and lab computers and more recently cloud environments. Agile workflows use tools that share a common worldview: in an agile environment, there may be more that one valid version of data, code or environment in play at any given time. All of these versions need references and identifiers. For example, a team of developers following the git-flow conventions (github.com/nvie/gitflow) may have several active branches, one for each strand of development. These workflows allow rapid and parallel iteration while maintaining identifiers pointing to individual snapshots of data and code and allowing rapid switching between strands. In contrast, the current focus of versioning in research data management is geared towards managing data for reproducibility and long-term preservation of the record of science. While both are important goals in the persistent curation domain of the institutional research data infrastructure, current tools emphasise planning over adaptation and can introduce unwanted rigidity by insisting on a single valid version or point of truth. In the collaborative curation domain of a research project, things are more fluid. However, there is no equivalent to the "versioning iso-surface" of the git protocol for the management and versioning of research data. At CSIRO we are developing concepts and tools for the agile management of software code and research data for virtual research environments, based on our experiences of actual data analytics projects in the

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

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.

WS-VLAM: A GT4 based workflow management system

NARCIS (Netherlands)

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

2007-01-01

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

Modelling and analysis of workflow for lean supply chains

Science.gov (United States)

Ma, Jinping; Wang, Kanliang; Xu, Lida

2011-11-01

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

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

Science.gov (United States)

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

2016-01-01

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

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

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...

MO-D-213-01: Workflow Monitoring for a High Volume Radiation Oncology Center

International Nuclear Information System (INIS)

Laub, S; Dunn, M; Galbreath, G; Gans, S; Pankuch, M

2015-01-01

Purpose: Implement a center wide communication system that increases interdepartmental transparency and accountability while decreasing redundant work and treatment delays by actively monitoring treatment planning workflow. Methods: Intake Management System (IMS), a program developed by ProCure Treatment Centers Inc., is a multi-function database that stores treatment planning process information. It was devised to work with the oncology information system (Mosaiq) to streamline interdepartmental workflow.Each step in the treatment planning process is visually represented and timelines for completion of individual tasks are established within the software. The currently active step of each patient’s planning process is highlighted either red or green according to whether the initially allocated amount of time has passed for the given process. This information is displayed as a Treatment Planning Process Monitor (TPPM), which is shown on screens in the relevant departments throughout the center. This display also includes the individuals who are responsible for each task.IMS is driven by Mosaiq’s quality checklist (QCL) functionality. Each step in the workflow is initiated by a Mosaiq user sending the responsible party a QCL assignment. IMS is connected to Mosaiq and the sending or completing of a QCL updates the associated field in the TPPM to the appropriate status. Results: Approximately one patient a week is identified during the workflow process as needing to have his/her treatment start date modified or resources re-allocated to address the most urgent cases. Being able to identify a realistic timeline for planning each patient and having multiple departments communicate their limitations and time constraints allows for quality plans to be developed and implemented without overburdening any one department. Conclusion: Monitoring the progression of the treatment planning process has increased transparency between departments, which enables efficient

MO-D-213-01: Workflow Monitoring for a High Volume Radiation Oncology Center

Energy Technology Data Exchange (ETDEWEB)

Laub, S [CDH Proton Center, Warrenville, IL (United States); Dunn, M [Proton Collaborative Group, Warrenville, Illinois (United States); Galbreath, G [ProCure Treatment Centers Inc., New York, NY (United States); Gans, S [Northwestern Memorial Chicago Proton Center, Warrenville, Illinois (United States); Pankuch, M [Northwestern Medicine Chicago Proton Center, Warrenville, IL (United States)

2015-06-15

Purpose: Implement a center wide communication system that increases interdepartmental transparency and accountability while decreasing redundant work and treatment delays by actively monitoring treatment planning workflow. Methods: Intake Management System (IMS), a program developed by ProCure Treatment Centers Inc., is a multi-function database that stores treatment planning process information. It was devised to work with the oncology information system (Mosaiq) to streamline interdepartmental workflow.Each step in the treatment planning process is visually represented and timelines for completion of individual tasks are established within the software. The currently active step of each patient’s planning process is highlighted either red or green according to whether the initially allocated amount of time has passed for the given process. This information is displayed as a Treatment Planning Process Monitor (TPPM), which is shown on screens in the relevant departments throughout the center. This display also includes the individuals who are responsible for each task.IMS is driven by Mosaiq’s quality checklist (QCL) functionality. Each step in the workflow is initiated by a Mosaiq user sending the responsible party a QCL assignment. IMS is connected to Mosaiq and the sending or completing of a QCL updates the associated field in the TPPM to the appropriate status. Results: Approximately one patient a week is identified during the workflow process as needing to have his/her treatment start date modified or resources re-allocated to address the most urgent cases. Being able to identify a realistic timeline for planning each patient and having multiple departments communicate their limitations and time constraints allows for quality plans to be developed and implemented without overburdening any one department. Conclusion: Monitoring the progression of the treatment planning process has increased transparency between departments, which enables efficient

Federated Database Services for Wind Tunnel Experiment Workflows

Directory of Open Access Journals (Sweden)

A. Paventhan

2006-01-01

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

Analysing scientific workflows: Why workflows not only connect web services

NARCIS (Netherlands)

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

2009-01-01

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

Analysing scientific workflows: why workflows not only connect web services

NARCIS (Netherlands)

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

2009-01-01

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

Workflow Fault Tree Generation Through Model Checking

DEFF Research Database (Denmark)

Herbert, Luke Thomas; Sharp, Robin

2014-01-01

We present a framework for the automated generation of fault trees from models of realworld process workflows, expressed in a formalised subset of the popular Business Process Modelling and Notation (BPMN) language. To capture uncertainty and unreliability in workflows, we extend this formalism...

IBEX: An open infrastructure software platform to facilitate collaborative work in radiomics

Energy Technology Data Exchange (ETDEWEB)

Zhang, Lifei; Yang, Jinzhong [Department of Radiation Physics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030 (United States); Fried, David V.; Fave, Xenia J.; Hunter, Luke A.; Court, Laurence E., E-mail: LECourt@mdanderson.org [Department of Radiation Physics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030 and The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, Texas 77030 (United States)

2015-03-15

Purpose: Radiomics, which is the high-throughput extraction and analysis of quantitative image features, has been shown to have considerable potential to quantify the tumor phenotype. However, at present, a lack of software infrastructure has impeded the development of radiomics and its applications. Therefore, the authors developed the imaging biomarker explorer (IBEX), an open infrastructure software platform that flexibly supports common radiomics workflow tasks such as multimodality image data import and review, development of feature extraction algorithms, model validation, and consistent data sharing among multiple institutions. Methods: The IBEX software package was developed using the MATLAB and C/C++ programming languages. The software architecture deploys the modern model-view-controller, unit testing, and function handle programming concepts to isolate each quantitative imaging analysis task, to validate if their relevant data and algorithms are fit for use, and to plug in new modules. On one hand, IBEX is self-contained and ready to use: it has implemented common data importers, common image filters, and common feature extraction algorithms. On the other hand, IBEX provides an integrated development environment on top of MATLAB and C/C++, so users are not limited to its built-in functions. In the IBEX developer studio, users can plug in, debug, and test new algorithms, extending IBEX’s functionality. IBEX also supports quality assurance for data and feature algorithms: image data, regions of interest, and feature algorithm-related data can be reviewed, validated, and/or modified. More importantly, two key elements in collaborative workflows, the consistency of data sharing and the reproducibility of calculation result, are embedded in the IBEX workflow: image data, feature algorithms, and model validation including newly developed ones from different users can be easily and consistently shared so that results can be more easily reproduced between

IBEX: An open infrastructure software platform to facilitate collaborative work in radiomics

International Nuclear Information System (INIS)

Zhang, Lifei; Yang, Jinzhong; Fried, David V.; Fave, Xenia J.; Hunter, Luke A.; Court, Laurence E.

2015-01-01

Purpose: Radiomics, which is the high-throughput extraction and analysis of quantitative image features, has been shown to have considerable potential to quantify the tumor phenotype. However, at present, a lack of software infrastructure has impeded the development of radiomics and its applications. Therefore, the authors developed the imaging biomarker explorer (IBEX), an open infrastructure software platform that flexibly supports common radiomics workflow tasks such as multimodality image data import and review, development of feature extraction algorithms, model validation, and consistent data sharing among multiple institutions. Methods: The IBEX software package was developed using the MATLAB and C/C++ programming languages. The software architecture deploys the modern model-view-controller, unit testing, and function handle programming concepts to isolate each quantitative imaging analysis task, to validate if their relevant data and algorithms are fit for use, and to plug in new modules. On one hand, IBEX is self-contained and ready to use: it has implemented common data importers, common image filters, and common feature extraction algorithms. On the other hand, IBEX provides an integrated development environment on top of MATLAB and C/C++, so users are not limited to its built-in functions. In the IBEX developer studio, users can plug in, debug, and test new algorithms, extending IBEX’s functionality. IBEX also supports quality assurance for data and feature algorithms: image data, regions of interest, and feature algorithm-related data can be reviewed, validated, and/or modified. More importantly, two key elements in collaborative workflows, the consistency of data sharing and the reproducibility of calculation result, are embedded in the IBEX workflow: image data, feature algorithms, and model validation including newly developed ones from different users can be easily and consistently shared so that results can be more easily reproduced between

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

CERN Document Server

FARRELL, Steven; The ATLAS collaboration

2015-01-01

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

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

CERN Document Server

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

2015-01-01

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

Nontargeted diagnostic ion network analysis (NINA): A software to streamline the analytical workflow for untargeted characterization of natural medicines.

Science.gov (United States)

Ye, Hui; Zhu, Lin; Sun, Di; Luo, Xiaozhuo; Lu, Gaoyuan; Wang, Hong; Wang, Jing; Cao, Guoxiu; Xiao, Wei; Wang, Zhenzhong; Wang, Guangji; Hao, Haiping

2016-11-30

The characterization of herbal prescriptions serves as a foundation for quality control and regulation of herbal medicines. Previously, the characterization of herbal chemicals from natural medicines often relied on the analysis of signature fragment ions from the acquired tandem mass spectrometry (MS/MS) spectra with prior knowledge of the herbal species present in the herbal prescriptions of interest. Nevertheless, such an approach is often limited to target components, and it risks missing the critical components that we have no prior knowledge of. We previously reported a "diagnostic ion-guided network bridging" strategy. It is a generally applicable and robust approach to analyze unknown substances from complex mixtures in an untargeted manner. In this study, we have developed a standalone software named "Nontargeted Diagnostic Ion Network Analysis (NINA)" with a graphical user interface based on a strategy for post-acquisition data analysis. NINA allows one to rapidly determine the nontargeted diagnostic ions (NIs) by summarizing all of the fragment ions shared by the precursors from the acquired MS/MS spectra. A NI-guided network using bridging components that possess two or more NIs can then be established via NINA. With such a network, we could sequentially identify the structures of all the NIs once a single compound has been identified de novo. The structures of NIs can then be used as "priori" knowledge to narrow the candidates containing the sub-structure of the corresponding NI from the database hits. Subsequently, we applied the NINA software to the characterization of a model herbal prescription, Re-Du-Ning injection, and rapidly identified 56 herbal chemicals from the prescription using an ultra-performance liquid chromatography quadrupole time-of-flight system in the negative mode with no knowledge of the herbal species or herbal chemicals in the mixture. Therefore, we believe the applications of NINA will greatly facilitate the characterization

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

An open source workflow for 3D printouts of scientific data volumes

Science.gov (United States)

Loewe, P.; Klump, J. F.; Wickert, J.; Ludwig, M.; Frigeri, A.

2013-12-01

As the amount of scientific data continues to grow, researchers need new tools to help them visualize complex data. Immersive data-visualisations are helpful, yet fail to provide tactile feedback and sensory feedback on spatial orientation, as provided from tangible objects. The gap in sensory feedback from virtual objects leads to the development of tangible representations of geospatial information to solve real world problems. Examples are animated globes [1], interactive environments like tangible GIS [2], and on demand 3D prints. The production of a tangible representation of a scientific data set is one step in a line of scientific thinking, leading from the physical world into scientific reasoning and back: The process starts with a physical observation, or from a data stream generated by an environmental sensor. This data stream is turned into a geo-referenced data set. This data is turned into a volume representation which is converted into command sequences for the printing device, leading to the creation of a 3D printout. As a last, but crucial step, this new object has to be documented and linked to the associated metadata, and curated in long term repositories to preserve its scientific meaning and context. The workflow to produce tangible 3D data-prints from science data at the German Research Centre for Geosciences (GFZ) was implemented as a software based on the Free and Open Source Geoinformatics tools GRASS GIS and Paraview. The workflow was successfully validated in various application scenarios at GFZ using a RapMan printer to create 3D specimens of elevation models, geological underground models, ice penetrating radar soundings for planetology, and space time stacks for Tsunami model quality assessment. While these first pilot applications have demonstrated the feasibility of the overall approach [3], current research focuses on the provision of the workflow as Software as a Service (SAAS), thematic generalisation of information content and

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....

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...

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.

Assessment of two different software solutions for the evaluation of CT colonography

International Nuclear Information System (INIS)

Andersen, K.; Blondin, D.; Moedder, U.; Cohnen, M.; Beck, A.; Aurich, V.; Vogt, C.

2005-01-01

Purpose: To compare a commercial CT colonography software ('Colonography', Siemens, Forchheim) with a non-commercial post-processing system ('Colotux', Department of Informatics). Material and methods: Identical data sets of 10 patients, who underwent an ultra-low-dose multi-detector CT colonography (ULD-MDCTC) (4 x 1 mm collimation, 8 mm pitch, 120 kVp, 10 mAs) were analyzed retrospectively. Assessment was performed using both software solutions by two resident radiologists, who did not have any experience with any colonography software tool before and who did not know the clinical symptoms of the patients or the results of the conventional colonoscopy. Both systems were analyzed using several subjective quality criteria including workflow, handling, image quality, endoluminal navigation and analysis of lesions with grading on a 5-point-scale. Results concerning polyps were compared between the two systems as well as with conventional colonoscopy. Results: Both colonography systems detected the same number of polyps. Although both showed some advantages for single criteria, no relevant difference was noted in general for subjective assessment. The time for calculation of three dimensional interactive volumes was three times longer for 'Colotux' compared to 'Colonography'. Linux-based 'Colotux' showed a trend towards better subjective image quality and easier measurement of polyp size. An intuitive desktop and 'Syngo'-workflow integration were advantages of 'Colonography'. Conclusion: The analysis of CT colonographies (4-detector-row-CT-scanner, ultra low dose technique, supine position) can adequately be achieved by both software solutions. There was no significant subjective or objective difference of quality between a 'stand-alone' individual system and a commerical workflow-integrated solution. A relevant factor for decision between the two systems may be the difference in time needed for the 3D volume calculation, especially in institutes with a high frequency

Selecting Advanced Software Technology in Two Small Manufacturing Enterprises

Science.gov (United States)

2004-05-01

improving workflow to further reduce delivery times, enhance customer service, and obtain a competitive advantage . The company wanted help... environment , stakeholders’ needs, ecommerce , shop floor visualization, and collaboration capability. These statements are not significantly different...for the purpose of describing a software environment . This identification does not imply any recommendation or endorsement by NIST, the SEI, CMU, or

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

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...

Resilient workflows for computational mechanics platforms

Science.gov (United States)

Nguyên, Toàn; Trifan, Laurentiu; Désidéri, Jean-Antoine

2010-06-01

Workflow management systems have recently been the focus of much interest and many research and deployment for scientific applications worldwide [26, 27]. Their ability to abstract the applications by wrapping application codes have also stressed the usefulness of such systems for multidiscipline applications [23, 24]. When complex applications need to provide seamless interfaces hiding the technicalities of the computing infrastructures, their high-level modeling, monitoring and execution functionalities help giving production teams seamless and effective facilities [25, 31, 33]. Software integration infrastructures based on programming paradigms such as Python, Mathlab and Scilab have also provided evidence of the usefulness of such approaches for the tight coupling of multidisciplne application codes [22, 24]. Also high-performance computing based on multi-core multi-cluster infrastructures open new opportunities for more accurate, more extensive and effective robust multi-discipline simulations for the decades to come [28]. This supports the goal of full flight dynamics simulation for 3D aircraft models within the next decade, opening the way to virtual flight-tests and certification of aircraft in the future [23, 24, 29].

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.

Usability and Workflow Evaluation of “RhEumAtic Disease Activity” (READY)

Science.gov (United States)

Yen, Po-Yin; Lara, Barbara; Lopetegui, Marcelo; Bharat, Aseem; Ardoin, Stacy; Johnson, Bernadette; Mathur, Puneet; Embi, Peter J.

2016-01-01

Summary Background RhEumAtic Disease activitY (READY) is a mobile health (mHealth) application that aims to create a shared platform integrating data from both patients and physicians, with a particular emphasis on arthritis disease activity. Methods We made READY available on an iPad and pilot implemented it at a rheumatology out-patient clinic. We conducted 1) a usability evaluation study to explore patients’ and physicians’ interactions with READY, and 2) a time motion study (TMS) to observe the clinical workflow before and after the implementation. Results A total of 33 patients and 15 physicians participated in the usability evaluation. We found usability problems in navigation, data entry, pain assessment, documentation, and instructions along with error messages. Despite these issues, 25 (75,76%) patients reported they liked READY. Physicians provided mixed feedback because they were concerned about the impact of READY on clinical workflow. Six physicians participated in the TMS. We observed 47 patient visits (44.72 hours) in the pre-implementation phase, and 42 patient visits (37.82 hours) in the post-implementation phase. We found that patients spent more time on READY than paper (4.39mins vs. 2.26mins), but overall, READY did not delay the workflow (pre = 52.08 mins vs. post = 45.46 mins). This time difference may be compensated with READY eliminating a workflow step for the staff. Conclusion Patients preferred READY to paper documents. Many found it easier to input information because of the larger font size and the ease of ‘tapping’ rather than writing-out or circling answers. Even though patients spent more time on READY than using paper documents, the longer usage of READY was mainly due to when troubleshooting was needed. Most patients did not have problems after receiving initial support from the staff. This study not only enabled improvements to the software but also serves as good reference for other researchers or institutional decision

Declarative Modelling and Safe Distribution of Healthcare Workflows

DEFF Research Database (Denmark)

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

2012-01-01

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

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.

Integration of PACS and HIS info the workflow of a nuclear medicine department. Experience in Regensburg

International Nuclear Information System (INIS)

Maenner, P.; Fuchs, E.; Marienhagen, J.; Schoenberger, J.; Eilles, C.; Tege, B.; Reicherzer, H.G.; Kurz, M.; Boerner, W.

2006-01-01

Aim: the development of new diagnostic techniques and the implementation of a modern quality control management system requires the continuous adaptation of existing data processing tools to the nuclear medicine diagnostic workflow. Furthermore, PACS connected to HIS facilitates and enhances the transfer of data and pictures, and satisfies the legal requirements for data retention as regulated by law. Therefore, the aim of this work is to present the architecture, structure and results of such a system newly installed in a department of nuclear medicine. Methods: initially, the nuclear medicine workflow was carefully analyzed and each step was correlated to the corresponding module. The standard SAP R/3 and IS-H / IS-H*med based software used for patient administration at the University of Regensburg Hospital was adapted to the needs of the Nuclear Medicine Department. The networking of the imaging systems was done by integration of a PACS. Finally, the PACS was connected to the HIS to allow the attachment of images to the medical report. Results, conclusion: by connecting the HIS to the nuclear medicine PACS, the workflow was significantly improved. The data management sequence starting at the reception desk, continuing through the nuclear medical examination, to the physician's final written and image report is clearly structured. Although high demands exist on technical support and administration the integration of PACS and HIS into the nuclear medicine workflow leads to enhanced efficiency and reduction in hospital costs. Patient and data management are considerably improved in this way. (orig.)

Custom software development for use in a clinical laboratory.

Science.gov (United States)

Sinard, John H; Gershkovich, Peter

2012-01-01

In-house software development for use in a clinical laboratory is a controversial issue. Many of the objections raised are based on outdated software development practices, an exaggeration of the risks involved, and an underestimation of the benefits that can be realized. Buy versus build analyses typically do not consider total costs of ownership, and unfortunately decisions are often made by people who are not directly affected by the workflow obstacles or benefits that result from those decisions. We have been developing custom software for clinical use for over a decade, and this article presents our perspective on this practice. A complete analysis of the decision to develop or purchase must ultimately examine how the end result will mesh with the departmental workflow, and custom-developed solutions typically can have the greater positive impact on efficiency and productivity, substantially altering the decision balance sheet. Involving the end-users in preparation of the functional specifications is crucial to the success of the process. A large development team is not needed, and even a single programmer can develop significant solutions. Many of the risks associated with custom development can be mitigated by a well-structured development process, use of open-source tools, and embracing an agile development philosophy. In-house solutions have the significant advantage of being adaptable to changing departmental needs, contributing to efficient and higher quality patient care.

SpaceWire Driver Software for Special DSPs

Science.gov (United States)

Clark, Douglas; Lux, James; Nishimoto, Kouji; Lang, Minh

2003-01-01

A computer program provides a high-level C-language interface to electronics circuitry that controls a SpaceWire interface in a system based on a space qualified version of the ADSP-21020 digital signal processor (DSP). SpaceWire is a spacecraft-oriented standard for packet-switching data-communication networks that comprise nodes connected through bidirectional digital serial links that utilize low-voltage differential signaling (LVDS). The software is tailored to the SMCS-332 application-specific integrated circuit (ASIC) (also available as the TSS901E), which provides three highspeed (150 Mbps) serial point-to-point links compliant with the proposed Institute of Electrical and Electronics Engineers (IEEE) Standard 1355.2 and equivalent European Space Agency (ESA) Standard ECSS-E-50-12. In the specific application of this software, the SpaceWire ASIC was combined with the DSP processor, memory, and control logic in a Multi-Chip Module DSP (MCM-DSP). The software is a collection of low-level driver routines that provide a simple message-passing application programming interface (API) for software running on the DSP. Routines are provided for interrupt-driven access to the two styles of interface provided by the SMCS: (1) the "word at a time" conventional host interface (HOCI); and (2) a higher performance "dual port memory" style interface (COMI).

LHCb: LHCbDirac is a DIRAC extension to support LHCb specific workflows

CERN Multimedia

Stagni, Federico

2012-01-01

We present LHCbDIRAC, an extension of the DIRAC community Grid solution to handle the LHCb specificities. The DIRAC software has been developed for many years within LHCb only. Nowadays it is a generic software, used by many scientific communities worldwide. Each community wanting to take advantage of DIRAC has to develop an extension, containing all the necessary code for handling their specific cases. LHCbDIRAC is an actively developed extension, implementing the LHCb computing model and workflows. LHCbDIRAC extends DIRAC to handle all the distributed computing activities of LHCb. Such activities include real data processing (reconstruction, stripping and streaming), Monte-Carlo simulation and data replication. Other activities are groups and user analysis, data management, resources management and monitoring, data provenance, accounting for user and production jobs. LHCbDIRAC also provides extensions of the DIRAC interfaces, including a secure web client, python APIs and CLIs. While DIRAC and LHCbDIRAC f...

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.

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

Science.gov (United States)

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

2017-01-01

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

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

Directory of Open Access Journals (Sweden)

Iván Tomás Cotes-Ruiz

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

A Workflow for Automated Satellite Image Processing: from Raw VHSR Data to Object-Based Spectral Information for Smallholder Agriculture

Directory of Open Access Journals (Sweden)

Dimitris Stratoulias

2017-10-01

Full Text Available Earth Observation has become a progressively important source of information for land use and land cover services over the past decades. At the same time, an increasing number of reconnaissance satellites have been set in orbit with ever increasing spatial, temporal, spectral, and radiometric resolutions. The available bulk of data, fostered by open access policies adopted by several agencies, is setting a new landscape in remote sensing in which timeliness and efficiency are important aspects of data processing. This study presents a fully automated workflow able to process a large collection of very high spatial resolution satellite images to produce actionable information in the application framework of smallholder farming. The workflow applies sequential image processing, extracts meaningful statistical information from agricultural parcels, and stores them in a crop spectrotemporal signature library. An important objective is to follow crop development through the season by analyzing multi-temporal and multi-sensor images. The workflow is based on free and open-source software, namely R, Python, Linux shell scripts, the Geospatial Data Abstraction Library, custom FORTRAN, C++, and the GNU Make utilities. We tested and applied this workflow on a multi-sensor image archive of over 270 VHSR WorldView-2, -3, QuickBird, GeoEye, and RapidEye images acquired over five different study areas where smallholder agriculture prevails.

Linear algebra applications using Matlab software

Directory of Open Access Journals (Sweden)

Cornelia Victoria Anghel

2005-10-01

Full Text Available The paper presents two ways of special matrix generating using some functions included in the MatLab software package. The MatLab software package contains a set of functions that generate special matrixes used in the linear algebra applications and the signal processing from different activity fields. The paper presents two tipes of special matrixes that can be generated using written sintaxes in the dialog window of the MatLab software and for the command validity we need to press the Enter task. The applications presented in the paper represent eamples of numerical calculus using the MatLab software and belong to the scientific field „Computer Assisted Mathematics” thus creating the symbiosis between mathematics and informatics.

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.

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.

ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry

Directory of Open Access Journals (Sweden)

Ramos Hector

2011-03-01

Full Text Available Abstract Background Since its inception, proteomics has essentially operated in a discovery mode with the goal of identifying and quantifying the maximal number of proteins in a sample. Increasingly, proteomic measurements are also supporting hypothesis-driven studies, in which a predetermined set of proteins is consistently detected and quantified in multiple samples. Selected reaction monitoring (SRM is a targeted mass spectrometric technique that supports the detection and quantification of specific proteins in complex samples at high sensitivity and reproducibility. Here, we describe ATAQS, an integrated software platform that supports all stages of targeted, SRM-based proteomics experiments including target selection, transition optimization and post acquisition data analysis. This software will significantly facilitate the use of targeted proteomic techniques and contribute to the generation of highly sensitive, reproducible and complete datasets that are particularly critical for the discovery and validation of targets in hypothesis-driven studies in systems biology. Result We introduce a new open source software pipeline, ATAQS (Automated and Targeted Analysis with Quantitative SRM, which consists of a number of modules that collectively support the SRM assay development workflow for targeted proteomic experiments (project management and generation of protein, peptide and transitions and the validation of peptide detection by SRM. ATAQS provides a flexible pipeline for end-users by allowing the workflow to start or end at any point of the pipeline, and for computational biologists, by enabling the easy extension of java algorithm classes for their own algorithm plug-in or connection via an external web site. This integrated system supports all steps in a SRM-based experiment and provides a user-friendly GUI that can be run by any operating system that allows the installation of the Mozilla Firefox web browser. Conclusions Targeted

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.

ICSSP 2015–Special Issue Introduction

DEFF Research Database (Denmark)

Pfahl, Dietmar; Kuhrmann, Marco; Bendraou, Reda

2016-01-01

Introduction to the Special Issue of the International Conference on Software and System Process......Introduction to the Special Issue of the International Conference on Software and System Process...

The use of Graphic User Interface for development of a user-friendly CRS-Stack software

Science.gov (United States)

Sule, Rachmat; Prayudhatama, Dythia; Perkasa, Muhammad D.; Hendriyana, Andri; Fatkhan; Sardjito; Adriansyah

2017-04-01

The development of a user-friendly Common Reflection Surface (CRS) Stack software that has been built by implementing Graphical User Interface (GUI) is described in this paper. The original CRS-Stack software developed by WIT Consortium is compiled in the unix/linux environment, which is not a user-friendly software, so that a user must write the commands and parameters manually in a script file. Due to this limitation, the CRS-Stack become a non popular method, although applying this method is actually a promising way in order to obtain better seismic sections, which have better reflector continuity and S/N ratio. After obtaining successful results that have been tested by using several seismic data belong to oil companies in Indonesia, it comes to an idea to develop a user-friendly software in our own laboratory. Graphical User Interface (GUI) is a type of user interface that allows people to interact with computer programs in a better way. Rather than typing commands and module parameters, GUI allows the users to use computer programs in much simple and easy. Thus, GUI can transform the text-based interface into graphical icons and visual indicators. The use of complicated seismic unix shell script can be avoided. The Java Swing GUI library is used to develop this CRS-Stack GUI. Every shell script that represents each seismic process is invoked from Java environment. Besides developing interactive GUI to perform CRS-Stack processing, this CRS-Stack GUI is design to help geophysicists to manage a project with complex seismic processing procedures. The CRS-Stack GUI software is composed by input directory, operators, and output directory, which are defined as a seismic data processing workflow. The CRS-Stack processing workflow involves four steps; i.e. automatic CMP stack, initial CRS-Stack, optimized CRS-Stack, and CRS-Stack Supergather. Those operations are visualized in an informative flowchart with self explanatory system to guide the user inputting the

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

Using CyberShake Workflows to Manage Big Seismic Hazard Data on Large-Scale Open-Science HPC Resources

Science.gov (United States)

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

2015-12-01

The CyberShake computational platform, developed by the Southern California Earthquake Center (SCEC), is an integrated collection of scientific software and middleware that performs 3D physics-based probabilistic seismic hazard analysis (PSHA) for Southern California. CyberShake integrates large-scale and high-throughput research codes to produce probabilistic seismic hazard curves for individual locations of interest and hazard maps for an entire region. A recent CyberShake calculation produced about 500,000 two-component seismograms for each of 336 locations, resulting in over 300 million synthetic seismograms in a Los Angeles-area probabilistic seismic hazard model. CyberShake calculations require a series of scientific software programs. Early computational stages produce data used as inputs by later stages, so we describe CyberShake calculations using a workflow definition language. Scientific workflow tools automate and manage the input and output data and enable remote job execution on large-scale HPC systems. To satisfy the requests of broad impact users of CyberShake data, such as seismologists, utility companies, and building code engineers, we successfully completed CyberShake Study 15.4 in April and May 2015, calculating a 1 Hz urban seismic hazard map for Los Angeles. We distributed the calculation between the NSF Track 1 system NCSA Blue Waters, the DOE Leadership-class system OLCF Titan, and USC's Center for High Performance Computing. This study ran for over 5 weeks, burning about 1.1 million node-hours and producing over half a petabyte of data. The CyberShake Study 15.4 results doubled the maximum simulated seismic frequency from 0.5 Hz to 1.0 Hz as compared to previous studies, representing a factor of 16 increase in computational complexity. We will describe how our workflow tools supported splitting the calculation across multiple systems. We will explain how we modified CyberShake software components, including GPU implementations and

Monitoring of Computing Resource Use of Active Software Releases in ATLAS

CERN Document Server

Limosani, Antonio; The ATLAS collaboration

2016-01-01

The LHC is the world's most powerful particle accelerator, colliding protons at centre of mass energy of 13 TeV. As the energy and frequency of collisions has grown in the search for new physics, so too has demand for computing resources needed for event reconstruction. We will report on the evolution of resource usage in terms of CPU and RAM in key ATLAS offline reconstruction workflows at the Tier0 at CERN and on the WLCG. Monitoring of workflows is achieved using the ATLAS PerfMon package, which is the standard ATLAS performance monitoring system running inside Athena jobs. Systematic daily monitoring has recently been expanded to include all workflows beginning at Monte Carlo generation through to end user physics analysis, beyond that of event reconstruction. Moreover, the move to a multiprocessor mode in production jobs has facilitated the use of tools, such as "MemoryMonitor", to measure the memory shared across processors in jobs. Resource consumption is broken down into software domains and displayed...

Research and practice of application software verification and validation for nuclear safety digital I and C system

International Nuclear Information System (INIS)

Dong Yaxin; Xu Xianzhu; Bai Xiangji

2014-01-01

Application software V and V activities determine whether the output results are consistent with the requirements of tasks throughout each stage of application software development process, and confirm whether the ultimately generated application software is conform to its intended use and other related requirements. A set of reasonable and feasible workflow for application software V and V activities was proposed based on the characteristics of the application software in this paper, and was demonstrated with the application software V and V activities in transformation project of in-core instrumentation system (RIC) in a nuclear power plant. (authors)

CO2 Storage Feasibility: A Workflow for Site Characterisation

Directory of Open Access Journals (Sweden)

Nepveu Manuel

2015-04-01

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

Reasoning about repairability of workflows at design time

NARCIS (Netherlands)

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

2009-01-01

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

Distributed Global Transaction Support for Workflow Management Applications

NARCIS (Netherlands)

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

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

XML schemas for common bioinformatic data types and their application in workflow systems.

Science.gov (United States)

Seibel, Philipp N; Krüger, Jan; Hartmeier, Sven; Schwarzer, Knut; Löwenthal, Kai; Mersch, Henning; Dandekar, Thomas; Giegerich, Robert

2006-11-06

Today, there is a growing need in bioinformatics to combine available software tools into chains, thus building complex applications from existing single-task tools. To create such workflows, the tools involved have to be able to work with each other's data--therefore, a common set of well-defined data formats is needed. Unfortunately, current bioinformatic tools use a great variety of heterogeneous formats. Acknowledging the need for common formats, the Helmholtz Open BioInformatics Technology network (HOBIT) identified several basic data types used in bioinformatics and developed appropriate format descriptions, formally defined by XML schemas, and incorporated them in a Java library (BioDOM). These schemas currently cover sequence, sequence alignment, RNA secondary structure and RNA secondary structure alignment formats in a form that is independent of any specific program, thus enabling seamless interoperation of different tools. All XML formats are available at http://bioschemas.sourceforge.net, the BioDOM library can be obtained at http://biodom.sourceforge.net. The HOBIT XML schemas and the BioDOM library simplify adding XML support to newly created and existing bioinformatic tools, enabling these tools to interoperate seamlessly in workflow scenarios.

XML schemas for common bioinformatic data types and their application in workflow systems

Science.gov (United States)

Seibel, Philipp N; Krüger, Jan; Hartmeier, Sven; Schwarzer, Knut; Löwenthal, Kai; Mersch, Henning; Dandekar, Thomas; Giegerich, Robert

2006-01-01

Background Today, there is a growing need in bioinformatics to combine available software tools into chains, thus building complex applications from existing single-task tools. To create such workflows, the tools involved have to be able to work with each other's data – therefore, a common set of well-defined data formats is needed. Unfortunately, current bioinformatic tools use a great variety of heterogeneous formats. Results Acknowledging the need for common formats, the Helmholtz Open BioInformatics Technology network (HOBIT) identified several basic data types used in bioinformatics and developed appropriate format descriptions, formally defined by XML schemas, and incorporated them in a Java library (BioDOM). These schemas currently cover sequence, sequence alignment, RNA secondary structure and RNA secondary structure alignment formats in a form that is independent of any specific program, thus enabling seamless interoperation of different tools. All XML formats are available at , the BioDOM library can be obtained at . Conclusion The HOBIT XML schemas and the BioDOM library simplify adding XML support to newly created and existing bioinformatic tools, enabling these tools to interoperate seamlessly in workflow scenarios. PMID:17087823

Schedule-Aware Workflow Management Systems

Science.gov (United States)

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

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

Building and documenting workflows with python-based snakemake

NARCIS (Netherlands)

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

2012-01-01

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

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.

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.

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.

Sustaining an Online, Shared Community Resource for Models, Robust Open source Software Tools and Data for Volcanology - the Vhub Experience

Science.gov (United States)

Patra, A. K.; Valentine, G. A.; Bursik, M. I.; Connor, C.; Connor, L.; Jones, M.; Simakov, N.; Aghakhani, H.; Jones-Ivey, R.; Kosar, T.; Zhang, B.

2015-12-01

Over the last 5 years we have created a community collaboratory Vhub.org [Palma et al, J. App. Volc. 3:2 doi:10.1186/2191-5040-3-2] as a place to find volcanology-related resources, and a venue for users to disseminate tools, teaching resources, data, and an online platform to support collaborative efforts. As the community (current active users > 6000 from an estimated community of comparable size) embeds the tools in the collaboratory into educational and research workflows it became imperative to: a) redesign tools into robust, open source reusable software for online and offline usage/enhancement; b) share large datasets with remote collaborators and other users seamlessly with security; c) support complex workflows for uncertainty analysis, validation and verification and data assimilation with large data. The focus on tool development/redevelopment has been twofold - firstly to use best practices in software engineering and new hardware like multi-core and graphic processing units. Secondly we wish to enhance capabilities to support inverse modeling, uncertainty quantification using large ensembles and design of experiments, calibration, validation. Among software engineering practices we practice are open source facilitating community contributions, modularity and reusability. Our initial targets are four popular tools on Vhub - TITAN2D, TEPHRA2, PUFF and LAVA. Use of tools like these requires many observation driven data sets e.g. digital elevation models of topography, satellite imagery, field observations on deposits etc. These data are often maintained in private repositories that are privately shared by "sneaker-net". As a partial solution to this we tested mechanisms using irods software for online sharing of private data with public metadata and access limits. Finally, we adapted use of workflow engines (e.g. Pegasus) to support the complex data and computing workflows needed for usage like uncertainty quantification for hazard analysis using physical

Text mining meets workflow: linking U-Compare with Taverna

Science.gov (United States)

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

2010-01-01

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

Distributed execution of aggregated multi domain workflows using an agent framework

NARCIS (Netherlands)

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

2007-01-01

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

Integrating prediction, provenance, and optimization into high energy workflows

Energy Technology Data Exchange (ETDEWEB)

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

2017-10-01

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

The P2P approach to interorganizational workflows

NARCIS (Netherlands)

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

2001-01-01

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

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

Security aspects in teleradiology workflow

Science.gov (United States)

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

2000-05-01

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

Verification of Timed Healthcare Workflows Using Component Timed-Arc Petri Nets

DEFF Research Database (Denmark)

Bertolini, Cristiano; Liu, Zhiming; Srba, Jiri

2013-01-01

Workflows in modern healthcare systems are becoming increasingly complex and their execution involves concurrency and sharing of resources. The definition, analysis and management of collaborative healthcare workflows requires abstract model notations with a precisely defined semantics and a supp......Workflows in modern healthcare systems are becoming increasingly complex and their execution involves concurrency and sharing of resources. The definition, analysis and management of collaborative healthcare workflows requires abstract model notations with a precisely defined semantics...

The ATLAS Data Management Software Engineering Process

CERN Document Server

Lassnig, M; The ATLAS collaboration; Stewart, G A; Barisits, M; Beermann, T; Vigne, R; Serfon, C; Goossens, L; Nairz, A; Molfetas, A

2014-01-01

Rucio is the next-generation data management system of the ATLAS experiment. The software engineering process to develop Rucio is fundamentally different to existing software development approaches in the ATLAS distributed computing community. Based on a conceptual design document, development takes place using peer-reviewed code in a test-driven environment. The main objectives are to ensure that every engineer understands the details of the full project, even components usually not touched by them, that the design and architecture are coherent, that temporary contributors can be productive without delay, that programming mistakes are prevented before being committed to the source code, and that the source is always in a fully functioning state. This contribution will illustrate the workflows and products used, and demonstrate the typical development cycle of a component from inception to deployment within this software engineering process. Next to the technological advantages, this contribution will also hi...

The ATLAS Data Management Software Engineering Process

CERN Document Server

Lassnig, M; The ATLAS collaboration; Stewart, G A; Barisits, M; Beermann, T; Vigne, R; Serfon, C; Goossens, L; Nairz, A

2013-01-01

Rucio is the next-generation data management system of the ATLAS experiment. The software engineering process to develop Rucio is fundamentally different to existing software development approaches in the ATLAS distributed computing community. Based on a conceptual design document, development takes place using peer-reviewed code in a test-driven environment. The main objectives are to ensure that every engineer understands the details of the full project, even components usually not touched by them, that the design and architecture are coherent, that temporary contributors can be productive without delay, that programming mistakes are prevented before being committed to the source code, and that the source is always in a fully functioning state. This contribution will illustrate the workflows and products used, and demonstrate the typical development cycle of a component from inception to deployment within this software engineering process. Next to the technological advantages, this contribution will also hi...

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.

Software Productivity of Field Experiments Using the Mobile Agents Open Architecture with Workflow Interoperability

Science.gov (United States)

Clancey, William J.; Lowry, Michael R.; Nado, Robert Allen; Sierhuis, Maarten

2011-01-01

We analyzed a series of ten systematically developed surface exploration systems that integrated a variety of hardware and software components. Design, development, and testing data suggest that incremental buildup of an exploration system for long-duration capabilities is facilitated by an open architecture with appropriate-level APIs, specifically designed to facilitate integration of new components. This improves software productivity by reducing changes required for reconfiguring an existing system.

A workflow to process 3D+time microscopy images of developing organisms and reconstruct their cell lineage

Science.gov (United States)

Faure, Emmanuel; Savy, Thierry; Rizzi, Barbara; Melani, Camilo; Stašová, Olga; Fabrèges, Dimitri; Špir, Róbert; Hammons, Mark; Čúnderlík, Róbert; Recher, Gaëlle; Lombardot, Benoît; Duloquin, Louise; Colin, Ingrid; Kollár, Jozef; Desnoulez, Sophie; Affaticati, Pierre; Maury, Benoît; Boyreau, Adeline; Nief, Jean-Yves; Calvat, Pascal; Vernier, Philippe; Frain, Monique; Lutfalla, Georges; Kergosien, Yannick; Suret, Pierre; Remešíková, Mariana; Doursat, René; Sarti, Alessandro; Mikula, Karol; Peyriéras, Nadine; Bourgine, Paul

2016-01-01

The quantitative and systematic analysis of embryonic cell dynamics from in vivo 3D+time image data sets is a major challenge at the forefront of developmental biology. Despite recent breakthroughs in the microscopy imaging of living systems, producing an accurate cell lineage tree for any developing organism remains a difficult task. We present here the BioEmergences workflow integrating all reconstruction steps from image acquisition and processing to the interactive visualization of reconstructed data. Original mathematical methods and algorithms underlie image filtering, nucleus centre detection, nucleus and membrane segmentation, and cell tracking. They are demonstrated on zebrafish, ascidian and sea urchin embryos with stained nuclei and membranes. Subsequent validation and annotations are carried out using Mov-IT, a custom-made graphical interface. Compared with eight other software tools, our workflow achieved the best lineage score. Delivered in standalone or web service mode, BioEmergences and Mov-IT offer a unique set of tools for in silico experimental embryology. PMID:26912388

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.

The Five 'R's' for Developing Trusted Software Frameworks to increase confidence in, and maximise reuse of, Open Source Software.

Science.gov (United States)

Fraser, Ryan; Gross, Lutz; Wyborn, Lesley; Evans, Ben; Klump, Jens

2015-04-01

benchmark cases. This will be achieved by linking the code in the software framework to peer review forums such as Mozilla Science or appropriate Journals (e.g. Geoscientific Model Development Journal) to assist users to know which codes to trust. 3) Referencing will be accomplished by linking the Software Framework to groups such as Figshare or ImpactStory that help disseminate and measure the impact of scientific research, including program code. 4) The Run component will draw on information supplied in the registration process, benchmark cases described in the review and relevant information to instantiate the scientific code on the selected environment. 5) The Repeat component will tap into existing Provenance Workflow engines that will automatically capture information that relate to a particular run of that software, including identification of all input and output artefacts, and all elements and transactions within that workflow. The proposed trusted software framework will enable users to rapidly discover and access reliable code, reduce the time to deploy it and greatly facilitate sharing, reuse and reinstallation of code. Properly designed it could enable an ability to scale out to massively parallel systems and be accessed nationally/ internationally for multiple use cases, including Supercomputer centres, cloud facilities, and local computers.

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...

Coupled RipCAS-DFLOW (CoRD) Software and Data Management System for Reproducible Floodplain Vegetation Succession Modeling

Science.gov (United States)

Turner, M. A.; Miller, S.; Gregory, A.; Cadol, D. D.; Stone, M. C.; Sheneman, L.

2016-12-01

We present the Coupled RipCAS-DFLOW (CoRD) modeling system created to encapsulate the workflow to analyze the effects of stream flooding on vegetation succession. CoRD provides an intuitive command-line and web interface to run DFLOW and RipCAS in succession over many years automatically, which is a challenge because, for our application, DFLOW must be run on a supercomputing cluster via the PBS job scheduler. RipCAS is a vegetation succession model, and DFLOW is a 2D open channel flow model. Data adaptors have been developed to seamlessly connect DFLOW output data to be RipCAS inputs, and vice-versa. CoRD provides automated statistical analysis and visualization, plus automatic syncing of input and output files and model run metadata to the hydrological data management system HydroShare using its excellent Python REST client. This combination of technologies and data management techniques allows the results to be shared with collaborators and eventually published. Perhaps most importantly, it allows results to be easily reproduced via either the command-line or web user interface. This system is a result of collaboration between software developers and hydrologists participating in the Western Consortium for Watershed Analysis, Visualization, and Exploration (WC-WAVE). Because of the computing-intensive nature of this particular workflow, including automating job submission/monitoring and data adaptors, software engineering expertise is required. However, the hydrologists provide the software developers with a purpose and ensure a useful, intuitive tool is developed. Our hydrologists contribute software, too: RipCAS was developed from scratch by hydrologists on the team as a specialized, open-source version of the Computer Aided Simulation Model for Instream Flow and Riparia (CASiMiR) vegetation model; our hydrologists running DFLOW provided numerous examples and help with the supercomputing system. This project is written in Python, a popular language in the

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.

Free software and free culture in Higher Education: pipelines and workflows for creative purposes

OpenAIRE

Gonçalves, Nelson; Figueiredo, Maria Pacheco

2015-01-01

OpenLab ESEV is a project of the School of Education of the Polytechnic Institute of Viseu (ESEV), Portugal, that aims to promote, foster and support the use of Free/Libre Software and Open Source Software, Open Educational Resources, Free Culture, Free file formats and more flexible copyright licenses for creative and educational purposes in the ESEV's domains of activity (education, arts, media). Most of the OpenLab ESEV activities are related to the teacher education and arts a...

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.

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.

Build and Execute Environment

Energy Technology Data Exchange (ETDEWEB)

2017-04-21

workflows for repeatable and partial re-execution. We will coordinate the physical snapshots of virtual machines with parallel programming constructs, such as barriers, to automate checkpoint and restart. We will also integrate with HPC-specific container runtimes to gain access to accelerators and other specialized hardware to preserve native performance. Containers will link development to continuous integration. When application developers check code in, it will automatically be tested on a suite of different software and hardware architectures.

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

Science.gov (United States)

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

2014-08-01

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

Text mining for the biocuration workflow.

Science.gov (United States)

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

2012-01-01

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

Workflow management: an overview

NARCIS (Netherlands)

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

2010-01-01

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

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.

Digital Workflows for Restoration and Management of the Museum Affandi - a Case Study in Challenging Circumstances

Science.gov (United States)

Herbig, U.; Styhler-Aydın, G.; Grandits, D.; Stampfer, L.; Pont, U.; Mayer, I.

2017-08-01

The appropriate restoration of architectural heritage needs a careful and comprehensive documentation of the existing structures, which even elaborates, if the function of the building needs special attention, like in museums. In a collaborative project between the Universitas Gadjah Mada, Yogyakarta, Indonesia and two universities in Austria (TU Wien and the Danube University Krems) a restoration and adaptation concept of the Affandi Museum in Yogyakarta is currently in progress. It provides a perfect case study for the development of a workflow to combine data from a building survey, architectural research, indoor climate measurements and the documentation of artwork in a challenging environment, from hot and humid tropical climate to continuous threads by natural hazards like earthquakes or volcanic eruptions. The Affandi Museum houses the collection of Affandi, who is considered to be Indonesia's foremost Expressionist painter and partly designed and constructed the museum by himself. With the spirit of the artist still perceptible in the complex the Affandi Museum is an important part of the Indonesian cultural heritage. Thus its preservation takes special attention and adds to the complexity of the development of a monitoring and maintenance concept. This paper describes the ongoing development of an approach to a workflow from the measurement and research of the objects, both architectural and artwork, to the semantically enriched BIM Model as the base for a sustainable monitoring tool for the Affandi Museum.

Concerning the problem of polygraphic wire calculation: theoretical aspects, software, practical implementation

Directory of Open Access Journals (Sweden)

Selkina A. V.

2016-05-01

Full Text Available the article analyzes the problems arising while organizing the workflow in printing companies. We suggest to address these problems by means of implementing computer-based accounting systems. Online and offline calculators used by printing enterprises for accounting are discussed. The author outlined the functional and specified requirements to such software. They were considered in the calculation module of accounting polygraphic wire used for block bonding. The software allows to increase the calculation process speed, to reduce the amount of errors in calculation and to decrease the labour intensity of the accounting process.

Computer software.

Science.gov (United States)

Rosenthal, L E

1986-10-01

Software is the component in a computer system that permits the hardware to perform the various functions that a computer system is capable of doing. The history of software and its development can be traced to the early nineteenth century. All computer systems are designed to utilize the "stored program concept" as first developed by Charles Babbage in the 1850s. The concept was lost until the mid-1940s, when modern computers made their appearance. Today, because of the complex and myriad tasks that a computer system can perform, there has been a differentiation of types of software. There is software designed to perform specific business applications. There is software that controls the overall operation of a computer system. And there is software that is designed to carry out specialized tasks. Regardless of types, software is the most critical component of any computer system. Without it, all one has is a collection of circuits, transistors, and silicone chips.

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.

A recommended workflow methodology in the creation of an educational and training application incorporating a digital reconstruction of the cerebral ventricular system and cerebrospinal fluid circulation to aid anatomical understanding.

Science.gov (United States)

Manson, Amy; Poyade, Matthieu; Rea, Paul

2015-10-19

The use of computer-aided learning in education can be advantageous, especially when interactive three-dimensional (3D) models are used to aid learning of complex 3D structures. The anatomy of the ventricular system of the brain is difficult to fully understand as it is seldom seen in 3D, as is the flow of cerebrospinal fluid (CSF). This article outlines a workflow for the creation of an interactive training tool for the cerebral ventricular system, an educationally challenging area of anatomy. This outline is based on the use of widely available computer software packages. Using MR images of the cerebral ventricular system and several widely available commercial and free software packages, the techniques of 3D modelling, texturing, sculpting, image editing and animations were combined to create a workflow in the creation of an interactive educational and training tool. This was focussed on cerebral ventricular system anatomy, and the flow of cerebrospinal fluid. We have successfully created a robust methodology by using key software packages in the creation of an interactive education and training tool. This has resulted in an application being developed which details the anatomy of the ventricular system, and flow of cerebrospinal fluid using an anatomically accurate 3D model. In addition to this, our established workflow pattern presented here also shows how tutorials, animations and self-assessment tools can also be embedded into the training application. Through our creation of an established workflow in the generation of educational and training material for demonstrating cerebral ventricular anatomy and flow of cerebrospinal fluid, it has enormous potential to be adopted into student training in this field. With the digital age advancing rapidly, this has the potential to be used as an innovative tool alongside other methodologies for the training of future healthcare practitioners and scientists. This workflow could be used in the creation of other tools

The ATLAS data management software engineering process

International Nuclear Information System (INIS)

Lassnig, M; Garonne, V; Stewart, G A; Barisits, M; Serfon, C; Goossens, L; Nairz, A; Beermann, T; Vigne, R; Molfetas, A

2014-01-01

Rucio is the next-generation data management system of the ATLAS experiment. The software engineering process to develop Rucio is fundamentally different to existing software development approaches in the ATLAS distributed computing community. Based on a conceptual design document, development takes place using peer-reviewed code in a test-driven environment. The main objectives are to ensure that every engineer understands the details of the full project, even components usually not touched by them, that the design and architecture are coherent, that temporary contributors can be productive without delay, that programming mistakes are prevented before being committed to the source code, and that the source is always in a fully functioning state. This contribution will illustrate the workflows and products used, and demonstrate the typical development cycle of a component from inception to deployment within this software engineering process. Next to the technological advantages, this contribution will also highlight the social aspects of an environment where every action is subject to detailed scrutiny.

The ATLAS data management software engineering process

Science.gov (United States)

Lassnig, M.; Garonne, V.; Stewart, G. A.; Barisits, M.; Beermann, T.; Vigne, R.; Serfon, C.; Goossens, L.; Nairz, A.; Molfetas, A.; Atlas Collaboration

2014-06-01

Rucio is the next-generation data management system of the ATLAS experiment. The software engineering process to develop Rucio is fundamentally different to existing software development approaches in the ATLAS distributed computing community. Based on a conceptual design document, development takes place using peer-reviewed code in a test-driven environment. The main objectives are to ensure that every engineer understands the details of the full project, even components usually not touched by them, that the design and architecture are coherent, that temporary contributors can be productive without delay, that programming mistakes are prevented before being committed to the source code, and that the source is always in a fully functioning state. This contribution will illustrate the workflows and products used, and demonstrate the typical development cycle of a component from inception to deployment within this software engineering process. Next to the technological advantages, this contribution will also highlight the social aspects of an environment where every action is subject to detailed scrutiny.

Inverse IMRT workflow process at Austin health

International Nuclear Information System (INIS)

Rykers, K.; Fernando, W.; Grace, M.; Liu, G.; Rolfo, A.; Viotto, A.; Mantle, C.; Lawlor, M.; Au-Yeung, D.; Quong, G.; Feigen, M.; Lim-Joon, D.; Wada, M.

2004-01-01

Full text: The work presented here will review the strategies adopted at Austin Health to bring IMRT into clinical use. IMRT is delivered using step and shoot mode on an Elekta Precise machine with 40 pairs of 1cm wide MLC leaves. Planning is done using CMS Focus/XiO. A collaborative approach for RO's, Physicists and RTs from concept to implementation was adopted. An overview will be given of the workflow for the clinic, the equipment used, tolerance levels and the lessons learned. 1. Strategic Planning for IMRT 2. Training a. MSKCC (New York) b.ESTRO (Amsterdam) c.Elekta (US and UK) 3. Linac testing and data acquisition a. Equipment and software review and selection b. Linac reliability/geometric and mechanical checks c. Draft Patient QA procedure d. EPI Image matching checks and procedures 4. Planning system checks a. export of dose matrix (options) b. dose calculation choices 5. IMRT Research Initiatives a. IMRT Planning Studies, Stabilisation, On-line Imaging 6. Equipment Procurement and testing a. Physics and Linac Equipment, Hardware, Software/Licences, Stabilisation 7. Establishing a DICOM Environment a. Prescription sending, Image transfer for EPI checks b. QA Files 8. Physics QA (Pre-Treatment) a.Clinical plan review; DVH checks b. geometry; dosimetry checks; DICOM checks c. 2D Distance to agreement; mm difference reports; Gamma function index 9. Documentation a.Protocol Development i. ICRU 50/62 reporting and prescribing b. QA for Physics c. QA for RT's d. Generation of a report for RO/patient history. Copyright (2004) Australasian College of Physical Scientists and Engineers in Medicine

A history-tracing XML-based provenance framework for workflows

NARCIS (Netherlands)

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

2010-01-01

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

Conceptual framework and architecture for service mediating workflow management

NARCIS (Netherlands)

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

2003-01-01

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

Monitoring of computing resource use of active software releases at ATLAS

CERN Document Server

AUTHOR|(INSPIRE)INSPIRE-00219183; The ATLAS collaboration

2017-01-01

The LHC is the world’s most powerful particle accelerator, colliding protons at centre of mass energy of 13 TeV. As the energy and frequency of collisions has grown in the search for new physics, so too has demand for computing resources needed for event reconstruction. We will report on the evolution of resource usage in terms of CPU and RAM in key ATLAS offline reconstruction workflows at the TierO at CERN and on the WLCG. Monitoring of workflows is achieved using the ATLAS PerfMon package, which is the standard ATLAS performance monitoring system running inside Athena jobs. Systematic daily monitoring has recently been expanded to include all workflows beginning at Monte Carlo generation through to end-user physics analysis, beyond that of event reconstruction. Moreover, the move to a multiprocessor mode in production jobs has facilitated the use of tools, such as “MemoryMonitor”, to measure the memory shared across processors in jobs. Resource consumption is broken down into software domains and dis...

Planning, Coordinating, and Managing Off-Site Storage is an Area of Increasing, Professional Responsibility for Special Collections Departments

Directory of Open Access Journals (Sweden)

Melissa Goertzen

2016-03-01

Full Text Available Objective – To measure the use of off-site storage for special collections materials and to examine how this use impacts core special collections activities. Design – Survey questionnaire containing both structured and open ended questions. Follow-up interviews were also conducted. Setting – Association of Research Libraries (ARL member institutions in the United States of America. Subjects – 108 directors of special collections. Methods – Participants were recruited via email; contact information was compiled through professional directories, web searches, and referrals from professionals at ARL member libraries. The survey was sent out on October 31, 2013, and two reminder emails were distributed before it closed three weeks later. The survey was created and distributed using Qualtrics, a research software that supports online data collection and analysis. All results were analyzed using Microsoft Excel and Qualtrics. Main Results – The final response rate was 58% (63 out of 108. The majority (51 participants, or 81% reported use of off-site storage for library collections. Of this group, 91% (47 out of 51 house a variety of special collections in off-site storage. The criteria most frequently utilized to designate these materials to off-site storage are use (87%, size (66%, format (60%, and value (57%. The authors found that special collections directors are most likely to send materials to off-site storage facilities that are established and in use by other departments at their home institution; access to established workflows, especially those linked to transit and delivery, and space for expanding collections are benefits. In regard to core special collections activities, results indicated that public service was most impacted by off-site storage. The authors discussed challenges related to patron use and satisfaction. In regard to management and processing, directors faced challenges using the same level of staff to maintain

Exploring Dental Providers’ Workflow in an Electronic Dental Record Environment

Science.gov (United States)

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

2016-01-01

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

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

International Nuclear Information System (INIS)

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

2010-01-01

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

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

Science.gov (United States)

Plale, B.

2009-05-01

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

Patterns for Parallel Software Design

CERN Document Server

Ortega-Arjona, Jorge Luis

2010-01-01

Essential reading to understand patterns for parallel programming Software patterns have revolutionized the way we think about how software is designed, built, and documented, and the design of parallel software requires you to consider other particular design aspects and special skills. From clusters to supercomputers, success heavily depends on the design skills of software developers. Patterns for Parallel Software Design presents a pattern-oriented software architecture approach to parallel software design. This approach is not a design method in the classic sense, but a new way of managin

Halden project activities on software dependability

International Nuclear Information System (INIS)

Dahll, G.; Sivertsen.

1994-01-01

Since 1977, the OECD Halden Reactor Project has been working in the field of software dependability. Special emphasis has been put on the use of software in safety critical systems. All phases in software development, from specification through software development, verification, and validation have been covered and are discussed in this article

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

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.

PlantRNA_Sniffer: A SVM-Based Workflow to Predict Long Intergenic Non-Coding RNAs in Plants.

Science.gov (United States)

Vieira, Lucas Maciel; Grativol, Clicia; Thiebaut, Flavia; Carvalho, Thais G; Hardoim, Pablo R; Hemerly, Adriana; Lifschitz, Sergio; Ferreira, Paulo Cavalcanti Gomes; Walter, Maria Emilia M T

2017-03-04

Non-coding RNAs (ncRNAs) constitute an important set of transcripts produced in the cells of organisms. Among them, there is a large amount of a particular class of long ncRNAs that are difficult to predict, the so-called long intergenic ncRNAs (lincRNAs), which might play essential roles in gene regulation and other cellular processes. Despite the importance of these lincRNAs, there is still a lack of biological knowledge and, currently, the few computational methods considered are so specific that they cannot be successfully applied to other species different from those that they have been originally designed to. Prediction of lncRNAs have been performed with machine learning techniques. Particularly, for lincRNA prediction, supervised learning methods have been explored in recent literature. As far as we know, there are no methods nor workflows specially designed to predict lincRNAs in plants. In this context, this work proposes a workflow to predict lincRNAs on plants, considering a workflow that includes known bioinformatics tools together with machine learning techniques, here a support vector machine (SVM). We discuss two case studies that allowed to identify novel lincRNAs, in sugarcane ( Saccharum spp.) and in maize ( Zea mays ). From the results, we also could identify differentially-expressed lincRNAs in sugarcane and maize plants submitted to pathogenic and beneficial microorganisms.

PlantRNA_Sniffer: A SVM-Based Workflow to Predict Long Intergenic Non-Coding RNAs in Plants

Directory of Open Access Journals (Sweden)

Lucas Maciel Vieira

2017-03-01

Full Text Available Non-coding RNAs (ncRNAs constitute an important set of transcripts produced in the cells of organisms. Among them, there is a large amount of a particular class of long ncRNAs that are difficult to predict, the so-called long intergenic ncRNAs (lincRNAs, which might play essential roles in gene regulation and other cellular processes. Despite the importance of these lincRNAs, there is still a lack of biological knowledge and, currently, the few computational methods considered are so specific that they cannot be successfully applied to other species different from those that they have been originally designed to. Prediction of lncRNAs have been performed with machine learning techniques. Particularly, for lincRNA prediction, supervised learning methods have been explored in recent literature. As far as we know, there are no methods nor workflows specially designed to predict lincRNAs in plants. In this context, this work proposes a workflow to predict lincRNAs on plants, considering a workflow that includes known bioinformatics tools together with machine learning techniques, here a support vector machine (SVM. We discuss two case studies that allowed to identify novel lincRNAs, in sugarcane (Saccharum spp. and in maize (Zea mays. From the results, we also could identify differentially-expressed lincRNAs in sugarcane and maize plants submitted to pathogenic and beneficial microorganisms.

On Secure Workflow Decentralisation on the Internet

Directory of Open Access Journals (Sweden)

Petteri Kaskenpalo

2010-06-01

Full Text Available Decentralised workflow management systems are a new research area, where most work to-date has focused on the system's overall architecture. As little attention has been given to the security aspects in such systems, we follow a security driven approach, and consider, from the perspective of available security building blocks, how security can be implemented and what new opportunities are presented when empowering the decentralised environment with modern distributed security protocols. Our research is motivated by a more general question of how to combine the positive enablers that email exchange enjoys, with the general benefits of workflow systems, and more specifically with the benefits that can be introduced in a decentralised environment. This aims to equip email users with a set of tools to manage the semantics of a message exchange, contents, participants and their roles in the exchange in an environment that provides inherent assurances of security and privacy. This work is based on a survey of contemporary distributed security protocols, and considers how these protocols could be used in implementing a distributed workflow management system with decentralised control . We review a set of these protocols, focusing on the required message sequences in reviewing the protocols, and discuss how these security protocols provide the foundations for implementing core control-flow, data, and resource patterns in a distributed workflow environment.

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

NARCIS (Netherlands)

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

2006-01-01

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

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

Energy Technology Data Exchange (ETDEWEB)

Gunter, Daniel

2008-07-31

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

Developing software to "track and catch" missed follow-up of abnormal test results in a complex sociotechnical environment.

Science.gov (United States)

Smith, M; Murphy, D; Laxmisan, A; Sittig, D; Reis, B; Esquivel, A; Singh, H

2013-01-01

Abnormal test results do not always receive timely follow-up, even when providers are notified through electronic health record (EHR)-based alerts. High workload, alert fatigue, and other demands on attention disrupt a provider's prospective memory for tasks required to initiate follow-up. Thus, EHR-based tracking and reminding functionalities are needed to improve follow-up. The purpose of this study was to develop a decision-support software prototype enabling individual and system-wide tracking of abnormal test result alerts lacking follow-up, and to conduct formative evaluations, including usability testing. We developed a working prototype software system, the Alert Watch And Response Engine (AWARE), to detect abnormal test result alerts lacking documented follow-up, and to present context-specific reminders to providers. Development and testing took place within the VA's EHR and focused on four cancer-related abnormal test results. Design concepts emphasized mitigating the effects of high workload and alert fatigue while being minimally intrusive. We conducted a multifaceted formative evaluation of the software, addressing fit within the larger socio-technical system. Evaluations included usability testing with the prototype and interview questions about organizational and workflow factors. Participants included 23 physicians, 9 clinical information technology specialists, and 8 quality/safety managers. Evaluation results indicated that our software prototype fit within the technical environment and clinical workflow, and physicians were able to use it successfully. Quality/safety managers reported that the tool would be useful in future quality assurance activities to detect patients who lack documented follow-up. Additionally, we successfully installed the software on the local facility's "test" EHR system, thus demonstrating technical compatibility. To address the factors involved in missed test results, we developed a software prototype to account for

Data intensive ATLAS workflows in the Cloud

CERN Document Server

Rzehorz, Gerhard Ferdinand; The ATLAS collaboration

2018-01-01

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

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

Directory of Open Access Journals (Sweden)

Nazia Anwar

2018-01-01

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

Declarative Event-Based Workflow as Distributed Dynamic Condition Response Graphs

DEFF Research Database (Denmark)

Hildebrandt, Thomas; Mukkamala, Raghava Rao

2010-01-01

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

Specialization Patterns

OpenAIRE

Schultz , Ulrik Pagh; Lawall , Julia ,; Consel , Charles

1999-01-01

Design patterns offer numerous advantages for software development, but can introduce inefficiency into the finished program. Program specialization can eliminate such overheads, but is most effective when targeted by the user to specific bottlenecks. Consequently, we propose to consider program specialization and design patterns as complementary concepts. On the one hand, program specialization can optimize object-oriented programs written using design patterns. On the other hand, design pat...

Design decisions in workflow management and quality of work.

NARCIS (Netherlands)

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

2009-01-01

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

Job life cycle management libraries for CMS workflow management projects

International Nuclear Information System (INIS)

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

2010-01-01

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

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

DEFF Research Database (Denmark)

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

2014-01-01

This paper presents a framework for the automated restructuring of workflows that allows one to minimise the impact of errors on a production workflow. The framework allows for the modelling of workflows by means of a formalised subset of the Business Process Modelling and Notation (BPMN) language...

Secure software development training course

Directory of Open Access Journals (Sweden)

Victor S. Gorbatov

2017-06-01

Full Text Available Information security is one of the most important criteria for the quality of developed software. To obtain a sufficient level of application security companies implement security process into software development life cycle. At this stage software companies encounter with deficit employees who able to solve problems of software design, implementation and application security. This article provides a description of the secure software development training course. Training course of application security is designed for co-education students of different IT-specializations.

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.

Analysing sensory panel performance in a proficiency test using the PanelCheck software

DEFF Research Database (Denmark)

Tomic, O.; Luciano, G.; Nilsen, A.

2010-01-01

Check software, a workflow is proposed that guides the user through the data analysis process. This allows practitioners and non-statisticians to get an overview over panel performances in a rapid manner without the need to be familiar with details on the statistical methods. Visualisation of data analysis...... results plays an important role as this provides a time saving and efficient way of screening and investigating sensory panel performances. Most of the statistical methods used in this paper are available in the open source software PanelCheck, which may be downloaded and used for free....

The impact of software quality characteristics on healthcare outcome: a literature review.

Science.gov (United States)

Aghazadeh, Sakineh; Pirnejad, Habibollah; Moradkhani, Alireza; Aliev, Alvosat

2014-01-01

The aim of this study was to discover the effect of software quality characteristics on healthcare quality and efficiency indicators. Through a systematic literature review, we selected and analyzed 37 original research papers to investigate the impact of the software indicators (coming from the standard ISO 9126 quality characteristics and sub-characteristics) on some of healthcare important outcome indicators and finally ranked these software indicators. The results showed that the software characteristics usability, reliability and efficiency were mostly favored in the studies, indicating their importance. On the other hand, user satisfaction, quality of patient care, clinical workflow efficiency, providers' communication and information exchange, patient satisfaction and care costs were among the healthcare outcome indicators frequently evaluated in relation to the mentioned software characteristics. Regression Logistic Method was the most common assessment methodology, and Confirmatory Factor Analysis and Structural Equation Modeling were performed to test the structural model's fit. The software characteristics were considered to impact the healthcare outcome indicators through other intermediate factors (variables).

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

Specialization Patterns

DEFF Research Database (Denmark)

Schultz, Ulrik Pagh; Lawall, Julia Laetitia; Consel, Charles

2000-01-01

Design patterns offer many advantages for software development, but can introduce inefficiency into the final program. Program specialization can eliminate such overheads, but is most effective when targeted by the user to specific bottlenecks. Consequently, we propose that these concepts...... are complementary. Program specialization can optimize programs written using design patterns, and design patterns provide information about the program structure that can guide specialization. Concretely, we propose specialization patterns, which describe how to apply program specialization to optimize uses...... of design patterns. In this paper, we analyze the specialization opportunities provided by specific uses of design patterns. Based on the analysis of each design pattern, we define the associated specialization pattern. These specialization opportunities can be declared using the specialization classes...

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

Generic MIDI devices as new input for specialized software

Directory of Open Access Journals (Sweden)

Marcin Badurowicz

2016-12-01

Full Text Available There are plenty of sublime devices, including input devices, for all kinds of specialists working with computers available on the market. Furthermore, the more specific solutions are needed, the more expensive and complicated they are. At the time when many people prefer to try as many things as possible before selecting the specific learning paths, both high price and high entry threshold, can appear as blockers. In the paper, there are selected some hardware and software solutions for facilitating the work of the professionals , who expect more analog-like interfaces and more natural ways to control computers presented. Additionally, the authors describe original software and hardware solution that allows the use of wide range MIDI devices as custom input devices. The concept of the software made is being presented, as well as some results of initial interaction of different kind of professionals and the proposed solution software and hardware.

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

Directory of Open Access Journals (Sweden)

Gryk Michael R

2007-01-01

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

High performance workflow implementation for protein surface characterization using grid technology

Directory of Open Access Journals (Sweden)

Clematis Andrea

2005-12-01

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

Optimizing perioperative decision making: improved information for clinical workflow planning.

Science.gov (United States)

Doebbeling, Bradley N; Burton, Matthew M; Wiebke, Eric A; Miller, Spencer; Baxter, Laurence; Miller, Donald; Alvarez, Jorge; Pekny, Joseph

2012-01-01

Perioperative care is complex and involves multiple interconnected subsystems. Delayed starts, prolonged cases and overtime are common. Surgical procedures account for 40-70% of hospital revenues and 30-40% of total costs. Most planning and scheduling in healthcare is done without modern planning tools, which have potential for improving access by assisting in operations planning support. We identified key planning scenarios of interest to perioperative leaders, in order to examine the feasibility of applying combinatorial optimization software solving some of those planning issues in the operative setting. Perioperative leaders desire a broad range of tools for planning and assessing alternate solutions. Our modeled solutions generated feasible solutions that varied as expected, based on resource and policy assumptions and found better utilization of scarce resources. Combinatorial optimization modeling can effectively evaluate alternatives to support key decisions for planning clinical workflow and improving care efficiency and satisfaction.

LipidMatch: an automated workflow for rule-based lipid identification using untargeted high-resolution tandem mass spectrometry data.

Science.gov (United States)

Koelmel, Jeremy P; Kroeger, Nicholas M; Ulmer, Candice Z; Bowden, John A; Patterson, Rainey E; Cochran, Jason A; Beecher, Christopher W W; Garrett, Timothy J; Yost, Richard A

2017-07-10

Lipids are ubiquitous and serve numerous biological functions; thus lipids have been shown to have great potential as candidates for elucidating biomarkers and pathway perturbations associated with disease. Methods expanding coverage of the lipidome increase the likelihood of biomarker discovery and could lead to more comprehensive understanding of disease etiology. We introduce LipidMatch, an R-based tool for lipid identification for liquid chromatography tandem mass spectrometry workflows. LipidMatch currently has over 250,000 lipid species spanning 56 lipid types contained in in silico fragmentation libraries. Unique fragmentation libraries, compared to other open source software, include oxidized lipids, bile acids, sphingosines, and previously uncharacterized adducts, including ammoniated cardiolipins. LipidMatch uses rule-based identification. For each lipid type, the user can select which fragments must be observed for identification. Rule-based identification allows for correct annotation of lipids based on the fragments observed, unlike typical identification based solely on spectral similarity scores, where over-reporting structural details that are not conferred by fragmentation data is common. Another unique feature of LipidMatch is ranking lipid identifications for a given feature by the sum of fragment intensities. For each lipid candidate, the intensities of experimental fragments with exact mass matches to expected in silico fragments are summed. The lipid identifications with the greatest summed intensity using this ranking algorithm were comparable to other lipid identification software annotations, MS-DIAL and Greazy. For example, for features with identifications from all 3 software, 92% of LipidMatch identifications by fatty acyl constituents were corroborated by at least one other software in positive mode and 98% in negative ion mode. LipidMatch allows users to annotate lipids across a wide range of high resolution tandem mass spectrometry

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.

PhenoTips: patient phenotyping software for clinical and research use.

Science.gov (United States)

Girdea, Marta; Dumitriu, Sergiu; Fiume, Marc; Bowdin, Sarah; Boycott, Kym M; Chénier, Sébastien; Chitayat, David; Faghfoury, Hanna; Meyn, M Stephen; Ray, Peter N; So, Joyce; Stavropoulos, Dimitri J; Brudno, Michael

2013-08-01

We have developed PhenoTips: open source software for collecting and analyzing phenotypic information for patients with genetic disorders. Our software combines an easy-to-use interface, compatible with any device that runs a Web browser, with a standardized database back end. The PhenoTips' user interface closely mirrors clinician workflows so as to facilitate the recording of observations made during the patient encounter. Collected data include demographics, medical history, family history, physical and laboratory measurements, physical findings, and additional notes. Phenotypic information is represented using the Human Phenotype Ontology; however, the complexity of the ontology is hidden behind a user interface, which combines simple selection of common phenotypes with error-tolerant, predictive search of the entire ontology. PhenoTips supports accurate diagnosis by analyzing the entered data, then suggesting additional clinical investigations and providing Online Mendelian Inheritance in Man (OMIM) links to likely disorders. By collecting, classifying, and analyzing phenotypic information during the patient encounter, PhenoTips allows for streamlining of clinic workflow, efficient data entry, improved diagnosis, standardization of collected patient phenotypes, and sharing of anonymized patient phenotype data for the study of rare disorders. Our source code and a demo version of PhenoTips are available at http://phenotips.org. © 2013 WILEY PERIODICALS, INC.

Software Defined Cyberinfrastructure

Energy Technology Data Exchange (ETDEWEB)

Foster, Ian; Blaiszik, Ben; Chard, Kyle; Chard, Ryan

2017-07-17

Within and across thousands of science labs, researchers and students struggle to manage data produced in experiments, simulations, and analyses. Largely manual research data lifecycle management processes mean that much time is wasted, research results are often irreproducible, and data sharing and reuse remain rare. In response, we propose a new approach to data lifecycle management in which researchers are empowered to define the actions to be performed at individual storage systems when data are created or modified: actions such as analysis, transformation, copying, and publication. We term this approach software-defined cyberinfrastructure because users can implement powerful data management policies by deploying rules to local storage systems, much as software-defined networking allows users to configure networks by deploying rules to switches.We argue that this approach can enable a new class of responsive distributed storage infrastructure that will accelerate research innovation by allowing any researcher to associate data workflows with data sources, whether local or remote, for such purposes as data ingest, characterization, indexing, and sharing. We report on early experiments with this approach in the context of experimental science, in which a simple if-trigger-then-action (IFTA) notation is used to define rules.

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.

Low Latency Workflow Scheduling and an Application of Hyperspectral Brightness Temperatures

Science.gov (United States)

Nguyen, P. T.; Chapman, D. R.; Halem, M.

2012-12-01

New system analytics for Big Data computing holds the promise of major scientific breakthroughs and discoveries from the exploration and mining of the massive data sets becoming available to the science community. However, such data intensive scientific applications face severe challenges in accessing, managing and analyzing petabytes of data. While the Hadoop MapReduce environment has been successfully applied to data intensive problems arising in business, there are still many scientific problem domains where limitations in the functionality of MapReduce systems prevent its wide adoption by those communities. This is mainly because MapReduce does not readily support the unique science discipline needs such as special science data formats, graphic and computational data analysis tools, maintaining high degrees of computational accuracies, and interfacing with application's existing components across heterogeneous computing processors. We address some of these limitations by exploiting the MapReduce programming model for satellite data intensive scientific problems and address scalability, reliability, scheduling, and data management issues when dealing with climate data records and their complex observational challenges. In addition, we will present techniques to support the unique Earth science discipline needs such as dealing with special science data formats (HDF and NetCDF). We have developed a Hadoop task scheduling algorithm that improves latency by 2x for a scientific workflow including the gridding of the EOS AIRS hyperspectral Brightness Temperatures (BT). This workflow processing algorithm has been tested at the Multicore Computing Center private Hadoop based Intel Nehalem cluster, as well as in a virtual mode under the Open Source Eucalyptus cloud. The 55TB AIRS hyperspectral L1b Brightness Temperature record has been gridded at the resolution of 0.5x1.0 degrees, and we have computed a 0.9 annual anti-correlation to the El Nino Southern oscillation in

Developing Software to “Track and Catch” Missed Follow-up of Abnormal Test Results in a Complex Sociotechnical Environment

Science.gov (United States)

Smith, M.; Murphy, D.; Laxmisan, A.; Sittig, D.; Reis, B.; Esquivel, A.; Singh, H.

2013-01-01

Summary Background Abnormal test results do not always receive timely follow-up, even when providers are notified through electronic health record (EHR)-based alerts. High workload, alert fatigue, and other demands on attention disrupt a provider’s prospective memory for tasks required to initiate follow-up. Thus, EHR-based tracking and reminding functionalities are needed to improve follow-up. Objectives The purpose of this study was to develop a decision-support software prototype enabling individual and system-wide tracking of abnormal test result alerts lacking follow-up, and to conduct formative evaluations, including usability testing. Methods We developed a working prototype software system, the Alert Watch And Response Engine (AWARE), to detect abnormal test result alerts lacking documented follow-up, and to present context-specific reminders to providers. Development and testing took place within the VA’s EHR and focused on four cancer-related abnormal test results. Design concepts emphasized mitigating the effects of high workload and alert fatigue while being minimally intrusive. We conducted a multifaceted formative evaluation of the software, addressing fit within the larger socio-technical system. Evaluations included usability testing with the prototype and interview questions about organizational and workflow factors. Participants included 23 physicians, 9 clinical information technology specialists, and 8 quality/safety managers. Results Evaluation results indicated that our software prototype fit within the technical environment and clinical workflow, and physicians were able to use it successfully. Quality/safety managers reported that the tool would be useful in future quality assurance activities to detect patients who lack documented follow-up. Additionally, we successfully installed the software on the local facility’s “test” EHR system, thus demonstrating technical compatibility. Conclusion To address the factors involved in missed

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.)

An Introduction to the Special Volume on

Directory of Open Access Journals (Sweden)

Micah Altman

2011-08-01

Full Text Available This special volume of the Journal of Statistical Software on political methodology includes 14 papers, with wide-ranging software contributions of political scientists to their own field, and more generally to statistical data analysis in the the social sciences and beyond. Special emphasis is given to software that is written in or can cooperate with the R system for statistical computing.

Electronic Health Record-Driven Workflow for Diagnostic Radiologists.

Science.gov (United States)

Geeslin, Matthew G; Gaskin, Cree M

2016-01-01

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

Styx Grid Services: Lightweight Middleware for Efficient Scientific Workflows

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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.

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.

DIGITAL WORKFLOWS FOR RESTORATION AND MANAGEMENT OF THE MUSEUM AFFANDI - A CASE STUDY IN CHALLENGING CIRCUMSTANCES

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U. Herbig

2017-08-01

Full Text Available The appropriate restoration of architectural heritage needs a careful and comprehensive documentation of the existing structures, which even elaborates, if the function of the building needs special attention, like in museums. In a collaborative project between the Universitas Gadjah Mada, Yogyakarta, Indonesia and two universities in Austria (TU Wien and the Danube University Krems a restoration and adaptation concept of the Affandi Museum in Yogyakarta is currently in progress. It provides a perfect case study for the development of a workflow to combine data from a building survey, architectural research, indoor climate measurements and the documentation of artwork in a challenging environment, from hot and humid tropical climate to continuous threads by natural hazards like earthquakes or volcanic eruptions. The Affandi Museum houses the collection of Affandi, who is considered to be Indonesia's foremost Expressionist painter and partly designed and constructed the museum by himself. With the spirit of the artist still perceptible in the complex the Affandi Museum is an important part of the Indonesian cultural heritage. Thus its preservation takes special attention and adds to the complexity of the development of a monitoring and maintenance concept. This paper describes the ongoing development of an approach to a workflow from the measurement and research of the objects, both architectural and artwork, to the semantically enriched BIM Model as the base for a sustainable monitoring tool for the Affandi Museum.

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.

Molecular Cloning Designer Simulator (MCDS: All-in-one molecular cloning and genetic engineering design, simulation and management software for complex synthetic biology and metabolic engineering projects

Directory of Open Access Journals (Sweden)

Zhenyu Shi

2016-12-01

Full Text Available Molecular Cloning Designer Simulator (MCDS is a powerful new all-in-one cloning and genetic engineering design, simulation and management software platform developed for complex synthetic biology and metabolic engineering projects. In addition to standard functions, it has a number of features that are either unique, or are not found in combination in any one software package: (1 it has a novel interactive flow-chart user interface for complex multi-step processes, allowing an integrated overview of the whole project; (2 it can perform a user-defined workflow of cloning steps in a single execution of the software; (3 it can handle multiple types of genetic recombineering, a technique that is rapidly replacing classical cloning for many applications; (4 it includes experimental information to conveniently guide wet lab work; and (5 it can store results and comments to allow the tracking and management of the whole project in one platform. MCDS is freely available from https://mcds.codeplex.com. Keywords: BioCAD, Genetic engineering software, Molecular cloning software, Synthetic biology, Workflow simulation and management

Parametric Room Acoustic workflows with real-time acoustic simulation

DEFF Research Database (Denmark)

Parigi, Dario

2017-01-01

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

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

Science.gov (United States)

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

2012-01-01

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

From Paper Based Clinical Practice Guidelines to Declarative Workflow Management

DEFF Research Database (Denmark)

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

2009-01-01

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

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

Science.gov (United States)

Elfering, Achim; Grebner, Simone; Ebener, Corinne

2015-01-01

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

Distributing Workflows over a Ubiquitous P2P Network

Directory of Open Access Journals (Sweden)

Eddie Al-Shakarchi

2007-01-01

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

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

Data mining workflow templates for intelligent discovery assistance in RapidMiner

OpenAIRE

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

2010-01-01

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

Requirements for Secure Logging of Decentralized Cross-Organizational Workflow Executions

NARCIS (Netherlands)

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

2005-01-01

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

CrossFlow: Cross-Organizational Workflow Management in Dynamic Virtual Enterprises

NARCIS (Netherlands)

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

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

CrossFlow : cross-organizational workflow management in dynamic virtual enterprises

NARCIS (Netherlands)

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

2000-01-01

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

The Symbiotic Relationship between Scientific Workflow and Provenance (Invited)

Science.gov (United States)

Stephan, E.

2010-12-01

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

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

Science.gov (United States)

Pan, Tianheng

2018-01-01

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

Integration of the radiotherapy irradiation planning in the digital workflow

International Nuclear Information System (INIS)

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

2013-01-01

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

Usability study of clinical exome analysis software: top lessons learned and recommendations.

Science.gov (United States)

Shyr, Casper; Kushniruk, Andre; Wasserman, Wyeth W

2014-10-01

New DNA sequencing technologies have revolutionized the search for genetic disruptions. Targeted sequencing of all protein coding regions of the genome, called exome analysis, is actively used in research-oriented genetics clinics, with the transition to exomes as a standard procedure underway. This transition is challenging; identification of potentially causal mutation(s) amongst ∼10(6) variants requires specialized computation in combination with expert assessment. This study analyzes the usability of user interfaces for clinical exome analysis software. There are two study objectives: (1) To ascertain the key features of successful user interfaces for clinical exome analysis software based on the perspective of expert clinical geneticists, (2) To assess user-system interactions in order to reveal strengths and weaknesses of existing software, inform future design, and accelerate the clinical uptake of exome analysis. Surveys, interviews, and cognitive task analysis were performed for the assessment of two next-generation exome sequence analysis software packages. The subjects included ten clinical geneticists who interacted with the software packages using the "think aloud" method. Subjects' interactions with the software were recorded in their clinical office within an urban research and teaching hospital. All major user interface events (from the user interactions with the packages) were time-stamped and annotated with coding categories to identify usability issues in order to characterize desired features and deficiencies in the user experience. We detected 193 usability issues, the majority of which concern interface layout and navigation, and the resolution of reports. Our study highlights gaps in specific software features typical within exome analysis. The clinicians perform best when the flow of the system is structured into well-defined yet customizable layers for incorporation within the clinical workflow. The results highlight opportunities to

Software for Managing Personal Files.

Science.gov (United States)

Lundeen, Gerald

1989-01-01

Discusses the special characteristics of personal file management software and compares four microcomputer software packages: Notebook II with Bibliography and Convert, Pro-Cite with Biblio-Links, askSam, and Reference Manager. Each package is evaluated in terms of the user interface, file maintenance, retrieval capabilities, output, and…

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.

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

Science.gov (United States)

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

2017-11-01

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

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

Science.gov (United States)

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

2017-10-12

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

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...

Multidetector-row helical CT: analysis of time management and workflow

Energy Technology Data Exchange (ETDEWEB)

Roos, Justus E.; Desbiolles, Lotus M.; Willmann, Juergen K.; Weishaupt, Dominik; Marincek, Borut; Hilfiker, Paul R. [Institute of Diagnostic Radiology, University Hospital Zurich (Switzerland)

2002-03-01

The purpose of this study was to evaluate time management and workflow for multidetector-row helical CT (MDCT). Time for patient and data handling of at total of 580 patients were evaluated at two different time periods (December 1999, August 2000), each for the following baseline measurements: (a) change of clothes/instruction; (b) patient placement on the CT table/i.v. catheter; (c) CT planning and programming; (d) CT data acquisition; (e) CT data reconstruction; (f) CT data storage/printing. All imaging was performed on a Somatom Volume Zoom (Siemens, Erlangen, Germany). Time measurements summarized for different CT protocols revealed the following: (a) 5:01 min ({+-}2.06 min); (b) 4:36 min ({+-}2.43 min); (c) 4:11 min ({+-}2.55 min); (d) 0:43 min ({+-}0.15 min); (e) 6:59 min ({+-}2.39 min); (f) 09:51 min ({+-}3.51 min). Planning and programming was most time-consuming for CT angiography, whereas chest and abdominal CT needed only 3:26 and 3:30 min, respectively. Reconstruction time was highest for HRCT (9:22 min) and CTA (9:03 min). Data storage/printing was most time-consuming for HRCT (13:02 min), followed by combined neck-chest-abdomen examinations (12:19 min). Comparing the two time periods, during which a software update was performed, a mean time reduction of 4:31 min per patient (15%, p<0.001) was achieved. Whereas CT data acquisition time is no longer a problem with MDCT, patient management, data reconstruction, and data storage are the most time-consuming parts. Well-trained technicians, state-of-the-art workstations, and fast networking are the most important factors to improve workflow. (orig.)

Software for nuclear data acquisition systems

International Nuclear Information System (INIS)

Christensen, P.

1983-01-01

The situation for experimenters and system designers needing software for instrumentation is described. It is stated that software for a data acquisition system can be divided into programmes described as the foundation software, the applications programme, and the analysis programme. Special attention is given to CAMAC. Two examples from Risoe describing data transportation and archiving are given. Finally the supply of software and the problems of documentation are described. (author)

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

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.

MIAWARE Software

DEFF Research Database (Denmark)

Wilkowski, Bartlomiej; Pereira, Oscar N. M.; Dias, Paulo

2008-01-01

is automatically generated. Furthermore, MIAWARE software is accompanied with an intelligent search engine for medical reports, based on the relations between parts of the lungs. A logical structure of the lungs is introduced to the search algorithm through the specially developed ontology. As a result...

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.

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

Simulation software: engineer processes before reengineering.

Science.gov (United States)

Lepley, C J

2001-01-01

People make decisions all the time using intuition. But what happens when you are asked: "Are you sure your predictions are accurate? How much will a mistake cost? What are the risks associated with this change?" Once a new process is engineered, it is difficult to analyze what would have been different if other options had been chosen. Simulating a process can help senior clinical officers solve complex patient flow problems and avoid wasted efforts. Simulation software can give you the data you need to make decisions. The author introduces concepts, methodologies, and applications of computer aided simulation to illustrate their use in making decisions to improve workflow design.

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.

CMS Alignement and Calibration workflows: lesson learned and future plans

CERN Document Server

AUTHOR|(CDS)2069172

2014-01-01

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

New Interactions with Workflow Systems

NARCIS (Netherlands)

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

2009-01-01

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

Logical provenance in data-oriented workflows?

KAUST Repository

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

2013-01-01

for general transformations, introducing the notions of correctness, precision, and minimality. We then determine when properties such as correctness and minimality carry over from the individual transformations' provenance to the workflow provenance. We

Workflow in clinical trial sites & its association with near miss events for data quality: ethnographic, workflow & systems simulation.

Science.gov (United States)

de Carvalho, Elias Cesar Araujo; Batilana, Adelia Portero; Claudino, Wederson; Reis, Luiz Fernando Lima; Schmerling, Rafael A; Shah, Jatin; Pietrobon, Ricardo

2012-01-01

With the exponential expansion of clinical trials conducted in (Brazil, Russia, India, and China) and VISTA (Vietnam, Indonesia, South Africa, Turkey, and Argentina) countries, corresponding gains in cost and enrolment efficiency quickly outpace the consonant metrics in traditional countries in North America and European Union. However, questions still remain regarding the quality of data being collected in these countries. We used ethnographic, mapping and computer simulation studies to identify/address areas of threat to near miss events for data quality in two cancer trial sites in Brazil. Two sites in Sao Paolo and Rio Janeiro were evaluated using ethnographic observations of workflow during subject enrolment and data collection. Emerging themes related to threats to near miss events for data quality were derived from observations. They were then transformed into workflows using UML-AD and modeled using System Dynamics. 139 tasks were observed and mapped through the ethnographic study. The UML-AD detected four major activities in the workflow evaluation of potential research subjects prior to signature of informed consent, visit to obtain subject́s informed consent, regular data collection sessions following study protocol and closure of study protocol for a given project. Field observations pointed to three major emerging themes: (a) lack of standardized process for data registration at source document, (b) multiplicity of data repositories and (c) scarcity of decision support systems at the point of research intervention. Simulation with policy model demonstrates a reduction of the rework problem. Patterns of threats to data quality at the two sites were similar to the threats reported in the literature for American sites. The clinical trial site managers need to reorganize staff workflow by using information technology more efficiently, establish new standard procedures and manage professionals to reduce near miss events and save time/cost. Clinical trial

A novel software assistant for the clinical analysis of MR spectroscopy with MeVisLab

Science.gov (United States)

Merkel, Bernd; Harz, Markus T.; Konrad, Olaf; Hahn, Horst K.; Peitgen, Heinz-Otto

2008-03-01

We present a novel software assistant for the analysis of multi-voxel 2D or 3D in-vivo-spectroscopy signals based on the rapid-prototyping platform MeVisLab. Magnetic Resonance Spectroscopy (MRS) is a valuable in-vivo metabolic window into tissue regions of interest, such as the brain, breast or prostate. With this method, the metabolic state can be investigated non-invasively. Different pathologies evoke characteristically different MRS signals, e.g., in prostate cancer, choline levels increase while citrate levels decrease compared to benign tissue. Concerning the majority of processing steps, available MRS tools lack performance in terms of speed. Our goal is to support clinicians in a fast and robust interpretation of MRS signals and to enable them to interactively work with large volumetric data sets. These data sets consist of 3D spatially resolved measurements of metabolite signals. The software assistant provides standard analysis methods for MRS data including data import and filtering, spatio-temporal Fourier transformation, and basic calculation of peak areas and spectroscopic metabolic maps. Visualization relies on the facilities of MeVisLab, a platform for developing clinically applicable software assistants. It is augmented by special-purpose viewing extensions and offers synchronized 1D, 2D, and 3D views of spectra and metabolic maps. A novelty in MRS processing tools is the side-by-side viewing ability of standard FT processed spectra with the results of time-domain frequency analysis algorithms like Linear Prediction and the Matrix Pencil Method. This enables research into the optimal toolset and workflow required to avoid misinterpretation and misapplication.

The economics of information systems and software

CERN Document Server

Veryard, Richard

2014-01-01

The Economics of Information Systems and Software focuses on the economic aspects of information systems and software, including advertising, evaluation of information systems, and software maintenance. The book first elaborates on value and values, software business, and scientific information as an economic category. Discussions focus on information products and information services, special economic properties of information, culture and convergence, hardware and software products, materiality and consumption, technological progress, and software flexibility. The text then takes a look at a

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.

SEER Data & Software

Science.gov (United States)

Options for accessing datasets for incidence, mortality, county populations, standard populations, expected survival, and SEER-linked and specialized data. Plus variable definitions, documentation for reporting and using datasets, statistical software (SEER*Stat), and observational research resources.

High Resolution Topography of Polar Regions from Commercial Satellite Imagery, Petascale Computing and Open Source Software

Science.gov (United States)

Morin, Paul; Porter, Claire; Cloutier, Michael; Howat, Ian; Noh, Myoung-Jong; Willis, Michael; Kramer, WIlliam; Bauer, Greg; Bates, Brian; Williamson, Cathleen

2017-04-01

Surface topography is among the most fundamental data sets for geosciences, essential for disciplines ranging from glaciology to geodynamics. Two new projects are using sub-meter, commercial imagery licensed by the National Geospatial-Intelligence Agency and open source photogrammetry software to produce a time-tagged 2m posting elevation model of the Arctic and an 8m posting reference elevation model for the Antarctic. When complete, this publically available data will be at higher resolution than any elevation models that cover the entirety of the Western United States. These two polar projects are made possible due to three equally important factors: 1) open-source photogrammetry software, 2) petascale computing, and 3) sub-meter imagery licensed to the United States Government. Our talk will detail the technical challenges of using automated photogrammetry software; the rapid workflow evolution to allow DEM production; the task of deploying the workflow on one of the world's largest supercomputers; the trials of moving massive amounts of data, and the management strategies the team needed to solve in order to meet deadlines. Finally, we will discuss the implications of this type of collaboration for future multi-team use of leadership-class systems such as Blue Waters, and for further elevation mapping.

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

Leveraging the Power of High Performance Computing for Next Generation Sequencing Data Analysis: Tricks and Twists from a High Throughput Exome Workflow

Science.gov (United States)

Wonczak, Stephan; Thiele, Holger; Nieroda, Lech; Jabbari, Kamel; Borowski, Stefan; Sinha, Vishal; Gunia, Wilfried; Lang, Ulrich; Achter, Viktor; Nürnberg, Peter

2015-01-01

Next generation sequencing (NGS) has been a great success and is now a standard method of research in the life sciences. With this technology, dozens of whole genomes or hundreds of exomes can be sequenced in rather short time, producing huge amounts of data. Complex bioinformatics analyses are required to turn these data into scientific findings. In order to run these analyses fast, automated workflows implemented on high performance computers are state of the art. While providing sufficient compute power and storage to meet the NGS data challenge, high performance computing (HPC) systems require special care when utilized for high throughput processing. This is especially true if the HPC system is shared by different users. Here, stability, robustness and maintainability are as important for automated workflows as speed and throughput. To achieve all of these aims, dedicated solutions have to be developed. In this paper, we present the tricks and twists that we utilized in the implementation of our exome data processing workflow. It may serve as a guideline for other high throughput data analysis projects using a similar infrastructure. The code implementing our solutions is provided in the supporting information files. PMID:25942438

Application of agile methodologies in software development

Directory of Open Access Journals (Sweden)

Jovanović Aca D.

2016-01-01

Full Text Available The paper presents the potentials for the development of software using agile methodologies. Special consideration is devoted to the potentials and advantages of use of the Scrum methodology in the development of software and the relationship between the implementation of agile methodologies and the software development projects.

From shared data to sharing workflow: Merging PACS and teleradiology

International Nuclear Information System (INIS)

Benjamin, Menashe; Aradi, Yinon; Shreiber, Reuven

2010-01-01

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

The CMS tracker calibration workflow: Experience with cosmic ray data

International Nuclear Information System (INIS)

Frosali, Simone

2010-01-01

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

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...

The eSMAF: a software for the assessment and follow-up of functional autonomy in geriatrics

Directory of Open Access Journals (Sweden)

Tousignant Michel

2007-02-01

Full Text Available Abstract Background Functional status or disability forms the core of most assessment instruments used to identify mix and level of resources and services needed by older adults who possess common characteristics. The Functional Autonomy Measurement System (SMAF is a 29-item scale measuring functional ability in five different areas. It has been recommended for use for home care, for allocation of chronic beds, for developing care plans in institutional settings and for epidemiological and evaluative studies. The SMAF can also be used with a case-mix classification system (Iso-SMAF to allocate resources based on patients' functional autonomy characteristics. The objective of this project was to develop a software version of the SMAF to facilitate the evaluation of the functional status of older adults in health services research and to optimize the clinical decision-making process. Results The eSMAF was developed over an 24-month period using a modified waterfall software engineering process. Requirements and functional specifications were determined using focus groups of stakeholders. Different versions of the software were iteratively field-tested in clinical and research environments and software adaptations made accordingly. User documentation and online help were created to assist the deployment of the software. The software is available in French or English versions under a 30-day unregistered demonstration license or a free restricted registered academic license. It can be used locally on a Windows-based PC or over a network to input SMAF data into a database, search and aggregate client data according to clinical and/or administrative criteria, and generate summary or detailed reports of selected data sets for print or export to another database. Conclusion In the last year, the software has been successfully deployed in the clinical workflow of different institutions in research and clinical applications. The software performed

Constructing reservoir-scale 3D geomechanical FE-models. A refined workflow for model generation and calculation

Energy Technology Data Exchange (ETDEWEB)

Fischer, K.; Henk, A. [Technische Univ. Darmstadt (Germany). Inst. fuer Angewandte Geowissenschaften

2013-08-01

The tectonic stress field strongly affects the optimal exploitation of conventional and unconventional hydrocarbon reservoirs. Amongst others, wellbore stability, orientation of hydraulically induced fractures and - particularly in fractured reservoirs - permeability anisotropies depend on the magnitudes and orientations of the recent stresses. Geomechanical reservoir models can provide unique insights into the tectonic stress field revealing the local perturbations resulting from faults and lithological changes. In order to provide robust predictions, such numerical models are based on the finite element (FE) method and account for the complexities of real reservoirs with respect to subsurface geometry, inhomogeneous material distribution and nonlinear rock mechanical behavior. We present a refined workflow for geomechanical reservoir modeling which allows for an easier set-up of the model geometry, high resolution submodels and faster calculation times due to element savings in the load frame. Transferring the reservoir geometry from the geological subsurface model, e.g., a Petrel {sup registered} project, to the FE model represents a special challenge as the faults are discontinuities in the numerical model and no direct interface exists between the two software packages used. Point clouds displaying faults and lithostratigraphic horizons can be used for geometry transfer but this labor-intensive approach is not feasible for complex field-scale models with numerous faults. Instead, so-called Coon's patches based on horizon lines, i.e. the intersection lines between horizons and faults, are well suited to re-generate the various surfaces in the FE software while maintaining their topology. High-resolution submodels of individual fault blocks can be incorporated into the field-scale model. This allows to consider both a locally refined mechanical stratigraphy and the impact of the large-scale fault pattern. A pressure load on top of the model represents the

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...

Testing Scientific Software: A Systematic Literature Review

Science.gov (United States)

Kanewala, Upulee; Bieman, James M.

2014-01-01

Context Scientific software plays an important role in critical decision making, for example making weather predictions based on climate models, and computation of evidence for research publications. Recently, scientists have had to retract publications due to errors caused by software faults. Systematic testing can identify such faults in code. Objective This study aims to identify specific challenges, proposed solutions, and unsolved problems faced when testing scientific software. Method We conducted a systematic literature survey to identify and analyze relevant literature. We identified 62 studies that provided relevant information about testing scientific software. Results We found that challenges faced when testing scientific software fall into two main categories: (1) testing challenges that occur due to characteristics of scientific software such as oracle problems and (2) testing challenges that occur due to cultural differences between scientists and the software engineering community such as viewing the code and the model that it implements as inseparable entities. In addition, we identified methods to potentially overcome these challenges and their limitations. Finally we describe unsolved challenges and how software engineering researchers and practitioners can help to overcome them. Conclusions Scientific software presents special challenges for testing. Specifically, cultural differences between scientist developers and software engineers, along with the characteristics of the scientific software make testing more difficult. Existing techniques such as code clone detection can help to improve the testing process. Software engineers should consider special challenges posed by scientific software such as oracle problems when developing testing techniques. PMID:25125798

Testing Scientific Software: A Systematic Literature Review.

Science.gov (United States)

Kanewala, Upulee; Bieman, James M

2014-10-01

Scientific software plays an important role in critical decision making, for example making weather predictions based on climate models, and computation of evidence for research publications. Recently, scientists have had to retract publications due to errors caused by software faults. Systematic testing can identify such faults in code. This study aims to identify specific challenges, proposed solutions, and unsolved problems faced when testing scientific software. We conducted a systematic literature survey to identify and analyze relevant literature. We identified 62 studies that provided relevant information about testing scientific software. We found that challenges faced when testing scientific software fall into two main categories: (1) testing challenges that occur due to characteristics of scientific software such as oracle problems and (2) testing challenges that occur due to cultural differences between scientists and the software engineering community such as viewing the code and the model that it implements as inseparable entities. In addition, we identified methods to potentially overcome these challenges and their limitations. Finally we describe unsolved challenges and how software engineering researchers and practitioners can help to overcome them. Scientific software presents special challenges for testing. Specifically, cultural differences between scientist developers and software engineers, along with the characteristics of the scientific software make testing more difficult. Existing techniques such as code clone detection can help to improve the testing process. Software engineers should consider special challenges posed by scientific software such as oracle problems when developing testing techniques.

A software tool for advanced MRgFUS prostate therapy planning and follow up

Science.gov (United States)

van Straaten, Dörte; Hoogenboom, Martijn; van Amerongen, Martinus J.; Weiler, Florian; Issawi, Jumana Al; Günther, Matthias; Fütterer, Jurgen; Jenne, Jürgen W.

2017-03-01

US guided HIFU/FUS ablation for the therapy of prostate cancer is a clinical established method, while MR guided HIFU/FUS applications for prostate recently started clinical evaluation. Even if MRI examination is an excellent diagnostic tool for prostate cancer, it is a time consuming procedure and not practicable within an MRgFUS therapy session. The aim of our ongoing work is to develop software to support therapy planning and post-therapy follow-up for MRgFUS on localized prostate cancer, based on multi-parametric MR protocols. The clinical workflow of diagnosis, therapy and follow-up of MR guided FUS on prostate cancer was deeply analyzed. Based on this, the image processing workflow was designed and all necessary components, e.g. GUI, viewer, registration tools etc. were defined and implemented. The software bases on MeVisLab with several implemented C++ modules for the image processing tasks. The developed software, called LTC (Local Therapy Control) will register and visualize automatically all images (T1w, T2w, DWI etc.) and ADC or perfusion maps gained from the diagnostic MRI session. This maximum of diagnostic information helps to segment all necessary ROIs, e.g. the tumor, for therapy planning. Final therapy planning will be performed based on these segmentation data in the following MRgFUS therapy session. In addition, the developed software should help to evaluate the therapy success, by synchronization and display of pre-therapeutic, therapy and follow-up image data including the therapy plan and thermal dose information. In this ongoing project, the first stand-alone prototype was completed and will be clinically evaluated.

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