WorldWideScience

Sample records for specialized workflow software

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

    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.

  2. Workflow Based Software Development Environment, Phase I

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

  3. Workflow Based Software Development Environment, Phase II

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

  4. Workflow-Based Software Development Environment

    Izygon, Michel E.

    2013-01-01

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

  5. CONNJUR Workflow Builder: a software integration environment for spectral reconstruction.

    Fenwick, Matthew; Weatherby, Gerard; Vyas, Jay; Sesanker, Colbert; Martyn, Timothy O; Ellis, Heidi J C; Gryk, Michael R

    2015-07-01

    CONNJUR Workflow Builder (WB) is an open-source software integration environment that leverages existing spectral reconstruction tools to create a synergistic, coherent platform for converting biomolecular NMR data from the time domain to the frequency domain. WB provides data integration of primary data and metadata using a relational database, and includes a library of pre-built workflows for processing time domain data. WB simplifies maximum entropy reconstruction, facilitating the processing of non-uniformly sampled time domain data. As will be shown in the paper, the unique features of WB provide it with novel abilities to enhance the quality, accuracy, and fidelity of the spectral reconstruction process. WB also provides features which promote collaboration, education, parameterization, and non-uniform data sets along with processing integrated with the Rowland NMR Toolkit (RNMRTK) and NMRPipe software packages. WB is available free of charge in perpetuity, dual-licensed under the MIT and GPL open source licenses.

  6. CONNJUR Workflow Builder: a software integration environment for spectral reconstruction

    Fenwick, Matthew; Weatherby, Gerard; Vyas, Jay; Sesanker, Colbert [UConn Health, Department of Molecular Biology and Biophysics (United States); Martyn, Timothy O. [Rensselaer at Hartford, Department of Engineering and Science (United States); Ellis, Heidi J. C. [Western New England College, Department of Computer Science and Information Technology (United States); Gryk, Michael R., E-mail: gryk@uchc.edu [UConn Health, Department of Molecular Biology and Biophysics (United States)

    2015-07-15

    CONNJUR Workflow Builder (WB) is an open-source software integration environment that leverages existing spectral reconstruction tools to create a synergistic, coherent platform for converting biomolecular NMR data from the time domain to the frequency domain. WB provides data integration of primary data and metadata using a relational database, and includes a library of pre-built workflows for processing time domain data. WB simplifies maximum entropy reconstruction, facilitating the processing of non-uniformly sampled time domain data. As will be shown in the paper, the unique features of WB provide it with novel abilities to enhance the quality, accuracy, and fidelity of the spectral reconstruction process. WB also provides features which promote collaboration, education, parameterization, and non-uniform data sets along with processing integrated with the Rowland NMR Toolkit (RNMRTK) and NMRPipe software packages. WB is available free of charge in perpetuity, dual-licensed under the MIT and GPL open source licenses.

  7. CONNJUR Workflow Builder: a software integration environment for spectral reconstruction

    Fenwick, Matthew; Weatherby, Gerard; Vyas, Jay; Sesanker, Colbert; Martyn, Timothy O.; Ellis, Heidi J. C.; Gryk, Michael R.

    2015-01-01

    CONNJUR Workflow Builder (WB) is an open-source software integration environment that leverages existing spectral reconstruction tools to create a synergistic, coherent platform for converting biomolecular NMR data from the time domain to the frequency domain. WB provides data integration of primary data and metadata using a relational database, and includes a library of pre-built workflows for processing time domain data. WB simplifies maximum entropy reconstruction, facilitating the processing of non-uniformly sampled time domain data. As will be shown in the paper, the unique features of WB provide it with novel abilities to enhance the quality, accuracy, and fidelity of the spectral reconstruction process. WB also provides features which promote collaboration, education, parameterization, and non-uniform data sets along with processing integrated with the Rowland NMR Toolkit (RNMRTK) and NMRPipe software packages. WB is available free of charge in perpetuity, dual-licensed under the MIT and GPL open source licenses

  8. Reference and PDF-manager software: complexities, support and workflow.

    Mead, Thomas L; Berryman, Donna R

    2010-10-01

    In the past, librarians taught reference management by training library users to use established software programs such as RefWorks or EndNote. In today's environment, there is a proliferation of Web-based programs that are being used by library clientele that offer a new twist on the well-known reference management programs. Basically, these new programs are PDF-manager software (e.g., Mendeley or Papers). Librarians are faced with new questions, issues, and concerns, given the new workflows and pathways that these PDF-manager programs present. This article takes a look at some of those.

  9. Managing Written Directives: A Software Solution to Streamline Workflow.

    Wagner, Robert H; Savir-Baruch, Bital; Gabriel, Medhat S; Halama, James R; Bova, Davide

    2017-06-01

    A written directive is required by the U.S. Nuclear Regulatory Commission for any use of 131 I above 1.11 MBq (30 μCi) and for patients receiving radiopharmaceutical therapy. This requirement has also been adopted and must be enforced by the agreement states. As the introduction of new radiopharmaceuticals increases therapeutic options in nuclear medicine, time spent on regulatory paperwork also increases. The pressure of managing these time-consuming regulatory requirements may heighten the potential for inaccurate or incomplete directive data and subsequent regulatory violations. To improve on the paper-trail method of directive management, we created a software tool using a Health Insurance Portability and Accountability Act (HIPAA)-compliant database. This software allows for secure data-sharing among physicians, technologists, and managers while saving time, reducing errors, and eliminating the possibility of loss and duplication. Methods: The software tool was developed using Visual Basic, which is part of the Visual Studio development environment for the Windows platform. Patient data are deposited in an Access database on a local HIPAA-compliant secure server or hard disk. Once a working version had been developed, it was installed at our institution and used to manage directives. Updates and modifications of the software were released regularly until no more significant problems were found with its operation. Results: The software has been used at our institution for over 2 y and has reliably kept track of all directives. All physicians and technologists use the software daily and find it superior to paper directives. They can retrieve active directives at any stage of completion, as well as completed directives. Conclusion: We have developed a software solution for the management of written directives that streamlines and structures the departmental workflow. This solution saves time, centralizes the information for all staff to share, and decreases

  10. Introducing students to digital geological mapping: A workflow based on cheap hardware and free software

    Vrabec, Marko; Dolžan, Erazem

    2016-04-01

    The undergraduate field course in Geological Mapping at the University of Ljubljana involves 20-40 students per year, which precludes the use of specialized rugged digital field equipment as the costs would be way beyond the capabilities of the Department. A different mapping area is selected each year with the aim to provide typical conditions that a professional geologist might encounter when doing fieldwork in Slovenia, which includes rugged relief, dense tree cover, and moderately-well- to poorly-exposed bedrock due to vegetation and urbanization. It is therefore mandatory that the digital tools and workflows are combined with classical methods of fieldwork, since, for example, full-time precise GNSS positioning is not viable under such circumstances. Additionally, due to the prevailing combination of complex geological structure with generally poor exposure, students cannot be expected to produce line (vector) maps of geological contacts on the go, so there is no need for such functionality in hardware and software that we use in the field. Our workflow therefore still relies on paper base maps, but is strongly complemented with digital tools to provide robust positioning, track recording, and acquisition of various point-based data. Primary field hardware are students' Android-based smartphones and optionally tablets. For our purposes, the built-in GNSS chips provide adequate positioning precision most of the time, particularly if they are GLONASS-capable. We use Oruxmaps, a powerful free offline map viewer for the Android platform, which facilitates the use of custom-made geopositioned maps. For digital base maps, which we prepare in free Windows QGIS software, we use scanned topographic maps provided by the National Geodetic Authority, but also other maps such as aerial imagery, processed Digital Elevation Models, scans of existing geological maps, etc. Point data, like important outcrop locations or structural measurements, are entered into Oruxmaps as

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

    Ma, Tianle; Zhang, Aidong

    2017-01-01

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

  12. A comprehensive evaluation of popular proteomics software workflows for label-free proteome quantification and imputation.

    Välikangas, Tommi; Suomi, Tomi; Elo, Laura L

    2017-05-31

    Label-free mass spectrometry (MS) has developed into an important tool applied in various fields of biological and life sciences. Several software exist to process the raw MS data into quantified protein abundances, including open source and commercial solutions. Each software includes a set of unique algorithms for different tasks of the MS data processing workflow. While many of these algorithms have been compared separately, a thorough and systematic evaluation of their overall performance is missing. Moreover, systematic information is lacking about the amount of missing values produced by the different proteomics software and the capabilities of different data imputation methods to account for them.In this study, we evaluated the performance of five popular quantitative label-free proteomics software workflows using four different spike-in data sets. Our extensive testing included the number of proteins quantified and the number of missing values produced by each workflow, the accuracy of detecting differential expression and logarithmic fold change and the effect of different imputation and filtering methods on the differential expression results. We found that the Progenesis software performed consistently well in the differential expression analysis and produced few missing values. The missing values produced by the other software decreased their performance, but this difference could be mitigated using proper data filtering or imputation methods. Among the imputation methods, we found that the local least squares (lls) regression imputation consistently increased the performance of the software in the differential expression analysis, and a combination of both data filtering and local least squares imputation increased performance the most in the tested data sets. © The Author 2017. Published by Oxford University Press.

  13. Special software for computing the special functions of wave catastrophes

    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.

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

    Klimek Radosław

    2014-12-01

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

  15. BioMoby extensions to the Taverna workflow management and enactment software

    Senger Martin

    2006-11-01

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

  16. A software-aided workflow for precinct-scale residential redevelopment

    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.

  17. A software-aided workflow for precinct-scale residential redevelopment

    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.

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

    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

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

    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.

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

    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

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

    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.

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

    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

  3. ERROR HANDLING IN INTEGRATION WORKFLOWS

    Alexey M. Nazarenko

    2017-01-01

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

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

    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.

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

    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...

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

    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

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

    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

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

    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...

  9. Workflow in Almaraz NPP

    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)

  10. Biowep: a workflow enactment portal for bioinformatics applications.

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

    2007-03-08

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

  11. Biowep: a workflow enactment portal for bioinformatics applications

    Romano Paolo

    2007-03-01

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

  12. Development of workflow planning software and a tracking study of the decay B+- --> J / Psi at the D0 Experiment

    Evans, David Edward

    2003-01-01

    A description of the development of the mc( ) runjob software package used to manage large scale computing tasks for the D0 Experiment at Fermilab is presented, along with a review of the Digital Front End Trigger electronics and the software used to control them. A tracking study is performed on detector data to determine that the D0 Experiment can detect charged B mesons, and that these results are in accordance with current results. B mesons are found by searching for the decay channel B ± → J/ψK ±

  13. Generic MIDI devices as new input for specialized software

    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.

  14. 3-D Animation, NL Editing & Special Effects Software Lab

    Federal Laboratory Consortium — The Visual Effects Team of the Indirect Fire Division is a team of highly skilled people with specialized training and experience in Multimedia Production. Utilizing...

  15. SpaceWire Driver Software for Special DSPs

    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).

  16. Generating statements at whole-body imaging with a workflow-optimized software tool - first experiences with multireader analysis

    Mueller-Horvat, C.; Plathow, C.; Ludescher, B.; Lichy, M.P.; Claussen, C.D.; Schlemmer, H.P.; Canda, V.; Zindel, C.; Hahn, H.K.; Peitgen, H.O.; Kuhnigk, J.

    2007-01-01

    Introduction: Due to technical innovations in sectional diagram methods, whole-body imaging has increased in importance for clinical radiology, particularly for the diagnosis of systemic tumor disease. Large numbers of images have to be evaluated in increasingly shorter time periods. The aim was to create and evaluate a new software tool to assist and automate the process of diagnosing whole-body datasets. Material and Methods: Thirteen whole-body datasets were evaluated by 3 readers using the conventional system and the new software tool. The times for loading the datasets, examining 5 different regions (head, neck, thorax, abdomen and pelvis/skeletal system) and retrieving a relevant finding for demonstration were acquired. Additionally a Student T-Test was performed. For qualitative analysis the 3 readers used a scale from 0 - 4 (0 = bad, 4 = very good) to assess dataset loading convenience, lesion location assistance, and ease of use. Additionally a kappa value was calculated. Results: The average loading time was 39.7 s (± 5.5) with the conventional system and 6.5 s (± 1.4) (p 0.9). The qualitative analysis showed a significant advantage with respect to convenience (p 0.9). (orig.)

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

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

    2018-02-01

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

  18. Evaluation of the Android Software for Special Needs Children

    Soykan, Emrah; Özdamli, Fezile

    2017-01-01

    It is clearly understood that technology oriented education on special training is neither sound nor adequate when considered from the literary point of view in our country. Limited studies held in country not only support this point of view but also demonstrate the lack of resource and studies carried out in this area. During the designing and…

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

    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

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

    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...

  1. ATLAS Grid Workflow Performance Optimization

    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.

  2. Special issue on new ideas and emerging results in understanding software

    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.

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

    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.

  4. Modeling Complex Workflow in Molecular Diagnostics

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

    2010-01-01

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

  5. Integration of services into workflow applications

    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

  6. Scientific Workflow Management in Proteomics

    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

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

    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)

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

    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.

  9. Parametric Room Acoustic Workflows

    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...

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

    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.

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

    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.

  12. Software

    Macedo, R.; Budd, G.; Ross, E.; Wells, P.

    2010-07-15

    The software section of this journal presented new software programs that have been developed to help in the exploration and development of hydrocarbon resources. Software provider IHS Inc. has made additions to its geological and engineering analysis software tool, IHS PETRA, a product used by geoscientists and engineers to visualize, analyze and manage well production, well log, drilling, reservoir, seismic and other related information. IHS PETRA also includes a directional well module and a decline curve analysis module to improve analysis capabilities in unconventional reservoirs. Petris Technology Inc. has developed a software to help manage the large volumes of data. PetrisWinds Enterprise (PWE) helps users find and manage wellbore data, including conventional wireline and MWD core data; analysis core photos and images; waveforms and NMR; and external files documentation. Ottawa-based Ambercore Software Inc. has been collaborating with Nexen on the Petroleum iQ software for steam assisted gravity drainage (SAGD) producers. Petroleum iQ integrates geology and geophysics data with engineering data in 3D and 4D. Calgary-based Envirosoft Corporation has developed a software that reduces the costly and time-consuming effort required to comply with Directive 39 of the Alberta Energy Resources Conservation Board. The product includes an emissions modelling software. Houston-based Seismic Micro-Technology (SMT) has developed the Kingdom software that features the latest in seismic interpretation. Holland-based Joa Oil and Gas and Calgary-based Computer Modelling Group have both supplied the petroleum industry with advanced reservoir simulation software that enables reservoir interpretation. The 2010 software survey included a guide to new software applications designed to facilitate petroleum exploration, drilling and production activities. Oil and gas producers can use the products for a range of functions, including reservoir characterization and accounting. In

  13. Development of workflow planning software and a tracking study of the decay B± → J / Ψ at the D0 Experiment

    Evans, David Edward [Lancaster Univ. (United Kingdom)

    2003-09-01

    A description of the development of the mc_runjob software package used to manage large scale computing tasks for the D0 Experiment at Fermilab is presented, along with a review of the Digital Front End Trigger electronics and the software used to control them. A tracking study is performed on detector data to determine that the D0 Experiment can detect charged B mesons, and that these results are in accordance with current results. B mesons are found by searching for the decay channel B± → J / Ψ K± .

  14. Dynamic Reusable Workflows for Ocean Science

    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

  15. Dynamic reusable workflows for ocean science

    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

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

    McCarthy, Ann

    2006-01-01

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

  17. Agreement Workflow Tool (AWT)

    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...

  18. A practical data processing workflow for multi-OMICS projects.

    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

  19. Large scale software building with CMake in ATLAS

    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...

  20. Large Scale Software Building with CMake in ATLAS

    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...

  1. A Model of Workflow Composition for Emergency Management

    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.

  2. The MPO system for automatic workflow documentation

    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.

  3. The MPO system for automatic workflow documentation

    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.

  4. Automation of Flexible Migration Workflows

    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

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

    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. 

  6. Open source workflow : a viable direction for BPM?

    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

  7. SU-G-JeP2-06: Dosimetric and Workflow Evaluation of First Commercial Synthetic CT Software for Clinical Use in Pelvis

    Tyagi, N; Zhang, J; Happersett, L; Kadbi, M; Mechalakos, J; Deasy, J; Hunt, M [Memorial Sloan Kettering Cancer Center, New York, NY (United States)

    2016-06-15

    Purpose: evaluate a commercial synthetic CT (syn-CT) software for use in prostate radiotherapy Methods: Twenty prostate patients underwent CT and MR simulation scans in treatment position on a 3T Philips scanner. The MR protocol consisted of a T2w turbo spin-echo for soft tissue contrast, a 2D balanced-fast field echo (b-FFE) for fiducial identification, a dual-echo 3D FFE B0 map for distortion analysis and a 3D mDIXON FFE sequence to generate syn-CT. Two echoes are acquired during mDIXON scan, allowing water, fat, and in-phase images to be derived using the frequency shift of the fat and water protons. Tissues were classified as: air, adipose, water, trabecular/spongy bone and compact/cortical bone and assigned specific bulk HU values. Bone structures are segmented based on a pelvis bone atlas. Accuracy of syn-CT for patient treatment planning was analyzed by transferring the original plan and structures from the CT to syn-CT via rigid registration and recalculating dose. In addition, new IMRT plans were generated on the syn-CT using structures contoured on MR and transferred to the syn-CT. Accuracy of fiducial-based localization at the treatment machine performed using syn-CT or DRRs generated from syn-CT was assessed by comparing to orthogonal kV radiographs or CBCT. Results: Dosimetric comparison between CT and syn-CT was within 0.5% for all structures. The de-novo optimized plans generated on the syn-CT met our institutional clinical objectives for target and normal structures. Patient-induced susceptibility distortion based on B0 maps was within 1mm and 0.4 mm in the body and prostate. The rectal and bladder outlines on the syn-CT were deemed sufficient for assessing rectal and bladder filling on the CBCT at the time of treatment. CBCT localization showed a median error of < ±1 mm in LR, AP and SI direction. Conclusion: MRI derived syn-CT can be used clinically in MR-alone planning and treatment process for prostate. Drs. Deasy, Hunt and Tyagi have Master

  8. A virtual radiation therapy workflow training simulation

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

    2016-01-01

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

  9. FOSS geospatial libraries in scientific workflow environments: experiences and directions

    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...

  10. Querying Workflow Logs

    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.

  11. Responsive web design workflow

    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...

  12. What is needed for effective open access workflows?

    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?

  13. Impact of CGNS on CFD Workflow

    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.

  14. Software Agents in Data and Workflow Management

    Barrass, T A; Metson, S; Newbold, D; Jank, W; García-Abia, P; Hernández, J M; Afaq, A; Ernst, M; Fisk, I; Wu, Y; Charlot, C; Semeniouk, I N; Bonacorsi, D; Fanfani, A; Grandi, C; De Filippis, N; Rabbertz, K; Rehn, J; Tuura, L; Wildish, T; Newbold, D

    2005-01-01

    CMS currently uses a number of tools to transfer data which, taken together, form the basis of a heterogeneous datagrid. The range of tools used, and the directed, rather than optimized nature of CMS recent large scale data challenge required the creation of a simple infrastructure that allowed a range of tools to operate in a complementary way. The system created comprises a hierarchy of simple processes (named agents) that propagate files through a number of transfer states. File locations and some application metadata were stored in POOL file catalogues, with LCG LRC or MySQL back-ends. Agents were assigned limited responsibilities, and were restricted to communicating state 9in a well-defined, indirect fashion through a central transfer management database. In this way, the task of distributing data was easily divided between different groups for implementation. The prototype system w as developed rapidly, and achieved the required sustained transfer rate of ~10 MBps, with O(10^6) files distributed to 6 s...

  15. The PBase Scientific Workflow Provenance Repository

    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.

  16. Workflows for Full Waveform Inversions

    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.

  17. Integrating configuration workflows with project management system

    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.

  18. Software Prototyping

    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

  19. Comparison of Resource Platform Selection Approaches for Scientific Workflows

    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.

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

    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

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

    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

  2. Is Chinese Software Engineering Professionalizing or Not?: Specialization of Knowledge, Subjective Identification and Professionalization

    Yang, Yan

    2012-01-01

    Purpose: This paper aims to discuss the challenge for the classical idea of professionalism in understanding the Chinese software engineering industry after giving a close insight into the development of this industry as well as individual engineers with a psycho-societal perspective. Design/methodology/approach: The study starts with the general…

  3. Workflow management: an overview

    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

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

    Ramakrishnan, Lavanya; Plale, Beth

    2010-04-05

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

  5. Ferret Workflow Anomaly Detection System

    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...

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

    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

  7. Recent software developments for special functions in the Santander-Amsterdam project

    A. Gil (Amparo); J. Segura (Javier); N.M. Temme (Nico)

    2014-01-01

    textabstractWe give an overview of published algorithms by our group and of current activities and future plans. In particular we give details on methods for computing special functions and discuss in detail two current lines of research. Firstly, we describe the recent developments for the

  8. Globalisation of Knowledge Production and Regional Innovation Policy: Supporting Specialized Hubs in the Bangalore Software Industry

    Chaminade, Cristina; Vang, Jan

    2008-01-01

    This paper is concerned with the changing role of regional innovation systems and regional policies in supporting the transition of indigenous firms in developing countries from competing on low costs towards becoming knowledge providers in global value chains. Special attention is paid to policies supporting the emergence and development of the regional innovation system in this transition process. Regional innovation systems in developing countries have very recently started to be conceptua...

  9. Insightful Workflow For Grid Computing

    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.

  10. Conventions and workflows for using Situs

    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

  11. Workflow User Interfaces Patterns

    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.

  12. Application of GESPECOR software for the calculation of coincidence summing effects in special cases

    Arnold, Dirk; Sima, Octavian

    2004-01-01

    In this work, coincidence summing correction factors have been measured for 133 Ba, 152 Eu and 88 Y point sources with a 50% relative efficiency p-type detector and a 25% relative efficiency n-type detector in two close-to-detector measurement geometries. The experimental data for 133 Ba and 152 Eu and the results obtained with the GESPECOR software reveal a complex structure of the conventional dead layer of the p-type detector. The high value of the coincidence summing correction factor for the 511 keV peak of 88 Y, in agreement with the values computed by GESPECOR, in this case cautions against the application of the semiempirical method for evaluating coincidence summing effects

  13. Distributed Workflow Service Composition Based on CTR Technology

    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.

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

    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.

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

    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.

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

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

    2012-01-01

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

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

    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.

  18. Special Issue: Software-engineering, Properites of Language and Aspect Technologies

    Bergmans, Lodewijk; Gybels, Kris; Ernst, Erik

    2008-01-01

    , comprehensibility and evolvability. As (aspect) languages are being pushed to meet their boundaries and limitations, the trade-offs in language design become increasingly difficult to make. In particular, a trade-off may be perfectly sensible in one application context, but much less so in another. In this special...... issue you will find three full papers, originating from the SPLAT workshop series, that address this last issue. Each of these papers resolves a fundamental language design trade-off by offering a language mechanism that lifts the design decisions to the application programmers: The first paper, "User......-Defined Join Point Selectors-An Extension Mechanism for Pointcut Languages" by Breuel and Reverbel, addresses the fact that aspect programmers are pushing the boundaries of pointcut languages. As a result, aspect language designers have to make a trade-off between limited expressiveness of traditional types...

  19. Radiology information system: a workflow-based approach

    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.)

  20. Planning bioinformatics workflows using an expert system

    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

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

    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.

  2. A Tool Supporting Collaborative Data Analytics Workflow Design and Management

    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.

  3. A standard-enabled workflow for synthetic biology

    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.

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

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

    2009-01-01

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

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

    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

  6. Security aspects in teleradiology workflow

    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.

  7. Deploying and sharing U-Compare workflows as web services.

    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.

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

    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

  9. Large Scale Software Building with CMake in ATLAS

    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.

  10. Implementing Oracle Workflow

    Mathieson, D W

    1999-01-01

    CERN (see [CERN]) is the world's largest physics research centre. Currently there are around 5,000 people working at the CERN site located on the border of France and Switzerland near Geneva along with another 4,000 working remotely at institutes situated all around the globe. CERN is currently working on the construction of our newest scientific instrument called the Large Hadron Collider (LHC); the construction alone of this 27-kilometre particle accelerator will not complete until 2005. Like many businesses in the current economic climate CERN is expected to continue growing, yet staff numbers are planned to fall in the coming years. In essence, do more with less. In an environment such as this, it is critical that the administration is as efficient as possible. One of the ways that administrative procedures are streamlined is by the use of an organisation-wide workflow system.

  11. Digital workflows in contemporary orthodontics

    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.

  12. Routine digital pathology workflow: The Catania experience

    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.

  13. Analog to digital workflow improvement: a quantitative study.

    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.

  14. Constructing Workflows from Script Applications

    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.

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

    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

  16. Privacy-aware workflow management

    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

  17. Summer Student Report - AV Workflow

    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.

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

    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.

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

    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.

  20. Application of Workflow Technology for Big Data Analysis Service

    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.

  1. The Prosthetic Workflow in the Digital Era

    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.

  2. Concurrency & Asynchrony in Declarative Workflows

    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...

  3. Similarity measures for scientific workflows

    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...

  4. Sci-Fri PM: Radiation Therapy, Planning, Imaging, and Special Techniques - 08: Retrospective Dose Accumulation Workflow in Head and Neck Cancer Patients Using RayStation 4.5.2

    Wong, Olive; Chan, Biu; Moseley, Joanne; McNiven, Andrea; Lindsay, Patricia; Bissonnette, Jean-Pierre; Waldron, John; Giuliani, Meredith; Zhang, Beibei

    2016-01-01

    Purpose: We have developed a semi-automated dose accumulation workflow for Head and Neck Cancer (HNC) patients to evaluate volumetric and dosimetric changes that take place during radiotherapy. This work will be used to assess how dosimetric changes affect both toxicity and disease control, hence inform the feasibility and design of a prospective HNC adaptive trial. Methods: RayStation 4.5.2 features deformable image registration (DIR), where structures already defined on the planning CT image set can be deformably mapped onto cone-beam computed tomography (CBCT) images, accounting for daily treatment set-up shifts and changes in patient anatomy. The daily delivered dose can be calculated on each CBCT and mapped back to the planning CT to allow dose accumulation. The process is partially automated using Python scripts developed in collaboration with RaySearch. Results: To date we have performed dose accumulation on 18 HNC patients treated at our institution during 2013–2015 under REB approval. Our semi-automated process establishes clinical feasibility. Generally, dose accumulation for the entire treatment course of one case takes 60–120 minutes: importing all CBCTs requires 20–30 minutes as each patient has 30 to 40 treated fractions; image registration and dose accumulation require 60–90 minutes. This is in contrast to the process without automated scripts where dose accumulation alone would take 3–5 hours. Conclusions: We have developed a reliable workflow for retrospective dose tracking in HNC using RayStation. The process has been validated for HNC patients treated on both Elekta and Varian linacs with CBCTs acquired on XVI and OBI platforms respectively.

  5. Sci-Fri PM: Radiation Therapy, Planning, Imaging, and Special Techniques - 08: Retrospective Dose Accumulation Workflow in Head and Neck Cancer Patients Using RayStation 4.5.2

    Wong, Olive; Chan, Biu; Moseley, Joanne; McNiven, Andrea; Lindsay, Patricia; Bissonnette, Jean-Pierre; Waldron, John; Giuliani, Meredith; Zhang, Beibei [Princess Margaret Cancer Centre-UHN (Canada)

    2016-08-15

    Purpose: We have developed a semi-automated dose accumulation workflow for Head and Neck Cancer (HNC) patients to evaluate volumetric and dosimetric changes that take place during radiotherapy. This work will be used to assess how dosimetric changes affect both toxicity and disease control, hence inform the feasibility and design of a prospective HNC adaptive trial. Methods: RayStation 4.5.2 features deformable image registration (DIR), where structures already defined on the planning CT image set can be deformably mapped onto cone-beam computed tomography (CBCT) images, accounting for daily treatment set-up shifts and changes in patient anatomy. The daily delivered dose can be calculated on each CBCT and mapped back to the planning CT to allow dose accumulation. The process is partially automated using Python scripts developed in collaboration with RaySearch. Results: To date we have performed dose accumulation on 18 HNC patients treated at our institution during 2013–2015 under REB approval. Our semi-automated process establishes clinical feasibility. Generally, dose accumulation for the entire treatment course of one case takes 60–120 minutes: importing all CBCTs requires 20–30 minutes as each patient has 30 to 40 treated fractions; image registration and dose accumulation require 60–90 minutes. This is in contrast to the process without automated scripts where dose accumulation alone would take 3–5 hours. Conclusions: We have developed a reliable workflow for retrospective dose tracking in HNC using RayStation. The process has been validated for HNC patients treated on both Elekta and Varian linacs with CBCTs acquired on XVI and OBI platforms respectively.

  6. wft4galaxy: a workflow testing tool for galaxy.

    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.

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

    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

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

    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

  9. Computer software.

    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.

  10. Office 2010 Workflow Developing Collaborative Solutions

    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

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

    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.

  12. Managing Library IT Workflow with Bugzilla

    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.

  13. CMS Distributed Computing Workflow Experience

    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...

  14. New Interactions with Workflow Systems

    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

  15. Using a Praxeology Approach to the Rational Choice of Specialized Software in the Preparation of the Computer Science Teacher

    Elena Semenikhina

    2018-02-01

    Full Text Available From the positions of Praxeology, the aspects of the forming of the future teachers’ abilities to choose software that turns out to be the most rational for the solving of the professional task are considered in the article (on the example of computer science teachers’ preparation to use dynamic mathematics software (DMS. The forming of such abilities based on a formula "one task – different software" is described. The methodology of organization of such experimental studies on the base of Sumy State Pedagogical University (Ukraine is described. The results of the statistical analysis of data are given on the basis of non-parametric sign test for dependent sample. It is educed that taking into account such approach provides the positive dynamics of the level of future informatics teachers’ preparation at the significance level of 0.05.

  16. CMS distributed computing workflow experience

    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.

  17. CMS distributed computing workflow experience

    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.

  18. Design Tools and Workflows for Braided Structures

    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...

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

    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

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

    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.

  1. Enhancing and Customizing Laboratory Information Systems to Improve/Enhance Pathologist Workflow.

    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.

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

    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.

  3. The Equivalency between Logic Petri Workflow Nets and Workflow Nets

    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

  4. Snakemake-a scalable bioinformatics workflow engine

    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

  5. Behavioral technique for workflow abstraction and matching

    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

  6. A performance study of grid workflow engines

    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

  7. Flexible Early Warning Systems with Workflows and Decision Tables

    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

  8. A standard-enabled workflow for synthetic biology.

    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.

  9. Specialized software utilities for gamma ray spectrometry. Final report of a co-ordinated research project 1996-2000

    2002-03-01

    A Co-ordinated Research Project (CRP) on Software Utilities for Gamma Ray Spectrometry was initiated by the International Atomic Energy Agency in 1996 for a three year period. In the CRP several basic applications of nuclear data handling were assayed which also dealt with the development of PC computer codes for various spectrometric purposes. The CRP produced several software packages: for the analysis of low level NaI spectra; user controlled analysis of gamma ray spectra from HPGe detectors; a set of routines for the definition of the detector resolution function and for the unfolding of experimental annihilation spectra; a program for the generation of gamma ray libraries for specific applications; a program to calculate true coincidence corrections; a program to calculate full-energy peak efficiency calibration curve for homogenous cylindrical sample geometries including self-attenuation correction; and a program for the library driven analysis of gamma ray spectra and for the quantification of radionuclide content in samples. In addition, the CRP addressed problems of the analysis of naturally occurring radioactive soil material gamma ray spectra, questions of quality assurance and quality control in gamma ray spectrometry, and verification of the expert system SHAMAN for the analysis of air filter spectra obtained within the framework of the Comprehensive Nuclear Test Ban Treaty. This TECDOC contains 10 presentations delivered at the meeting with the description of the software developed. Each of the papers has been indexed separately

  10. ESO Reflex: a graphical workflow engine for data reduction

    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.

  11. Climate Data Analytics Workflow Management

    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.

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

    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.

  13. Towards seamless workflows in agile data science

    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

  14. MIAWARE Software

    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...

  15. a Standardized Approach to Topographic Data Processing and Workflow Management

    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

  16. ESO Reflex: A Graphical Workflow Engine for Data Reduction

    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.

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

    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.

  18. Pro WF Windows Workflow in NET 40

    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

  19. Multidetector-row CT: economics and workflow

    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.)

  20. Software Agents for Workflows Support | Zakaria | Revue d ...

    No Abstract Available Revue d'Information Scientifique & Technique Vol.10(1-2) 2000: 27-40. Full Text: EMAIL FULL TEXT EMAIL FULL TEXT · DOWNLOAD FULL TEXT DOWNLOAD FULL TEXT · http://dx.doi.org/10.4314/rist.v10i1.26727 · AJOL African Journals Online. HOW TO USE AJOL... for Researchers · for Librarians ...

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

    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...

  2. Software and the Scientist: Coding and Citation Practices in Geodynamics

    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.

  3. Resilient workflows for computational mechanics platforms

    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.

  4. Resilient workflows for computational mechanics platforms

    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].

  5. A Component Based Approach to Scientific Workflow Management

    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.

  6. A component based approach to scientific workflow management

    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

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

    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

  8. Inverse IMRT workflow process at Austin health

    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

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

    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.

  10. Workflow patterns the definitive guide

    Russell, Nick; ter Hofstede, Arthur H M

    2016-01-01

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

  11. Complexity Metrics for Workflow Nets

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

    2009-01-01

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

  12. Contracts for Cross-Organizational Workflow Management

    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

  13. Verifying generalized soundness for workflow nets

    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

  14. Implementing bioinformatic workflows within the bioextract server

    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...

  15. Workflow Fault Tree Generation Through Model Checking

    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...

  16. Workflow Patterns for Business Process Modeling

    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

  17. Automated quality control in a file-based broadcasting workflow

    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.

  18. An integrated billing application to streamline clinician workflow.

    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.

  19. The MPO API: A tool for recording scientific workflows

    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.

  20. The MPO API: A tool for recording scientific workflows

    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

  1. Specialization Patterns

    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...

  2. A Formal Framework for Workflow Analysis

    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.

  3. Using Mobile Agents to Implement Workflow System

    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.

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

    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

  5. SOFTWARE SUPPORT FOR RICH PICTURES

    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...

  6. ADVANCED APPROACH TO PRODUCTION WORKFLOW COMPOSITION ON ENGINEERING KNOWLEDGE PORTALS

    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...

  7. The CASA Software Package

    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.

  8. Soarian--workflow management applied for health care.

    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.

  9. Specialization Patterns

    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...

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

    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

  11. Workflow Management in CLARIN-DK

    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...

  12. The Diabetic Retinopathy Screening Workflow

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

    2015-01-01

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

  13. Workflow Optimization in Vertebrobasilar Occlusion

    Kamper, Lars; Meyn, Hannes; Rybacki, Konrad; Nordmeyer, Simone; Kempkes, Udo; Piroth, Werner; Isenmann, Stefan; Haage, Patrick

    2012-01-01

    Objective: In vertebrobasilar occlusion, rapid recanalization is the only substantial means to improve the prognosis. We introduced a standard operating procedure (SOP) for interventional therapy to analyze the effects on interdisciplinary time management. Methods: Intrahospital time periods between hospital admission and neuroradiological intervention were retrospectively analyzed, together with the patients’ outcome, before (n = 18) and after (n = 20) implementation of the SOP. Results: After implementation of the SOP, we observed statistically significant improvement of postinterventional patient neurological status (p = 0.017). In addition, we found a decrease of 5:33 h for the mean time period from hospital admission until neuroradiological intervention. The recanalization rate increased from 72.2% to 80% after implementation of the SOP. Conclusion: Our results underscore the relevance of SOP implementation and analysis of time management for clinical workflow optimization. Both may trigger awareness for the need of efficient interdisciplinary time management. This could be an explanation for the decreased time periods and improved postinterventional patient status after SOP implementation.

  14. Integrative Workflows for Metagenomic Analysis

    Efthymios eLadoukakis

    2014-11-01

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

  15. Software development assurance for special control computer sets on the base of the Electronica-60M microcomputer in the stations of fuel element nondestructive testing

    Vasil'kova, A.D.; Grachev, S.N.; Salakatova, L.S.

    1987-01-01

    A special computational control complex (SCCC) including the ''Elektronika-60M'' microcomputer, a device for communication with an object (DCO) based on the typical microprocessing set (TMS) based on LIUS-2 KTS means and an adapter for communication of the ''Elektronika-60M'' microcomputer bus with IK1 TMS bus developed for their conjugation is used for development of nondestructive control post software. An instrumental SCCC including SM-4 microcomputer, TMS units as DCO, an adapter for communication of the common bus of the SM-4 minicomputer with the IK1 TMS bus developed for their conjugation and devices for simulation of the facility operation is suggested to increase labour productivity of programmers. The SM-4 microcomputer permits to develop programs in the FORTRAN language and to carry out their effective adjustment. A subprogram library for communication with TMS units is compiled, and the technique for testing FORTRAN programs in programmable read-only memory TMS as well as start of these programs are developed

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

    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

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

    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.

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

    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...

  19. COSMOS: Python library for massively parallel workflows.

    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.

  20. Implementing Workflow Reconfiguration in WS-BPEL

    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...

  1. Logical provenance in data-oriented workflows?

    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

  2. A Multilevel Secure Workflow Management System

    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...

  3. Integrated workflows for spiking neuronal network simulations

    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

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

    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.

  5. Multilevel Workflow System in the ATLAS Experiment

    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...

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

    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.

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

    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.

  8. Optimizing CyberShake Seismic Hazard Workflows for Large HPC Resources

    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

  9. Advancing the integration of hospital IT. Pitfalls and perspectives when replacing specialized software for high-risk environments with enterprise system extensions.

    Engelmann, Carsten; Ametowobla, Dzifa

    2017-05-17

    Planning and controlling surgical operations hugely impacts upon productivity, patient safety, and surgeons' careers. Established, specialized software for this task is being increasingly replaced by "Operating Room (OR)-modules" appended to enterprise-wide resource planning (ERP) systems. As a result, usability problems are re-emerging and require developers' attention. Systematic evaluation of the functionality and social repercussions of a global, market-leading IT business control system (SAP R3, Germany), adapted for real-time OR process steering. Field study involving document analyses, interviews, and a 73-item survey addressed to 77 qualified (> 1-year system experience) senior planning executives (end users; "planners") working in surgical departments of university hospitals. Planners reported that 57% of electronic operation requests contained contradictory information. Key screens contained clinically irrelevant areas (36 +/- 29%). Compared to the legacy system, users reported either no improvements or worse performance, in regard to co-ordination of OR stakeholders, intra-day program changes, and safety. Planners concluded that the ERP-planning module was "non-intuitive" (66%), increased planning work (56%, p=0.002), and did not impact upon either organizational mishap spectrum or frequency. Interviews evidenced intra-institutional power shifts due to increased system complexity. Planners resented e.g. a trend towards increased personal culpability for mishap. Highly complex enterprise system extensions may not be directly suited to specific process steering tasks in a high risk/low error-environment like the OR. In view of surgeons' high primary task load, the repeated call for simpler IT is an imperative for ERP extensions. System design should consider a) that current OR IT suffers from an input limitation regarding planning-relevant real-time data, and b) that there are social processes that strongly affect planning and particularly ERP use beyond

  10. Multilevel Workflow System in the ATLAS Experiment

    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)

  11. A method to mine workflows from provenance for assisting scientific workflow composition

    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

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

    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

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

    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

  14. An Adaptable Seismic Data Format for Modern Scientific Workflows

    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.

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

    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.

  16. Recommendation systems in software engineering

    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...

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

    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

  18. Data intensive ATLAS workflows in the Cloud

    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

  19. Data intensive ATLAS workflows in the Cloud

    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.

  20. Data intensive ATLAS workflows in the Cloud

    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...

  1. Logical provenance in data-oriented workflows?

    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.

  2. Quantitative analysis of probabilistic BPMN workflows

    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....

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

    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

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

    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.

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

    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.

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

    David Bruce Stockton

    2015-10-01

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

  7. SEER Data & Software

    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.

  8. Quantitative analysis of probabilistic BPMN workflows

    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...

  9. A Prudent Approach to Fair Use Workflow

    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.

  10. Perti Net-Based Workflow Access Control Model

    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.

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

    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.

  12. Software livre de produção textual com predição de palavras: um aliado do aluno especial Text production with a word predicition free-ware software: support for the special student

    Monica Jordan

    2009-12-01

    discusses the results obtained when keyboard simulator were applied along with word prediction techniques based on grammatical class groups for the Portuguese language; this proposal facilitates writing production with good grammatical quality. Data obtained with adolescents with sequelae from cerebral palsy showed that the use of the software was positive, as it enhanced communication and was useful in the learning process for the Portuguese language. Broadening communication possibilities without prejudice to grammatical quality is a means of aiding in the educational process and social inclusion for people with special needs, so as to enhance social participation and improve quality of life.

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

    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.

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

    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

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

    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

  16. Soundness of Timed-Arc Workflow Nets

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

    2014-01-01

    , we demonstrate the usability of our theory on the case studies of a Brake System Control Unit used in aircraft certification, the MPEG2 encoding algorithm, and a blood transfusion workflow. The implementation of the algorithms is freely available as a part of the model checker TAPAAL....

  17. Distributed interoperable workflow support for electronic commerce

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

    1998-01-01

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

  18. Using workflow for projects in higher education

    van der Veen, Johan (CTIT); Jones, Valerie M.; Collis, Betty

    2000-01-01

    The WWW is increasingly used as a medium to support education and training. A course at the University of Twente in which groups of students collaborate in the design and production of multimedia instructional materials has now been supported by a website since 1995. Workflow was integrated with

  19. Workflow Automation: A Collective Case Study

    Harlan, Jennifer

    2013-01-01

    Knowledge management has proven to be a sustainable competitive advantage for many organizations. Knowledge management systems are abundant, with multiple functionalities. The literature reinforces the use of workflow automation with knowledge management systems to benefit organizations; however, it was not known if process automation yielded…

  20. On Secure Workflow Decentralisation on the Internet

    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.

  1. Text mining for the biocuration workflow.

    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.

  2. Adaptive workflow simulation of emergency response

    Bruinsma, Guido Wybe Jan

    2010-01-01

    Recent incidents and major training exercises in and outside the Netherlands have persistently shown that not having or not sharing information during emergency response are major sources of emergency response inefficiency and error, and affect incident mitigation outcomes through workflow planning

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

    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...

  4. Challenges and benefits of digital workflow implementation in aerospace manufacturing engineering

    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...

  5. Performing Workflows in Pervasive Environments Based on Context Specifications

    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...

  6. Workflow Support for Advanced Grid-Enabled Computing

    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...

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

    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

  8. On Lifecycle Constraints of Artifact-Centric Workflows

    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.

  9. WS-VLAM: A GT4 based workflow management system

    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

  10. Optimal resource assignment in workflows for maximizing cooperation

    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

  11. Database Support for Workflow Management: The WIDE Project

    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

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

    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.

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

    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

  14. Grid workflow job execution service 'Pilot'

    Shamardin, Lev; Kryukov, Alexander; Demichev, Andrey; Ilyin, Vyacheslav

    2011-12-01

    'Pilot' is a grid job execution service for workflow jobs. The main goal for the service is to automate computations with multiple stages since they can be expressed as simple workflows. Each job is a directed acyclic graph of tasks and each task is an execution of something on a grid resource (or 'computing element'). Tasks may be submitted to any WS-GRAM (Globus Toolkit 4) service. The target resources for the tasks execution are selected by the Pilot service from the set of available resources which match the specific requirements from the task and/or job definition. Some simple conditional execution logic is also provided. The 'Pilot' service is built on the REST concepts and provides a simple API through authenticated HTTPS. This service is deployed and used in production in a Russian national grid project GridNNN.

  15. Grid workflow job execution service 'Pilot'

    Shamardin, Lev; Kryukov, Alexander; Demichev, Andrey; Ilyin, Vyacheslav

    2011-01-01

    'Pilot' is a grid job execution service for workflow jobs. The main goal for the service is to automate computations with multiple stages since they can be expressed as simple workflows. Each job is a directed acyclic graph of tasks and each task is an execution of something on a grid resource (or 'computing element'). Tasks may be submitted to any WS-GRAM (Globus Toolkit 4) service. The target resources for the tasks execution are selected by the Pilot service from the set of available resources which match the specific requirements from the task and/or job definition. Some simple conditional execution logic is also provided. The 'Pilot' service is built on the REST concepts and provides a simple API through authenticated HTTPS. This service is deployed and used in production in a Russian national grid project GridNNN.

  16. Workflow optimization beyond RIS and PACS

    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

  17. Patterns for Parallel Software Design

    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

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

    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).

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

    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.

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

    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.)

  1. Designing Flexible E-Business Workflow Systems

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

    2010-01-01

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

  2. SPECT/CT workflow and imaging protocols

    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.)

  3. IDD Archival Hardware Architecture and Workflow

    Mendonsa, D; Nekoogar, F; Martz, H

    2008-10-09

    This document describes the functionality of every component in the DHS/IDD archival and storage hardware system shown in Fig. 1. The document describes steps by step process of image data being received at LLNL then being processed and made available to authorized personnel and collaborators. Throughout this document references will be made to one of two figures, Fig. 1 describing the elements of the architecture and the Fig. 2 describing the workflow and how the project utilizes the available hardware.

  4. SPECT/CT workflow and imaging protocols

    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.)

  5. Human factors in software development: On its underlying theories and the value of learning from related disciplines. A guest editorial introduction to the special issue

    Amrit, C.; Daneva, Maia; Damian, D.

    2014-01-01

    Human factors play a very important role in Software Development [1]. According to Avison et al. [2] ‘‘Failure to include human factors may explain some of the dissatisfaction with conventional information systems development methodologies; they do not address real organizations’’ (p95 [2]).

  6. Schedule-Aware Workflow Management Systems

    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.

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

    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.

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

    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

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

    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...

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

    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.)

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

    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.)

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

    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...

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

    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

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

    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.

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

    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

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

    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

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

    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

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

    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.

  19. Text mining for the biocuration workflow

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

    2012-01-01

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

  20. ICSSP 2015–Special Issue Introduction

    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...

  1. Electronic resource management systems a workflow approach

    Anderson, Elsa K

    2014-01-01

    To get to the bottom of a successful approach to Electronic Resource Management (ERM), Anderson interviewed staff at 11 institutions about their ERM implementations. Among her conclusions, presented in this issue of Library Technology Reports, is that grasping the intricacies of your workflow-analyzing each step to reveal the gaps and problems-at the beginning is crucial to selecting and implementing an ERM. Whether the system will be used to fill a gap, aggregate critical data, or replace a tedious manual process, the best solution for your library depends on factors such as your current soft

  2. Evolutionary optimization of production materials workflow processes

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

    2014-01-01

    We present an evolutionary optimisation technique for stochastic production processes, which is able to find improved production materials workflow processes with respect to arbitrary combinations of numerical quantities associated with the production process. Working from a core fragment...... of the BPMN language, we employ an evolutionary algorithm where stochastic model checking is used as a fitness function to determine the degree of improvement of candidate processes derived from the original process through mutation and cross-over operations. We illustrate this technique using a case study...

  3. Reenginering of the i4 workflow engine

    Likar, Tilen

    2013-01-01

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

  4. CMS data and workflow management system

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

    2008-01-01

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

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

    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

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

    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.

  7. Declarative Modelling and Safe Distribution of Healthcare Workflows

    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....

  8. Building and documenting workflows with python-based snakemake

    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....

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

    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%.

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

    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.

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

    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.

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

    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.

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

    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.

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

    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

  15. Business and scientific workflows a web service-oriented approach

    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

  16. Design, Modelling and Analysis of a Workflow Reconfiguration

    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...

  17. A Strategy for an MLS Workflow Management System

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

    1999-01-01

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

  18. Deriving DICOM surgical extensions from surgical workflows

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

    2007-03-01

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

  19. Workflow management for a cosmology collaboratory

    Loken, Stewart C.; McParland, Charles

    2001-01-01

    The Nearby Supernova Factory Project will provide a unique opportunity to bring together simulation and observation to address crucial problems in particle and nuclear physics. Its goal is to significantly enhance our understanding of the nuclear processes in supernovae and to improve our ability to use both Type Ia and Type II supernovae as reference light sources (standard candles) in precision measurements of cosmological parameters. Over the past several years, astronomers and astrophysicists have been conducting in-depth sky searches with the goal of identifying supernovae in their earliest evolutionary stages and, during the 4 to 8 weeks of their most ''explosive'' activity, measure their changing magnitude and spectra. The search program currently under development at LBNL is an earth-based observation program utilizing observational instruments at Haleakala and Mauna Kea, Hawaii and Mt. Palomar, California. This new program provides a demanding testbed for the integration of computational, data management and collaboratory technologies. A critical element of this effort is the use of emerging workflow management tools to permit collaborating scientists to manage data processing and storage and to integrate advanced supernova simulation into the real-time control of the experiments. This paper describes the workflow management framework for the project, discusses security and resource allocation requirements and reviews emerging tools to support this important aspect of collaborative work

  20. Software engineering

    Sommerville, Ian

    2010-01-01

    The ninth edition of Software Engineering presents a broad perspective of software engineering, focusing on the processes and techniques fundamental to the creation of reliable, software systems. Increased coverage of agile methods and software reuse, along with coverage of 'traditional' plan-driven software engineering, gives readers the most up-to-date view of the field currently available. Practical case studies, a full set of easy-to-access supplements, and extensive web resources make teaching the course easier than ever.

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

    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.

  2. The economics of information systems and software

    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

  3. Automated Finite State Workflow for Distributed Data Production

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

    2016-10-01

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

  4. Automated Finite State Workflow for Distributed Data Production

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

    2016-01-01

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

  5. Accelerating the scientific exploration process with scientific workflows

    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

  6. Halden project activities on software dependability

    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

  7. 3D Printing of CT Dataset: Validation of an Open Source and Consumer-Available Workflow.

    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.

  8. Software for noise measurements

    Zyryanov, V.A.

    1987-01-01

    The CURS program library comprising 38 fortran-programs, designed for processing descrete experimental data in the form of random or determined periodic processes is described. The library is based on the modular construction principle which allows one to create on its base any sets of programs to solve tasks related to NPP operation, and to develop special software

  9. Swabs to genomes: a comprehensive workflow

    Madison I. Dunitz

    2015-05-01

    Full Text Available The sequencing, assembly, and basic analysis of microbial genomes, once a painstaking and expensive undertaking, has become much easier for research labs with access to standard molecular biology and computational tools. However, there are a confusing variety of options available for DNA library preparation and sequencing, and inexperience with bioinformatics can pose a significant barrier to entry for many who may be interested in microbial genomics. The objective of the present study was to design, test, troubleshoot, and publish a simple, comprehensive workflow from the collection of an environmental sample (a swab to a published microbial genome; empowering even a lab or classroom with limited resources and bioinformatics experience to perform it.

  10. SOFTWARE OPEN SOURCE, SOFTWARE GRATIS?

    Nur Aini Rakhmawati

    2006-01-01

    Full Text Available Normal 0 false false false IN X-NONE X-NONE MicrosoftInternetExplorer4 Berlakunya Undang – undang Hak Atas Kekayaan Intelektual (HAKI, memunculkan suatu alternatif baru untuk menggunakan software open source. Penggunaan software open source menyebar seiring dengan isu global pada Information Communication Technology (ICT saat ini. Beberapa organisasi dan perusahaan mulai menjadikan software open source sebagai pertimbangan. Banyak konsep mengenai software open source ini. Mulai dari software yang gratis sampai software tidak berlisensi. Tidak sepenuhnya isu software open source benar, untuk itu perlu dikenalkan konsep software open source mulai dari sejarah, lisensi dan bagaimana cara memilih lisensi, serta pertimbangan dalam memilih software open source yang ada. Kata kunci :Lisensi, Open Source, HAKI

  11. The P2P approach to interorganizational workflows

    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

  12. Reasoning about repairability of workflows at design time

    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

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

    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

  14. Conceptual framework and architecture for service mediating workflow management

    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

  15. Building and documenting workflows with python-based snakemake

    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

  16. Analyzing the Gap between Workflows and their Natural Language Descriptions

    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

  17. Modelling and analysis of workflow for lean supply chains

    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.

  18. Two-Layer Transaction Management for Workflow Management Applications

    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

  19. Parametric Room Acoustic workflows with real-time acoustic simulation

    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...

  20. Distributed Global Transaction Support for Workflow Management Applications

    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

  1. A Collaborative Workflow for the Digitization of Unique Materials

    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…

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

    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

  3. Workflow automation based on OSI job transfer and manipulation

    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

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

    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....

  5. Data and Workflow Management Challenges in Global Adjoint Tomography

    Lei, W.; Ruan, Y.; Smith, J. A.; Modrak, R. T.; Orsvuran, R.; Krischer, L.; Chen, Y.; Balasubramanian, V.; Hill, J.; Turilli, M.; Bozdag, E.; Lefebvre, M. P.; Jha, S.; Tromp, J.

    2017-12-01

    It is crucial to take the complete physics of wave propagation into account in seismic tomography to further improve the resolution of tomographic images. The adjoint method is an efficient way of incorporating 3D wave simulations in seismic tomography. However, global adjoint tomography is computationally expensive, requiring thousands of wavefield simulations and massive data processing. Through our collaboration with the Oak Ridge National Laboratory (ORNL) computing group and an allocation on Titan, ORNL's GPU-accelerated supercomputer, we are now performing our global inversions by assimilating waveform data from over 1,000 earthquakes. The first challenge we encountered is dealing with the sheer amount of seismic data. Data processing based on conventional data formats and processing tools (such as SAC), which are not designed for parallel systems, becomes our major bottleneck. To facilitate the data processing procedures, we designed the Adaptive Seismic Data Format (ASDF) and developed a set of Python-based processing tools to replace legacy FORTRAN-based software. These tools greatly enhance reproducibility and accountability while taking full advantage of highly parallel system and showing superior scaling on modern computational platforms. The second challenge is that the data processing workflow contains more than 10 sub-procedures, making it delicate to handle and prone to human mistakes. To reduce human intervention as much as possible, we are developing a framework specifically designed for seismic inversion based on the state-of-the art workflow management research, specifically the Ensemble Toolkit (EnTK), in collaboration with the RADICAL team from Rutgers University. Using the initial developments of the EnTK, we are able to utilize the full computing power of the data processing cluster RHEA at ORNL while keeping human interaction to a minimum and greatly reducing the data processing time. Thanks to all the improvements, we are now able to

  6. The Live Access Server Scientific Product Generation Through Workflow Orchestration

    Hankin, S.; Calahan, J.; Li, J.; Manke, A.; O'Brien, K.; Schweitzer, R.

    2006-12-01

    The Live Access Server (LAS) is a well-established Web-application for display and analysis of geo-science data sets. The software, which can be downloaded and installed by anyone, gives data providers an easy way to establish services for their on-line data holdings, so their users can make plots; create and download data sub-sets; compare (difference) fields; and perform simple analyses. Now at version 7.0, LAS has been in operation since 1994. The current "Armstrong" release of LAS V7 consists of three components in a tiered architecture: user interface, workflow orchestration and Web Services. The LAS user interface (UI) communicates with the LAS Product Server via an XML protocol embedded in an HTTP "get" URL. Libraries (APIs) have been developed in Java, JavaScript and perl that can readily generate this URL. As a result of this flexibility it is common to find LAS user interfaces of radically different character, tailored to the nature of specific datasets or the mindset of specific users. When a request is received by the LAS Product Server (LPS -- the workflow orchestration component), business logic converts this request into a series of Web Service requests invoked via SOAP. These "back- end" Web services perform data access and generate products (visualizations, data subsets, analyses, etc.). LPS then packages these outputs into final products (typically HTML pages) via Jakarta Velocity templates for delivery to the end user. "Fine grained" data access is performed by back-end services that may utilize JDBC for data base access; the OPeNDAP "DAPPER" protocol; or (in principle) the OGC WFS protocol. Back-end visualization services are commonly legacy science applications wrapped in Java or Python (or perl) classes and deployed as Web Services accessible via SOAP. Ferret is the default visualization application used by LAS, though other applications such as Matlab, CDAT, and GrADS can also be used. Other back-end services may include generation of Google

  7. Software Epistemology

    2016-03-01

    in-vitro decision to incubate a startup, Lexumo [7], which is developing a commercial Software as a Service ( SaaS ) vulnerability assessment...LTS Label Transition System MUSE Mining and Understanding Software Enclaves RTEMS Real-Time Executive for Multi-processor Systems SaaS Software ...as a Service SSA Static Single Assignment SWE Software Epistemology UD/DU Def-Use/Use-Def Chains (Dataflow Graph)

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

    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.

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

    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.

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

    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.

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

    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.

  12. A practical workflow for making anatomical atlases for biological research.

    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.

  13. Federated Database Services for Wind Tunnel Experiment Workflows

    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.

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

    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.

  15. Secure software development training course

    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.

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

    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.

  17. Software quality concepts and practice

    Galin, Daniel

    2018-01-01

    The book presents a comprehensive discussion on software quality issues and software quality assurance (SQA) principles and practices, and lays special emphasis on implementing and managing SQA. Primarily designed to serve three audiences; universities and college students, vocational training participants, and software engineers and software development managers, the book may be applicable to all personnel engaged in a software projects Features: * A broad view of SQA. The book delves into SQA issues, going beyond the classic boundaries of custom-made software development to also cover in-house software development, subcontractors, and readymade software. * An up-to-date wide-range coverage of SQA and SQA related topics. Providing comprehensive coverage on multifarious SQA subjects, including topics, hardly explored till in SQA texts. * A systematic presentation of the SQA function and its tasks: establishing the SQA processes, planning, coordinating, follow-up, review and evaluation of SQA processes. * Fo...

  18. Distributed execution of aggregated multi domain workflows using an agent framework

    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

  19. Software reliability

    Bendell, A

    1986-01-01

    Software Reliability reviews some fundamental issues of software reliability as well as the techniques, models, and metrics used to predict the reliability of software. Topics covered include fault avoidance, fault removal, and fault tolerance, along with statistical methods for the objective assessment of predictive accuracy. Development cost models and life-cycle cost models are also discussed. This book is divided into eight sections and begins with a chapter on adaptive modeling used to predict software reliability, followed by a discussion on failure rate in software reliability growth mo

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

    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.

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

    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.

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

    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

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

    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

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

    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.

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

    Bistacchi, Andrea

    2015-04-01

    Different Remote Sensing technologies, including photogrammetry and LIDAR, allow collecting 3D dataset that can be used to create 3D digital representations of outcrop surfaces, called Digital Outcrop Models (DOM), or sometimes Virtual Outcrop Models (VOM). Irrespective of the Remote Sensing technique used, DOMs can be represented either by photorealistic point clouds (PC-DOM) or textured surfaces (TS-DOM). The first are datasets composed of millions of points with XYZ coordinates and RGB colour, whilst the latter are triangulated surfaces onto which images of the outcrop have been mapped or "textured" (applying a tech-nology originally developed for movies and videogames). Here we present a workflow that allows exploiting in an integrated and efficient, yet flexible way, both kinds of dataset: PC-DOMs and TS-DOMs. The workflow is composed of three main steps: (1) data collection and processing, (2) interpretation, and (3) modelling. Data collection can be performed with photogrammetry, LIDAR, or other techniques. The quality of photogrammetric datasets obtained with Structure From Motion (SFM) techniques has shown a tremendous improvement over the past few years, and this is becoming the more effective way to collect DOM datasets. The main advantages of photogrammetry over LIDAR are represented by the very simple and lightweight field equipment (a digital camera), and by the arbitrary spatial resolution, that can be increased simply getting closer to the out-crop or by using a different lens. It must be noted that concerns about the precision of close-range photogrammetric surveys, that were justified in the past, are no more a problem if modern software and acquisition schemas are applied. In any case, LIDAR is a well-tested technology and it is still very common. Irrespective of the data collection technology, the output will be a photorealistic point cloud and a collection of oriented photos, plus additional imagery in special projects (e.g. infrared images

  6. Software for Managing Personal Files.

    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…

  7. DataSpaces: An Interaction and Coordination Framework for Coupled Simulation Workflows

    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.

  8. Software Defined Cyberinfrastructure

    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.

  9. Image Classification Workflow Using Machine Learning Methods

    Christoffersen, M. S.; Roser, M.; Valadez-Vergara, R.; Fernández-Vega, J. A.; Pierce, S. A.; Arora, R.

    2016-12-01

    Recent increases in the availability and quality of remote sensing datasets have fueled an increasing number of scientifically significant discoveries based on land use classification and land use change analysis. However, much of the software made to work with remote sensing data products, specifically multispectral images, is commercial and often prohibitively expensive. The free to use solutions that are currently available come bundled up as small parts of much larger programs that are very susceptible to bugs and difficult to install and configure. What is needed is a compact, easy to use set of tools to perform land use analysis on multispectral images. To address this need, we have developed software using the Python programming language with the sole function of land use classification and land use change analysis. We chose Python to develop our software because it is relatively readable, has a large body of relevant third party libraries such as GDAL and Spectral Python, and is free to install and use on Windows, Linux, and Macintosh operating systems. In order to test our classification software, we performed a K-means unsupervised classification, Gaussian Maximum Likelihood supervised classification, and a Mahalanobis Distance based supervised classification. The images used for testing were three Landsat rasters of Austin, Texas with a spatial resolution of 60 meters for the years of 1984 and 1999, and 30 meters for the year 2015. The testing dataset was easily downloaded using the Earth Explorer application produced by the USGS. The software should be able to perform classification based on any set of multispectral rasters with little to no modification. Our software makes the ease of land use classification using commercial software available without an expensive license.

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

    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

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

    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.

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

    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.

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

    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.

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

    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

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

    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.

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

    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.

  17. CMS Alignement and Calibration workflows: lesson learned and future plans

    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.

  18. EDMS based workflow for Printing Industry

    Prathap Nayak

    2013-04-01

    Full Text Available Information is indispensable factor of any enterprise. It can be a record or a document generated for every transaction that is made, which is either a paper based or in electronic format for future reference. A Printing Industry is one such industry in which managing information of various formats, with latest workflows and technologies, could be a nightmare and a challenge for any operator or an user when each process from the least bit of information to a printed product are always dependendent on each other. Hence the information has to be harmonized artistically in order to avoid production downtime or employees pointing fingers at each other. This paper analyses how the implementation of Electronic Document Management System (EDMS could contribute to the Printing Industry for immediate access to stored documents within and across departments irrespective of geographical boundaries. The paper outlines initially with a brief history, contemporary EDMS system and some illustrated examples with a study done by choosing Library as a pilot area for evaluating EDMS. The paper ends with an imitative proposal that maps several document management based activities for implementation of EDMS for a Printing Industry.

  19. Workflow management in large distributed systems

    Legrand, I; Newman, H; Voicu, R; Dobre, C; Grigoras, C

    2011-01-01

    The MonALISA (Monitoring Agents using a Large Integrated Services Architecture) framework provides a distributed service system capable of controlling and optimizing large-scale, data-intensive applications. An essential part of managing large-scale, distributed data-processing facilities is a monitoring system for computing facilities, storage, networks, and the very large number of applications running on these systems in near realtime. All this monitoring information gathered for all the subsystems is essential for developing the required higher-level services—the components that provide decision support and some degree of automated decisions—and for maintaining and optimizing workflow in large-scale distributed systems. These management and global optimization functions are performed by higher-level agent-based services. We present several applications of MonALISA's higher-level services including optimized dynamic routing, control, data-transfer scheduling, distributed job scheduling, dynamic allocation of storage resource to running jobs and automated management of remote services among a large set of grid facilities.

  20. Workflow management in large distributed systems

    Legrand, I.; Newman, H.; Voicu, R.; Dobre, C.; Grigoras, C.

    2011-12-01

    The MonALISA (Monitoring Agents using a Large Integrated Services Architecture) framework provides a distributed service system capable of controlling and optimizing large-scale, data-intensive applications. An essential part of managing large-scale, distributed data-processing facilities is a monitoring system for computing facilities, storage, networks, and the very large number of applications running on these systems in near realtime. All this monitoring information gathered for all the subsystems is essential for developing the required higher-level services—the components that provide decision support and some degree of automated decisions—and for maintaining and optimizing workflow in large-scale distributed systems. These management and global optimization functions are performed by higher-level agent-based services. We present several applications of MonALISA's higher-level services including optimized dynamic routing, control, data-transfer scheduling, distributed job scheduling, dynamic allocation of storage resource to running jobs and automated management of remote services among a large set of grid facilities.

  1. An optimal big data workflow for biomedical image analysis

    Aurelle Tchagna Kouanou

    Full Text Available Background and objective: In the medical field, data volume is increasingly growing, and traditional methods cannot manage it efficiently. In biomedical computation, the continuous challenges are: management, analysis, and storage of the biomedical data. Nowadays, big data technology plays a significant role in the management, organization, and analysis of data, using machine learning and artificial intelligence techniques. It also allows a quick access to data using the NoSQL database. Thus, big data technologies include new frameworks to process medical data in a manner similar to biomedical images. It becomes very important to develop methods and/or architectures based on big data technologies, for a complete processing of biomedical image data. Method: This paper describes big data analytics for biomedical images, shows examples reported in the literature, briefly discusses new methods used in processing, and offers conclusions. We argue for adapting and extending related work methods in the field of big data software, using Hadoop and Spark frameworks. These provide an optimal and efficient architecture for biomedical image analysis. This paper thus gives a broad overview of big data analytics to automate biomedical image diagnosis. A workflow with optimal methods and algorithm for each step is proposed. Results: Two architectures for image classification are suggested. We use the Hadoop framework to design the first, and the Spark framework for the second. The proposed Spark architecture allows us to develop appropriate and efficient methods to leverage a large number of images for classification, which can be customized with respect to each other. Conclusions: The proposed architectures are more complete, easier, and are adaptable in all of the steps from conception. The obtained Spark architecture is the most complete, because it facilitates the implementation of algorithms with its embedded libraries. Keywords: Biomedical images, Big

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

    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

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

    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.

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

    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.

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

    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.

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

    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...

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

    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.

  8. A standard-enabled workflow for synthetic biology

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

    2017-01-01

    A synthetic biology workflow is composed of data repositories that provide information about genetic parts, sequence-level design tools to compose these parts into circuits, visualization tools to depict these designs, genetic design tools to select

  9. Text mining meets workflow: linking U-Compare with Taverna

    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

  10. Job life cycle management libraries for CMS workflow management projects

    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.

  11. A Community-Driven Workflow Recommendation and Reuse Infrastructure

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

  12. modeling workflow management in a distributed computing system

    Dr Obe

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

  13. Scientific workflows as productivity tools for drug discovery.

    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.

  14. Software Innovation

    Rose, Jeremy

      Innovation is the forgotten key to modern systems development - the element that defines the enterprising engineer, the thriving software firm and the cutting edge software application.  Traditional forms of technical education pay little attention to creativity - often encouraging overly...

  15. Workflows for microarray data processing in the Kepler environment

    Stropp Thomas

    2012-05-01

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

  16. Workflows for microarray data processing in the Kepler environment.

    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

  17. Workflows for microarray data processing in the Kepler environment

    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

  18. Selecting Advanced Software Technology in Two Small Manufacturing Enterprises

    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

  19. Software engineering

    Sommerville, Ian

    2016-01-01

    For courses in computer science and software engineering The Fundamental Practice of Software Engineering Software Engineering introduces readers to the overwhelmingly important subject of software programming and development. In the past few years, computer systems have come to dominate not just our technological growth, but the foundations of our world's major industries. This text seeks to lay out the fundamental concepts of this huge and continually growing subject area in a clear and comprehensive manner. The Tenth Edition contains new information that highlights various technological updates of recent years, providing readers with highly relevant and current information. Sommerville's experience in system dependability and systems engineering guides the text through a traditional plan-based approach that incorporates some novel agile methods. The text strives to teach the innovators of tomorrow how to create software that will make our world a better, safer, and more advanced place to live.

  20. Software Process Improvement

    Kuhrmann, Marco; Diebold, Philipp; Münch, Jürgen

    2016-01-01

    Software process improvement (SPI) is around for decades: frameworks are proposed, success factors are studied, and experiences have been reported. However, the sheer mass of concepts, approaches, and standards published over the years overwhelms practitioners as well as researchers. What is out...... to new specialized frameworks. New and specialized frameworks account for the majority of the contributions found (approx. 38%). Furthermore, we find a growing interest in success factors (approx. 16%) to aid companies in conducting SPI and in adapting agile principles and practices for SPI (approx. 10...

  1. Translating Unstructured Workflow Processes to Readable BPEL: Theory and Implementation

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

    2008-01-01

    and not easy to use by end-users. Therefore, we provide a mapping from Workflow Nets (WF-nets) to BPEL. This mapping builds on the rich theory of Petri nets and can also be used to map other languages (e.g., UML, EPC, BPMN, etc.) onto BPEL. In addition to this we have implemented the algorithm in a tool called...... WorkflowNet2BPEL4WS....

  2. Worklist handling in workflow-enabled radiological application systems

    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.

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

    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

  4. CO2 Storage Feasibility: A Workflow for Site Characterisation

    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.

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

    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.

  6. LabelFlow Framework for Annotating Workflow Provenance

    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.

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

    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.

  8. The CMS Data Quality Monitoring software experience and future improvements

    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.

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

    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.

  10. Rapid Energy Modeling Workflow Demonstration Project

    2014-01-01

    app FormIt for conceptual modeling with further refinement available in Revit or Vasari. Modeling can also be done in Revit (detailed and conceptual...referenced building model while in the field. • Autodesk® Revit is a BIM software application with integrated energy and carbon analyses driven by Green...FormIt, Revit and Vasari, and (3) comparative analysis. The energy results of these building analyses are represented as annual energy use for natural

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

    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.

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

    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.

  13. Software requirements

    Wiegers, Karl E

    2003-01-01

    Without formal, verifiable software requirements-and an effective system for managing them-the programs that developers think they've agreed to build often will not be the same products their customers are expecting. In SOFTWARE REQUIREMENTS, Second Edition, requirements engineering authority Karl Wiegers amplifies the best practices presented in his original award-winning text?now a mainstay for anyone participating in the software development process. In this book, you'll discover effective techniques for managing the requirements engineering process all the way through the development cy

  14. Application of agile methodologies in software development

    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.

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

    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.

  16. Software Reviews.

    Dwyer, Donna; And Others

    1989-01-01

    Reviewed are seven software packages for Apple and IBM computers. Included are: "Toxicology"; "Science Corner: Space Probe"; "Alcohol and Pregnancy"; "Science Tool Kit Plus"; Computer Investigations: Plant Growth"; "Climatrolls"; and "Animal Watch: Whales." (CW)

  17. Software Reviews.

    Davis, Shelly J., Ed.; Knaupp, Jon, Ed.

    1984-01-01

    Reviewed is computer software on: (1) classification of living things, a tutorial program for grades 5-10; and (2) polynomial practice using tiles, a drill-and-practice program for algebra students. (MNS)

  18. Software Reviews.

    Miller, Anne, Ed.; Radziemski, Cathy, Ed.

    1988-01-01

    Three pieces of computer software are described and reviewed: HyperCard, to build and use varied applications; Iggy's Gnees, for problem solving with shapes in grades kindergarten-two; and Algebra Shop, for practicing skills and problem solving. (MNS)

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

    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

  20. Visual Workflows for Oil and Gas Exploration

    Hollt, Thomas

    2013-04-14

    The most important resources to fulfill today’s energy demands are fossil fuels, such as oil and natural gas. When exploiting hydrocarbon reservoirs, a detailed and credible model of the subsurface structures to plan the path of the borehole, is crucial in order to minimize economic and ecological risks. Before that, the placement, as well as the operations of oil rigs need to be planned carefully, as off-shore oil exploration is vulnerable to hazards caused by strong currents. The oil and gas industry therefore relies on accurate ocean forecasting systems for planning their operations. This thesis presents visual workflows for creating subsurface models as well as planning the placement and operations of off-shore structures. Creating a credible subsurface model poses two major challenges: First, the structures in highly ambiguous seismic data are interpreted in the time domain. Second, a velocity model has to be built from this interpretation to match the model to depth measurements from wells. If it is not possible to obtain a match at all positions, the interpretation has to be updated, going back to the first step. This results in a lengthy back and forth between the different steps, or in an unphysical velocity model in many cases. We present a novel, integrated approach to interactively creating subsurface models from reflection seismics, by integrating the interpretation of the seismic data using an interactive horizon extraction technique based on piecewise global optimization with velocity modeling. Computing and visualizing the effects of changes to the interpretation and velocity model on the depth-converted model, on the fly enables an integrated feedback loop that enables a completely new connection of the seismic data in time domain, and well data in depth domain. For planning the operations of off-shore structures we present a novel integrated visualization system that enables interactive visual analysis of ensemble simulations used in ocean

  1. Automated Processing Workflow for Ambient Seismic Recordings

    Girard, A. J.; Shragge, J.

    2017-12-01

    Structural imaging using body-wave energy present in ambient seismic data remains a challenging task, largely because these wave modes are commonly much weaker than surface wave energy. In a number of situations body-wave energy has been extracted successfully; however, (nearly) all successful body-wave extraction and imaging approaches have focused on cross-correlation processing. While this is useful for interferometric purposes, it can also lead to the inclusion of unwanted noise events that dominate the resulting stack, leaving body-wave energy overpowered by the coherent noise. Conversely, wave-equation imaging can be applied directly on non-correlated ambient data that has been preprocessed to mitigate unwanted energy (i.e., surface waves, burst-like and electromechanical noise) to enhance body-wave arrivals. Following this approach, though, requires a significant preprocessing effort on often Terabytes of ambient seismic data, which is expensive and requires automation to be a feasible approach. In this work we outline an automated processing workflow designed to optimize body wave energy from an ambient seismic data set acquired on a large-N array at a mine site near Lalor Lake, Manitoba, Canada. We show that processing ambient seismic data in the recording domain, rather than the cross-correlation domain, allows us to mitigate energy that is inappropriate for body-wave imaging. We first develop a method for window selection that automatically identifies and removes data contaminated by coherent high-energy bursts. We then apply time- and frequency-domain debursting techniques to mitigate the effects of remaining strong amplitude and/or monochromatic energy without severely degrading the overall waveforms. After each processing step we implement a QC check to investigate improvements in the convergence rates - and the emergence of reflection events - in the cross-correlation plus stack waveforms over hour-long windows. Overall, the QC analyses suggest that

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

    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.

  3. Improving adherence to the Epic Beacon ambulatory workflow.

    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.

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

    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.

  5. The myth of standardized workflow in primary care.

    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.

  6. Exploring Dental Providers’ Workflow in an Electronic Dental Record Environment

    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

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

    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.

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

    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.

  9. Software for rapid prototyping in the pharmaceutical and biotechnology industries.

    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.

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

    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

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

    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

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

    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.

  13. Distributing Workflows over a Ubiquitous P2P Network

    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.

  14. Provenance-based refresh in data-oriented workflows

    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.

  15. Integration of the radiotherapy irradiation planning in the digital workflow

    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.)

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

    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.

  17. Software reengineering

    Fridge, Ernest M., III

    1991-01-01

    Today's software systems generally use obsolete technology, are not integrated properly with other software systems, and are difficult and costly to maintain. The discipline of reverse engineering is becoming prominent as organizations try to move their systems up to more modern and maintainable technology in a cost effective manner. JSC created a significant set of tools to develop and maintain FORTRAN and C code during development of the Space Shuttle. This tool set forms the basis for an integrated environment to re-engineer existing code into modern software engineering structures which are then easier and less costly to maintain and which allow a fairly straightforward translation into other target languages. The environment will support these structures and practices even in areas where the language definition and compilers do not enforce good software engineering. The knowledge and data captured using the reverse engineering tools is passed to standard forward engineering tools to redesign or perform major upgrades to software systems in a much more cost effective manner than using older technologies. A beta vision of the environment was released in Mar. 1991. The commercial potential for such re-engineering tools is very great. CASE TRENDS magazine reported it to be the primary concern of over four hundred of the top MIS executives.

  18. Software for nuclear data acquisition systems

    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)

  19. A workflow for the 3D visualization of meteorological data

    Helbig, Carolin; Rink, Karsten

    2014-05-01

    In the future, climate change will strongly influence our environment and living conditions. To predict possible changes, climate models that include basic and process conditions have been developed and big data sets are produced as a result of simulations. The combination of various variables of climate models with spatial data from different sources helps to identify correlations and to study key processes. For our case study we use results of the weather research and forecasting (WRF) model of two regions at different scales that include various landscapes in Northern Central Europe and Baden-Württemberg. We visualize these simulation results in combination with observation data and geographic data, such as river networks, to evaluate processes and analyze if the model represents the atmospheric system sufficiently. For this purpose, a continuous workflow that leads from the integration of heterogeneous raw data to visualization using open source software (e.g. OpenGeoSys Data Explorer, ParaView) is developed. These visualizations can be displayed on a desktop computer or in an interactive virtual reality environment. We established a concept that includes recommended 3D representations and a color scheme for the variables of the data based on existing guidelines and established traditions in the specific domain. To examine changes over time in observation and simulation data, we added the temporal dimension to the visualization. In a first step of the analysis, the visualizations are used to get an overview of the data and detect areas of interest such as regions of convection or wind turbulences. Then, subsets of data sets are extracted and the included variables can be examined in detail. An evaluation by experts from the domains of visualization and atmospheric sciences establish if they are self-explanatory and clearly arranged. These easy-to-understand visualizations of complex data sets are the basis for scientific communication. In addition, they have

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

    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.

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

    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

  2. Software Authentication

    Wolford, J.K.; Geelhood, B.D.; Hamilton, V.A.; Ingraham, J.; MacArthur, D.W.; Mitchell, D.J.; Mullens, J.A.; Vanier, P. E.; White, G.K.; Whiteson, R.

    2001-01-01

    The effort to define guidance for authentication of software for arms control and nuclear material transparency measurements draws on a variety of disciplines and has involved synthesizing established criteria and practices with newer methods. Challenges include the need to protect classified information that the software manipulates as well as deal with the rapid pace of innovation in the technology of nuclear material monitoring. The resulting guidance will shape the design of future systems and inform the process of authentication of instruments now being developed. This paper explores the technical issues underlying the guidance and presents its major tenets

  3. Software engineering

    Thorin, Marc

    1985-01-01

    Software Engineering describes the conceptual bases as well as the main methods and rules on computer programming. This book presents software engineering as a coherent and logically built synthesis and makes it possible to properly carry out an application of small or medium difficulty that can later be developed and adapted to more complex cases. This text is comprised of six chapters and begins by introducing the reader to the fundamental notions of entities, actions, and programming. The next two chapters elaborate on the concepts of information and consistency domains and show that a proc

  4. Dynamic Service Selection in Workflows Using Performance Data

    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.

  5. Task Delegation Based Access Control Models for Workflow Systems

    Gaaloul, Khaled; Charoy, François

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

  6. Implementation of the electronic DDA workflow for NSSS system design

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

    1996-06-01

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

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

    Krogel, Jaron T.

    2016-01-01

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

  8. Assessment of the Nurse Medication Administration Workflow Process

    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.

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

    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.

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

    FARRELL, Steven; The ATLAS collaboration

    2015-01-01

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

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

    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.

  12. Exformatics Declarative Case Management Workflows as DCR Graphs

    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...

  13. Addressing informatics challenges in Translational Research with workflow technology.

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

    2008-09-01

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

  14. Reviews, Software.

    Science Teacher, 1988

    1988-01-01

    Reviews two computer software packages for use in physical science, physics, and chemistry classes. Includes "Physics of Model Rocketry" for Apple II, and "Black Box" for Apple II and IBM compatible computers. "Black Box" is designed to help students understand the concept of indirect evidence. (CW)

  15. Software Reviews.

    Kinnaman, Daniel E.; And Others

    1988-01-01

    Reviews four educational software packages for Apple, IBM, and Tandy computers. Includes "How the West was One + Three x Four,""Mavis Beacon Teaches Typing,""Math and Me," and "Write On." Reviews list hardware requirements, emphasis, levels, publisher, purchase agreements, and price. Discusses the strengths…

  16. Software Review.

    McGrath, Diane, Ed.

    1989-01-01

    Reviewed is a computer software package entitled "Audubon Wildlife Adventures: Grizzly Bears" for Apple II and IBM microcomputers. Included are availability, hardware requirements, cost, and a description of the program. The murder-mystery flavor of the program is stressed in this program that focuses on illegal hunting and game…

  17. Software Reviews.

    Teles, Elizabeth, Ed.; And Others

    1990-01-01

    Reviewed are two computer software packages for Macintosh microcomputers including "Phase Portraits," an exploratory graphics tool for studying first-order planar systems; and "MacMath," a set of programs for exploring differential equations, linear algebra, and other mathematical topics. Features, ease of use, cost, availability, and hardware…

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

    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

  19. Lean software development in action

    Janes, Andrea

    2014-01-01

    This book illustrates how goal-oriented, automated measurement can be used to create Lean organizations and to facilitate the development of Lean software, while also demonstrating the practical implementation of Lean software development by combining tried and trusted tools. In order to be successful, a Lean orientation of software development has to go hand in hand with a company's overall business strategy. To achieve this, two interrelated aspects require special attention: measurement and experience management. In this book, Janes and Succi provide the necessary knowledge to establish "

  20. Matches, Mismatches, and Methods: Multiple-View Workflows for Energy Portfolio Analysis.

    Brehmer, Matthew; Ng, Jocelyn; Tate, Kevin; Munzner, Tamara

    2016-01-01

    The energy performance of large building portfolios is challenging to analyze and monitor, as current analysis tools are not scalable or they present derived and aggregated data at too coarse of a level. We conducted a visualization design study, beginning with a thorough work domain analysis and a characterization of data and task abstractions. We describe generalizable visual encoding design choices for time-oriented data framed in terms of matches and mismatches, as well as considerations for workflow design. Our designs address several research questions pertaining to scalability, view coordination, and the inappropriateness of line charts for derived and aggregated data due to a combination of data semantics and domain convention. We also present guidelines relating to familiarity and trust, as well as methodological considerations for visualization design studies. Our designs were adopted by our collaborators and incorporated into the design of an energy analysis software application that will be deployed to tens of thousands of energy workers in their client base.

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

    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

  2. Workflow management versus case handling: results from a controlled software experiment

    Mutschler, B.B.; Weber, B.; Reichert, M.U.

    2008-01-01

    Business Process Management (BPM) technology has become an important instrument for improving process performance. When considering its use, however, enterprises typically have to rely on vendor promises or qualitative reports. What is still missing and what is also demanded by IT decision makers

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

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

    2012-12-15

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

  4. The ATLAS Data Management Software Engineering Process

    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...

  5. The ATLAS Data Management Software Engineering Process

    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...

  6. The CMS Data Quality Monitoring software experience and future improvements

    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.

  7. Computing and software

    White, G. C.

    2004-06-01

    pieces of likelihood functions together to generate estimates. The idea is interesting, and maybe some bright young statistician can work out the specifics to implement the procedure. Choquet et al. (2004 describe MSURGE, a software package that implements the multistate capture–recapture models. The unique feature of MSURGE is that the design matrix is constructed with an interpreted language called GEMACO. Because MSURGE is limited to just multistate models, the special requirements of these likelihoods can be provided. The software and methods presented in these papers gives biologists and wildlife managers an expanding range of possibilities for data analysis. Although ease–of–use is generally getting better, it does not replace the need for understanding of the requirements and structure of the models being computed. The internet provides access to many free software packages as well as user–discussion groups to share knowledge and ideas. (A starting point for wildlife–related applications is (http://www.phidot.org.

  8. Testing Scientific Software: A Systematic Literature Review

    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

  9. Testing Scientific Software: A Systematic Literature Review.

    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.

  10. Software Tools for Software Maintenance

    1988-10-01

    COMMUNICATIONS, AND COMPUTER SCIENCES I ,(AIRMICS) FO~SOFTWARE TOOLS (.o FOR SOF1 ’ARE MAINTENANCE (ASQBG-1-89-001) October, 1988 DTIC ELECTE -ifB...SUNWW~. B..c Program An~Iysw HA.c C-Tractr C Cobol Stncturing Facility VS Cobol 11 F-Scan Foctma Futbol Cobol Fortran Sltiuc Code Anaiyaer Fortran IS

  11. Implementing Software Defined Radio

    Grayver, Eugene

    2013-01-01

    Software Defined Radio makes wireless communications easier, more efficient, and more reliable. This book bridges the gap between academic research and practical implementation. When beginning a project, practicing engineers, technical managers, and graduate students can save countless hours by considering the concepts presented in these pages. The author covers the myriad options and trade-offs available when selecting an appropriate hardware architecture. As demonstrated here, the choice between hardware- and software-centric architecture can mean the difference between meeting an aggressive schedule and bogging down in endless design iterations. Because of the author’s experience overseeing dozens of failed and successful developments, he is able to present many real-life examples. Some of the key concepts covered are: Choosing the right architecture for the market – laboratory, military, or commercial Hardware platforms – FPGAs, GPPs, specialized and hybrid devices Standardization efforts to ens...

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

    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.

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

    Ross, Peeter; Pohjonen, Hanna

    2011-04-01

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

  14. Implementation of a healthcare process in four different workflow systems

    Mans, R.S.; Aalst, van der W.M.P.; Russell, N.C.; Bakker, P.J.M.

    2009-01-01

    Currently, many hospitals are investigating the use of a work-flow management system in order to provide support for care processes. However, today's workow management systems fall short in supporting care processes as exibility is required for its execution. In this paper, we investigate the

  15. A Generalized Email Classification System for Workflow Analysis

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

    2017-01-01

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

  16. 3D workflows in orthodontics, maxillofacial surgery and prosthodontics

    van der Meer, Wicher Jurjen

    2016-01-01

    In this thesis different aspects of digital workflows in Orthodontics, Maxillofacial Surgery and Prosthodontics are discussed and, where possible, placed in a broader perspective thereby attempting to go both broader and deeper into the implications of the introduction of 3D digital technology in

  17. Collaborative e-Science Experiments and Scientific Workflows

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

    2011-01-01

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

  18. SHIWA workflow interoperability solutions for neuroimaging data analysis

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

    2012-01-01

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

  19. Supporting flexible processes with adaptive workflow and case handling

    Günther, C.W.; Reichert, M.; Aalst, van der W.M.P.

    2008-01-01

    Workflow management technology has profoundly transformed the way complex tasks are being handled in modern, large-scale organizations. However, it is mostly those systems' inherent lack of flexibility that hinders their broad acceptance, and that is perceived as annoyance by users. In this context,

  20. Styx Grid Services: Lightweight Middleware for Efficient Scientific Workflows

    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.

  1. CrossFlow: integrating workflow management and electronic commerce

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

    2001-01-01

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

  2. CrossFlow: Integrating Workflow Management and Electronic Commerce

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

    2001-01-01

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

  3. How to increase work autonomy in workflow management systems?

    Vanderfeesten, I.T.P.; Reijers, H.A.

    2006-01-01

    Abstract: Purpose – Current workflow management systems (WfMS's) are often too rigid and lead to "chain production" in the office. The paper proposes a number of "tuning measures" to reconfigure an implemented WfMS in such a way that it is more agreeable to the needs of its users.

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

    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.

  5. The CMS tracker calibration workflow: Experience with cosmic ray data

    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.

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

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

    2009-01-01

    We present a field study of oncology workflow, involving doctors, nurses and pharmacists at Danish hospitals and discuss the obstacles, enablers and challenges for the use of computer based clinical practice guidelines. Related to the CIGDec approach of Pesic and van der Aalst we then describe how...

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

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

    2017-01-01

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

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

    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

  9. EPIQR software

    Flourentzos, F. [Federal Institute of Technology, Lausanne (Switzerland); Droutsa, K. [National Observatory of Athens, Athens (Greece); Wittchen, K.B. [Danish Building Research Institute, Hoersholm (Denmark)

    1999-11-01

    The support of the EPIQR method is a multimedia computer program. Several modules help the users of the method to treat the data collected during a diagnosis survey, to set up refurbishment scenario and calculate their cost or energy performance, and finally to visualize the results in a comprehensive way and to prepare quality reports. This article presents the structure and the main features of the software. (au)

  10. Enabling scientific workflows in virtual reality

    Kreylos, O.; Bawden, G.; Bernardin, T.; Billen, M.I.; Cowgill, E.S.; Gold, R.D.; Hamann, B.; Jadamec, M.; Kellogg, L.H.; Staadt, O.G.; Sumner, D.Y.

    2006-01-01

    To advance research and improve the scientific return on data collection and interpretation efforts in the geosciences, we have developed methods of interactive visualization, with a special focus on immersive virtual reality (VR) environments. Earth sciences employ a strongly visual approach to the measurement and analysis of geologic data due to the spatial and temporal scales over which such data ranges, As observations and simulations increase in size and complexity, the Earth sciences are challenged to manage and interpret increasing amounts of data. Reaping the full intellectual benefits of immersive VR requires us to tailor exploratory approaches to scientific problems. These applications build on the visualization method's strengths, using both 3D perception and interaction with data and models, to take advantage of the skills and training of the geological scientists exploring their data in the VR environment. This interactive approach has enabled us to develop a suite of tools that are adaptable to a range of problems in the geosciences and beyond. Copyright ?? 2008 by the Association for Computing Machinery, Inc.

  11. Software preservation

    Tadej Vodopivec

    2011-01-01

    Full Text Available Comtrade Ltd. covers a wide range of activities related to information and communication technologies; its deliverables include web applications, locally installed programs,system software, drivers, embedded software (used e.g. in medical devices, auto parts,communication switchboards. Also the extensive knowledge and practical experience about digital long-term preservation technologies have been acquired. This wide spectrum of activities puts us in the position to discuss the often overlooked aspect of the digital preservation - preservation of software programs. There are many resources dedicated to digital preservation of digital data, documents and multimedia records,but not so many about how to preserve the functionalities and features of computer programs. Exactly these functionalities - dynamic response to inputs - render the computer programs rich compared to documents or linear multimedia. The article opens the questions on the beginning of the way to the permanent digital preservation. The purpose is to find a way in the right direction, where all relevant aspects will be covered in proper balance. The following questions are asked: why at all to preserve computer programs permanently, who should do this and for whom, when we should think about permanent program preservation, what should be persevered (such as source code, screenshots, documentation, and social context of the program - e.g. media response to it ..., where and how? To illustrate the theoretic concepts given the idea of virtual national museum of electronic banking is also presented.

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

    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

  13. Workflows Table: Herramienta de gestión de Workflows para Tiendeo

    Pellicero Argilaga, Francesc

    2015-01-01

    Diseño e implementación de un sistema software de gestión de tareas y peticiones para el equipo de desarrollo de Tiendeo Web Marketing S.L. Incluye todas las fases del desarrollo: toma de requisitos, estudio de soluciones actuales, especificación, diseño e implementación del sistema.

  14. A Workflow-Oriented Approach To Propagation Models In Heliophysics

    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

  15. Establishing software quality assurance

    Malsbury, J.

    1983-01-01

    This paper is concerned with four questions about establishing software QA: What is software QA. Why have software QA. What is the role of software QA. What is necessary to ensure the success of software QA

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

    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

  17. Contract-Based Transaction Management in Cross-Organizational Workflow Management

    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,

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

    Mthombeni, Thabo DM

    2011-12-01

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

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

    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.

  20. Finding the Right Educational Software for Your Child.

    Moore, Jack

    1990-01-01

    Ideas are presented for identifying, evaluating, and selecting instructional software for children with special needs. The article notes several library research tools as sources of information and lists specific questions to consider when evaluating software. (JDD)

  1. Simulation software: engineer processes before reengineering.

    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.

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

    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)

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

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

    2013-01-01

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

  4. Program specialization

    Marlet, Renaud

    2013-01-01

    This book presents the principles and techniques of program specialization - a general method to make programs faster (and possibly smaller) when some inputs can be known in advance. As an illustration, it describes the architecture of Tempo, an offline program specializer for C that can also specialize code at runtime, and provides figures for concrete applications in various domains. Technical details address issues related to program analysis precision, value reification, incomplete program specialization, strategies to exploit specialized program, incremental specialization, and data speci

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

    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...

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

    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.

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

    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.

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

    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.

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

    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

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

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

    2010-01-01

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

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

    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...

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

    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...

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

    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.

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

    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

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

    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.

  16. Networked Print Production: Does JDF Provide a Perfect Workflow?

    Bernd Zipper

    2004-12-01

    Full Text Available The "networked printing works" is a well-worn slogan used by many providers in the graphics industry and for the past number of years printing-works manufacturers have been working on the goal of achieving the "networked printing works". A turning point from the concept to real implementation can now be expected at drupa 2004: JDF (Job Definition Format and thus "networked production" will form the center of interest here. The first approaches towards a complete, networked workflow between prepress, print and postpress in production are already available - the products and solutions will now be presented publicly at drupa 2004. So, drupa 2004 will undoubtedly be the "JDF-drupa" - the drupa where machines learn to communicate with each other digitally - the drupa, where the dream of general system and job communication in the printing industry can be first realized. CIP3, which has since been renamed CIP4, is an international consortium of leading manufacturers from the printing and media industry who have taken on the task of integrating processes for prepress, print and postpress. The association, to which nearly all manufacturers in the graphics industry belong, has succeeded with CIP3 in developing a first international standard for the transmission of control data in the print workflow.Further development of the CIP4 standard now includes a more extensive "system language" called JDF, which will guarantee workflow communication beyond manufacturer boundaries. However, not only data for actual print production will be communicated with JDF (Job Definition Format: planning and calculation data for MIS (Management Information systems and calculation systems will also be prepared. The German printing specialist Hans-Georg Wenke defines JDF as follows: "JDF takes over data from MIS for machines, aggregates and their control desks, data exchange within office applications, and finally ensures that data can be incorporated in the technical workflow

  17. Global Software Engineering: A Software Process Approach

    Richardson, Ita; Casey, Valentine; Burton, John; McCaffery, Fergal

    Our research has shown that many companies are struggling with the successful implementation of global software engineering, due to temporal, cultural and geographical distance, which causes a range of factors to come into play. For example, cultural, project managementproject management and communication difficulties continually cause problems for software engineers and project managers. While the implementation of efficient software processes can be used to improve the quality of the software product, published software process models do not cater explicitly for the recent growth in global software engineering. Our thesis is that global software engineering factors should be included in software process models to ensure their continued usefulness in global organisations. Based on extensive global software engineering research, we have developed a software process, Global Teaming, which includes specific practices and sub-practices. The purpose is to ensure that requirements for successful global software engineering are stipulated so that organisations can ensure successful implementation of global software engineering.

  18. Handling of Multimedia Files in the Invenio Software

    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...

  19. Software system safety

    Uber, James G.

    1988-01-01

    Software itself is not hazardous, but since software and hardware share common interfaces there is an opportunity for software to create hazards. Further, these software systems are complex, and proven methods for the design, analysis, and measurement of software safety are not yet available. Some past software failures, future NASA software trends, software engineering methods, and tools and techniques for various software safety analyses are reviewed. Recommendations to NASA are made based on this review.

  20. Avionics Simulation, Development and Software Engineering

    2002-01-01

    During this reporting period, all technical responsibilities were accomplished as planned. A close working relationship was maintained with personnel of the MSFC Avionics Department Software Group (ED14), the MSFC EXPRESS Project Office (FD31), and the Huntsville Boeing Company. Accomplishments included: performing special tasks; supporting Software Review Board (SRB), Avionics Test Bed (ATB), and EXPRESS Software Control Panel (ESCP) activities; participating in technical meetings; and coordinating issues between the Boeing Company and the MSFC Project Office.