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Sample records for complex healthcare workflows

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

    DEFF Research Database (Denmark)

    Bertolini, Cristiano; Liu, Zhiming; Srba, Jiri

    2013-01-01

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

  2. Complexity Metrics for Workflow Nets

    DEFF Research Database (Denmark)

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

    2009-01-01

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

  3. Declarative Modelling and Safe Distribution of Healthcare Workflows

    DEFF Research Database (Denmark)

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

    2012-01-01

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

  4. Modeling Complex Workflow in Molecular Diagnostics

    Science.gov (United States)

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

    2010-01-01

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

  5. Leading healthcare in complexity.

    Science.gov (United States)

    Cohn, Jeffrey

    2014-12-01

    Healthcare institutions and providers are in complexity. Networks of interconnections from relationships and technology create conditions in which interdependencies and non-linear dynamics lead to surprising, unpredictable outcomes. Previous effective approaches to leadership, focusing on top-down bureaucratic methods, are no longer effective. Leading in complexity requires leaders to accept the complexity, create an adaptive space in which innovation and creativity can flourish and then integrate the successful practices that emerge into the formal organizational structure. Several methods for doing adaptive space work will be discussed. Readers will be able to contrast traditional leadership approaches with leading in complexity. They will learn new behaviours that are required of complexity leaders, along with challenges they will face, often from other leaders within the organization.

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

    Science.gov (United States)

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

    2017-06-01

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

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

    NARCIS (Netherlands)

    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

  8. Complexity leadership: a healthcare imperative.

    Science.gov (United States)

    Weberg, Dan

    2012-01-01

    The healthcare system is plagued with increasing cost and poor quality outcomes. A major contributing factor for these issues is that outdated leadership practices, such as leader-centricity, linear thinking, and poor readiness for innovation, are being used in healthcare organizations. Complexity leadership theory provides a new framework with which healthcare leaders may practice leadership. Complexity leadership theory conceptualizes leadership as a continual process that stems from collaboration, complex systems thinking, and innovation mindsets. Compared to transactional and transformational leadership concepts, complexity leadership practices hold promise to improve cost and quality in health care. © 2012 Wiley Periodicals, Inc.

  9. On predicting the results of applying workflow management in a healthcare context

    NARCIS (Netherlands)

    Chermin, B.; Frey, I.A.; Reijers, H.A.; Smeets, H.J.

    2012-01-01

    Even though workflow management systems are currently not being applied on a wide scale in healthcare settings, their benefits with respect to operational efficiency and reducing patient risk seem enticing. The authors show how an approach that is rooted in simulation can be useful to predict the

  10. An Assisted Workflow for the Early Design of Nearly Zero Emission Healthcare Buildings

    Directory of Open Access Journals (Sweden)

    Hassan A. Sleiman

    2017-07-01

    Full Text Available Energy efficiency in buildings is one of the main goals of many governmental policies due to their high impact on the carbon dioxide emissions in Europe. One of these targets is to reduce the energy consumption in healthcare buildings, which are known to be among the most energy-demanding building types. Although design decisions made at early design phases have a significant impact on the energy performance of the realized buildings, only a small portion of possible early designs is analyzed, which does not ensure an optimal building design. We propose an automated early design support workflow, accompanied by a set of tools, for achieving nearly zero emission healthcare buildings. It is intended to be used by decision makers during the early design phase. It starts with the user-defined brief and the design rules, which are the input for the Early Design Configurator (EDC. The EDC generates multiple design alternatives following an evolutionary algorithm while trying to satisfy user requirements and geometric constraints. The generated alternatives are then validated by means of an Early Design Validator (EDV, and then, early energy and cost assessments are made using two early assessment tools. A user-friendly dashboard is used to guide the user and to illustrate the workflow results, whereas the chosen alternative at the end of the workflow is considered as the starting point for the next design phases. Our proposal has been implemented using Building Information Models (BIM and validated by means of a case study on a healthcare building and several real demonstrations from different countries in the context of the European project STREAMER.

  11. Complexity science and leadership in healthcare.

    Science.gov (United States)

    Burns, J P

    2001-10-01

    The emerging field of complexity science offers an alternative leadership strategy for the chaotic, complex healthcare environment. A survey revealed that healthcare leaders intuitively support principles of complexity science. Leadership that uses complexity principles offers opportunities in the chaotic healthcare environment to focus less on prediction and control and more on fostering relationships and creating conditions in which complex adaptive systems can evolve to produce creative outcomes.

  12. A healthcare Lean Six Sigma System for postanesthesia care unit workflow improvement.

    Science.gov (United States)

    Kuo, Alex Mu-Hsing; Borycki, Elizabeth; Kushniruk, Andre; Lee, Te-Shu

    2011-01-01

    The aim of this article is to propose a new model called Healthcare Lean Six Sigma System that integrates Lean and Six Sigma methodologies to improve workflow in a postanesthesia care unit. The methodology of the proposed model is fully described. A postanesthesia care unit case study is also used to demonstrate the benefits of using the Healthcare Lean Six Sigma System model by combining Lean and Six Sigma methodologies together. The new model bridges the service gaps between health care providers and patients, balances the requirements of health care managers, and delivers health care services to patients by taking the benefits of the Lean speed and Six Sigma high-quality principles. The full benefits of the new model will be realized when applied at both strategic and operational levels. For further research, we will examine how the proposed model is used in different real-world case studies.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    Johnson, Kevin B; Lorenzi, Nancy M

    2011-01-01

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

  15. An assisted workflow for the early design of nearly zero emission healthcare buildings

    NARCIS (Netherlands)

    Sleiman, H.A.; Hempel, S.; Traversari, A.A.L.; Bruinenberg, S.

    2017-01-01

    Energy efficiency in buildings is one of the main goals of many governmental policies due to their high impact on the carbon dioxide emissions in Europe. One of these targets is to reduce the energy consumption in healthcare buildings, which are known to be among the most energy-demanding building

  16. The use of workflows in the design and implementation of complex experiments in macromolecular crystallography

    International Nuclear Information System (INIS)

    Brockhauser, Sandor; Svensson, Olof; Bowler, Matthew W.; Nanao, Max; Gordon, Elspeth; Leal, Ricardo M. F.; Popov, Alexander; Gerring, Matthew; McCarthy, Andrew A.; Gotz, Andy

    2012-01-01

    A powerful and easy-to-use workflow environment has been developed at the ESRF for combining experiment control with online data analysis on synchrotron beamlines. This tool provides the possibility of automating complex experiments without the need for expertise in instrumentation control and programming, but rather by accessing defined beamline services. The automation of beam delivery, sample handling and data analysis, together with increasing photon flux, diminishing focal spot size and the appearance of fast-readout detectors on synchrotron beamlines, have changed the way that many macromolecular crystallography experiments are planned and executed. Screening for the best diffracting crystal, or even the best diffracting part of a selected crystal, has been enabled by the development of microfocus beams, precise goniometers and fast-readout detectors that all require rapid feedback from the initial processing of images in order to be effective. All of these advances require the coupling of data feedback to the experimental control system and depend on immediate online data-analysis results during the experiment. To facilitate this, a Data Analysis WorkBench (DAWB) for the flexible creation of complex automated protocols has been developed. Here, example workflows designed and implemented using DAWB are presented for enhanced multi-step crystal characterizations, experiments involving crystal reorientation with kappa goniometers, crystal-burning experiments for empirically determining the radiation sensitivity of a crystal system and the application of mesh scans to find the best location of a crystal to obtain the highest diffraction quality. Beamline users interact with the prepared workflows through a specific brick within the beamline-control GUI MXCuBE

  17. Managing today's complex healthcare business enterprise: reflections on distinctive requirements of healthcare management education.

    Science.gov (United States)

    Welton, William E

    2004-01-01

    In early 2001, the community of educational programs offering master's-level education in healthcare management began an odyssey to modernize its approach to the organization and delivery of healthcare management education. The community recognized that cumulative long-term changes within healthcare management practice required a careful examination of healthcare management context and manpower requirements. This article suggests an evidence-based rationale for defining the distinctive elements of healthcare management, thus suggesting a basis for review and transformation of master's-level healthcare management curricula. It also suggests ways to modernize these curricula in a manner that recognizes the distinctiveness of the healthcare business enterprise as well as the changing management roles and careers within these complex organizations and systems. Through such efforts, the healthcare management master's-level education community would be better prepared to meet current and future challenges, to increase its relevance to the management practice community, and to allocate scarce faculty and program resources more effectively.

  18. A structured workflow for mapping human Sin3 histone deacetylase complex interactions using Halo-MudPIT AP-MS.

    Science.gov (United States)

    Banks, Charles A S; Thornton, Janet L; Eubanks, Cassandra G; Adams, Mark K; Miah, Sayem; Boanca, Gina; Liu, Xingyu; Katt, Maria; Parmely, Tari; Florens, Laurence A; Washburn, Michael P

    2018-03-29

    Although a variety of affinity purification mass spectrometry (AP-MS) strategies have been used to investigate complex interactions, many of these are susceptible to artifacts due to substantial overexpression of the exogenously expressed bait protein. Here we present a logical and systematic workflow that uses the multifunctional Halo tag to assess the correct localization and behavior of tagged subunits of the Sin3 histone deacetylase complex prior to further AP-MS analysis. Using this workflow, we modified our tagging/expression strategy with 21.7% of the tagged bait proteins that we constructed, allowing us to quickly develop validated reagents. Specifically, we apply the workflow to map interactions between stably expressed versions of the Sin3 subunits SUDS3, SAP30 or SAP30L and other cellular proteins.  Here we show that the SAP30 and SAP30L paralogues strongly associate with the core Sin3 complex, but SAP30L has unique associations with the proteasome and the myelin sheath.  Next, we demonstrate an advancement of the complex NSAF (cNSAF) approach, in which normalization to the scaffold protein SIN3A accounts for variations in the proportion of each bait capturing Sin3 complexes and allows a comparison between different baits capturing the same protein complex. This analysis reveals that although the Sin3 subunit SUDS3 appears to be used in both SIN3A and SIN3B based complexes, the SAP30 subunit is not used in SIN3B based complexes. Intriguingly, we do not detect the Sin3 subunits SAP18 and SAP25 among the 128 high-confidence interactions identified, suggesting that these subunits may not be common to all versions of the Sin3 complex in human cells. This workflow provides the framework for building validated reagents to assemble quantitative interaction networks for chromatin remodeling complexes and provides novel insights into focused protein interaction networks. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.

  19. Evaluating Complex Healthcare Systems: A Critique of Four Approaches

    Directory of Open Access Journals (Sweden)

    Heather Boon

    2007-01-01

    Full Text Available The purpose of this paper is to bring clarity to the emerging conceptual and methodological literature that focuses on understanding and evaluating complex or ‘whole’ systems of healthcare. An international working group reviewed literature from interdisciplinary or interprofessional groups describing approaches to the evaluation of complex systems of healthcare. The following four key approaches were identified: a framework from the MRC (UK, whole systems research, whole medical systems research described by NCCAM (USA and a model from NAFKAM (Norway. Main areas of congruence include acknowledgment of the inherent complexity of many healthcare interventions and the need to find new ways to evaluate these; the need to describe and understand the components of complex interventions in context (as they are actually practiced; the necessity of using mixed methods including randomized clinical trials (RCTs (explanatory and pragmatic and qualitative approaches; the perceived benefits of a multidisciplinary team approach to research; and the understanding that methodological developments in this field can be applied to both complementary and alternative medicine (CAM as well as conventional therapies. In contrast, the approaches differ in the following ways: terminology used, the extent to which the approach attempts to be applicable to both CAM and conventional medical interventions; the prioritization of research questions (in order of what should be done first especially with respect to how the ‘definitive’ RCT fits into the process of assessing complex healthcare systems; and the need for a staged approach. There appears to be a growing international understanding of the need for a new perspective on assessing complex healthcare systems.

  20. Embracing uncertainty, managing complexity: applying complexity thinking principles to transformation efforts in healthcare systems.

    Science.gov (United States)

    Khan, Sobia; Vandermorris, Ashley; Shepherd, John; Begun, James W; Lanham, Holly Jordan; Uhl-Bien, Mary; Berta, Whitney

    2018-03-21

    Complexity thinking is increasingly being embraced in healthcare, which is often described as a complex adaptive system (CAS). Applying CAS to healthcare as an explanatory model for understanding the nature of the system, and to stimulate changes and transformations within the system, is valuable. A seminar series on systems and complexity thinking hosted at the University of Toronto in 2016 offered a number of insights on applications of CAS perspectives to healthcare that we explore here. We synthesized topics from this series into a set of six insights on how complexity thinking fosters a deeper understanding of accepted ideas in healthcare, applications of CAS to actors within the system, and paradoxes in applications of complexity thinking that may require further debate: 1) a complexity lens helps us better understand the nebulous term "context"; 2) concepts of CAS may be applied differently when actors are cognizant of the system in which they operate; 3) actor responses to uncertainty within a CAS is a mechanism for emergent and intentional adaptation; 4) acknowledging complexity supports patient-centred intersectional approaches to patient care; 5) complexity perspectives can support ways that leaders manage change (and transformation) in healthcare; and 6) complexity demands different ways of implementing ideas and assessing the system. To enhance our exploration of key insights, we augmented the knowledge gleaned from the series with key articles on complexity in the literature. Ultimately, complexity thinking acknowledges the "messiness" that we seek to control in healthcare and encourages us to embrace it. This means seeing challenges as opportunities for adaptation, stimulating innovative solutions to ensure positive adaptation, leveraging the social system to enable ideas to emerge and spread across the system, and even more important, acknowledging that these adaptive actions are part of system behaviour just as much as periods of stability are. By

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

    Science.gov (United States)

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

    2013-01-01

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

  2. Compliance and High Reliability in a Complex Healthcare Organization.

    Science.gov (United States)

    Simon, Maxine dellaBadia

    2018-01-01

    When considering the impact of regulation on healthcare, visualize a spider's web. The spider weaves sections together to create the whole, with each fiber adding to the structure to support its success or lead to its failure. Each section is dependent on the others, and all must be aligned to maintain the structure. Outside forces can cause a shift in the web's fragile equilibrium.The interdependence of the sections of the spider's web is similar to the way hospital departments and services work together. An organization's structure must be shaped to support its mission and vision. At the same time, the business of healthcare requires the development and achievement of operational objectives and financial performance goals. Establishing a culture that is flexible enough to permit creativity, provide resiliency, and manage complexity as the organization grows is fundamental to success. An organization must address each of these factors while maintaining stability, carrying out its mission, and fostering improvement.Nature's order maintains the spider's web. Likewise, regulation can strengthen healthcare organizations by initiating disruptive changes that can support efforts to achieve and sustain high reliability in the delivery of care. To that end, leadership must be willing to provide the necessary vision and resources.

  3. Helping Older Adults Improve Their Medication Experience (HOME) by Addressing Medication Regimen Complexity in Home Healthcare.

    Science.gov (United States)

    Sheehan, Orla C; Kharrazi, Hadi; Carl, Kimberly J; Leff, Bruce; Wolff, Jennifer L; Roth, David L; Gabbard, Jennifer; Boyd, Cynthia M

    In skilled home healthcare (SHHC), communication between nurses and physicians is often inadequate for medication reconciliation and needed changes to the medication regimens are rarely made. Fragmentation of electronic health record (EHR) systems, transitions of care, lack of physician-nurse in-person contact, and poor understanding of medications by patients and their families put patients at risk for serious adverse outcomes. The aim of this study was to develop and test the HOME tool, an informatics tool to improve communication about medication regimens, share the insights of home care nurses with physicians, and highlight to physicians and nurses the complexity of medication schedules. We used human computer interaction design and evaluation principles, automated extraction from standardized forms, and modification of existing EHR fields to highlight key medication-related insights that had arisen during the SHHC visit. Separate versions of the tool were developed for physicians/nurses and patients/caregivers. A pilot of the tool was conducted using 20 SHHC encounters. Home care nurses and physicians found the tool useful for communication. Home care nurses were able to implement the HOME tool into their clinical workflow and reported improved communication with physicians about medications. This simple and largely automated tool improves understanding and communication around medications in SHHC.

  4. Coding for Language Complexity: The Interplay among Methodological Commitments, Tools, and Workflow in Writing Research

    Science.gov (United States)

    Geisler, Cheryl

    2018-01-01

    Coding, the analytic task of assigning codes to nonnumeric data, is foundational to writing research. A rich discussion of methodological pluralism has established the foundational importance of systematicity in the task of coding, but less attention has been paid to the equally important commitment to language complexity. Addressing the interplay…

  5. Tutorial at CNS 2013: Managing complex workflows in neural simulation and data analysis

    OpenAIRE

    Grün, Sonja; Davison, Andrew

    2013-01-01

    In our attempts to uncover the mechanisms that govern brain processing on the level of interacting neurons, neuroscientists have taken on the challenge of tackling the sheer complexity exhibited by neuronal networks. Neuronal simulations are nowadays performed with a high degree of detail, covering large, heterogeneous networks. Experimentally, electrophysiologists can simultaneously record from hundreds of neurons in complicated behavioral paradigms. The data streams of simulation and experi...

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

    Science.gov (United States)

    Ross, Peeter; Pohjonen, Hanna

    2011-04-01

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

  7. The myth of standardized workflow in primary care.

    Science.gov (United States)

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

    2016-01-01

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

  8. Constructing Workflows from Script Applications

    Directory of Open Access Journals (Sweden)

    Mikołaj Baranowski

    2012-01-01

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

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

    Science.gov (United States)

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

    2016-01-01

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

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

    OpenAIRE

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

    2016-01-01

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

  11. Healthcare

    Science.gov (United States)

    Carnevale, Anthony P.; Smith, Nicole; Gulish, Artem; Beach, Bennett H.

    2012-01-01

    This report, provides detailed analyses and projections of occupations in healthcare fields, and wages earned. In addition, the important skills and work values associated with workers in those fields of healthcare are discussed. Finally, the authors analyze the implications of research findings for the racial, ethnic, and class diversity of the…

  12. Complexity, flow, and antifragile healthcare systems: implications for nurse executives.

    Science.gov (United States)

    Clancy, Thomas R

    2015-04-01

    As systems evolve over time, their natural tendency is to become increasingly more complex. Studies in the field of complex systems have generated new perspectives on the application of management strategies in health systems. Much of this research appears as a natural extension of the cross-disciplinary field of systems theory. In this article, I further discuss the concept of fragility, its impact on system behavior, and ways to reduce it.

  13. Pro WF Windows Workflow in NET 40

    CERN Document Server

    Bukovics, Bruce

    2010-01-01

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

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

    Science.gov (United States)

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

    2014-06-01

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

  15. An ontological knowledge framework for adaptive medical workflow.

    Science.gov (United States)

    Dang, Jiangbo; Hedayati, Amir; Hampel, Ken; Toklu, Candemir

    2008-10-01

    As emerging technologies, semantic Web and SOA (Service-Oriented Architecture) allow BPMS (Business Process Management System) to automate business processes that can be described as services, which in turn can be used to wrap existing enterprise applications. BPMS provides tools and methodologies to compose Web services that can be executed as business processes and monitored by BPM (Business Process Management) consoles. Ontologies are a formal declarative knowledge representation model. It provides a foundation upon which machine understandable knowledge can be obtained, and as a result, it makes machine intelligence possible. Healthcare systems can adopt these technologies to make them ubiquitous, adaptive, and intelligent, and then serve patients better. This paper presents an ontological knowledge framework that covers healthcare domains that a hospital encompasses-from the medical or administrative tasks, to hospital assets, medical insurances, patient records, drugs, and regulations. Therefore, our ontology makes our vision of personalized healthcare possible by capturing all necessary knowledge for a complex personalized healthcare scenario involving patient care, insurance policies, and drug prescriptions, and compliances. For example, our ontology facilitates a workflow management system to allow users, from physicians to administrative assistants, to manage, even create context-aware new medical workflows and execute them on-the-fly.

  16. Using video-reflexive ethnography to capture the complexity of leadership enactment in the healthcare workplace.

    Science.gov (United States)

    Gordon, Lisi; Rees, Charlotte; Ker, Jean; Cleland, Jennifer

    2017-12-01

    Current theoretical thinking asserts that leadership should be distributed across many levels of healthcare organisations to improve the patient experience and staff morale. However, much healthcare leadership education focusses on the training and competence of individuals and little attention is paid to the interprofessional workplace and how its inherent complexities might contribute to the emergence of leadership. Underpinned by complexity theory, this research aimed to explore how interprofessional healthcare teams enact leadership at a micro-level through influential acts of organising. A whole (interprofessional) team workplace-based study utilising video-reflexive ethnography occurred in two UK clinical sites. Thematic framework analyses of the video data (video-observation and video-reflexivity sessions) were undertaken, followed by in-depth analyses of human-human and human-material interactions. Data analysis revealed a complex interprofessional environment where leadership is a dynamic process, negotiated and renegotiated in various ways throughout interactions (both formal and informal). Being able to "see" themselves at work gave participants the opportunity to discuss and analyse their everyday leadership practices and challenge some of their sometimes deeply entrenched values, beliefs, practices and assumptions about healthcare leadership. These study findings therefore indicate a need to redefine the way that medical and healthcare educators facilitate leadership development and argue for new approaches to research which shifts the focus from leaders to leadership.

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

    NARCIS (Netherlands)

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

    2007-01-01

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

  18. Addressing the Complexities of Big Data Analytics in Healthcare: The Diabetes Screening Case

    Directory of Open Access Journals (Sweden)

    Daswin De Silva

    2015-09-01

    Full Text Available The healthcare industry generates a high throughput of medical, clinical and omics data of varying complexity and features. Clinical decision-support is gaining widespread attention as medical institutions and governing bodies turn towards better management of this data for effective and efficient healthcare delivery and quality assured outcomes. Amass of data across all stages, from disease diagnosis to palliative care, is further indication of the opportunities and challenges to effective data management, analysis, prediction and optimization techniques as parts of knowledge management in clinical environments. Big Data analytics (BDA presents the potential to advance this industry with reforms in clinical decision-support and translational research. However, adoption of big data analytics has been slow due to complexities posed by the nature of healthcare data. The success of these systems is hard to predict, so further research is needed to provide a robust framework to ensure investment in BDA is justified. In this paper we investigate these complexities from the perspective of updated Information Systems (IS participation theory. We present a case study on a large diabetes screening project to integrate, converge and derive expedient insights from such an accumulation of data and make recommendations for a successful BDA implementation grounded in a participatory framework and the specificities of big data in healthcare context.

  19. Scientific Workflow Management in Proteomics

    Science.gov (United States)

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

    2012-01-01

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

  20. Digital Workflow for the Acquisition and Elaboration of 3d Data in a Monumental Complex: the Fortress of Saint John the Baptist in Florence

    Science.gov (United States)

    Tucci, G.; Bonora, V.; Conti, A.; Fiorini, L.

    2017-08-01

    In recent years, the GeCo Laboratory has undertaken numerous projects to digitalize vast and complex buildings; the specific nature of the different projects has resulted in a case-by-case approach, each time working on past experiences and updating not only the hardware and software tools but also the management and processing methods. This paper presents the workflow followed for the survey of the Fortress of Saint John the Baptist in Florence, an on-going interdisciplinary project. Presently Florence's main trade fair congress centre, at the same time it hosts various buildings that bear witness to the fortress's life-history, combining constructions from the Medici and Lorraine eras with recently built exhibition facilities. Now new research has been required due to the realization of new pavilions and the regeneration of the whole complex. This has included a critical survey, material testing, diagnostic investigations and stratigraphic analyses to define the building's state of preservation. The working group comprises specialists from different institutions, amongst which the Italian Military Geographic Institute, the University of Florence, the National Research Council Institute for the Preservation and Enhancement of the Cultural Heritage, and the Florence City Council.

  1. Extending the NIF DISCO framework to automate complex workflow: coordinating the harvest and integration of data from diverse neuroscience information resources.

    Science.gov (United States)

    Marenco, Luis N; Wang, Rixin; Bandrowski, Anita E; Grethe, Jeffrey S; Shepherd, Gordon M; Miller, Perry L

    2014-01-01

    This paper describes how DISCO, the data aggregator that supports the Neuroscience Information Framework (NIF), has been extended to play a central role in automating the complex workflow required to support and coordinate the NIF's data integration capabilities. The NIF is an NIH Neuroscience Blueprint initiative designed to help researchers access the wealth of data related to the neurosciences available via the Internet. A central component is the NIF Federation, a searchable database that currently contains data from 231 data and information resources regularly harvested, updated, and warehoused in the DISCO system. In the past several years, DISCO has greatly extended its functionality and has evolved to play a central role in automating the complex, ongoing process of harvesting, validating, integrating, and displaying neuroscience data from a growing set of participating resources. This paper provides an overview of DISCO's current capabilities and discusses a number of the challenges and future directions related to the process of coordinating the integration of neuroscience data within the NIF Federation.

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

    Science.gov (United States)

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

    2016-01-01

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

  3. The case of value-based healthcare for people living with complex long-term conditions.

    Science.gov (United States)

    Elf, Marie; Flink, Maria; Nilsson, Marie; Tistad, Malin; von Koch, Lena; Ytterberg, Charlotte

    2017-01-11

    There is a trend towards value-based health service, striving to cut costs while generating value for the patient. The overall objective comprises higher-quality health services and improved patient safety and cost efficiency. The approach could align with patient-centred care, as it entails a focus on the patient's experience of her or his entire cycle of care, including the use of well-defined outcome measurements. Challenges arise when the approach is applied to health services for people living with long-term complex conditions that require support from various healthcare services. The aim of this work is to critically discuss the value-based approach and its implications for patients with long-term complex conditions. Two cases from clinical practice and research form the foundation for our reasoning, illustrating several challenges regarding value-based health services for people living with long-term complex conditions. Achieving value-based health services that provide the health outcomes that matter to patients and providing greater patient-centredness will place increased demands on the healthcare system. Patients and their informal caregivers must be included in the development and establishment of outcome measures. The outcome measures must be standardized to allow evaluation of specific conditions at an aggregated level, but they must also be sensitive enough to capture each patient's individual needs and goals. Healthcare systems that strive to establish value-based services must collaborate beyond the organizational boundaries to create clear patient trajectories in order to avoid fragmentation. The shift towards value-based health services has the potential to align healthcare-service delivery with patient-centred care if serious efforts to take the patient's perspective into account are made. This is especially challenging in fragmented healthcare systems and for patients with long-term- and multi-setting-care needs.

  4. Communication in Healthcare: Opportunities for information technology and concerns for patient safety

    NARCIS (Netherlands)

    H. Pirnejad (Habibollah)

    2008-01-01

    textabstractUnderstanding healthcare workflow is fundamental for design and implementation of information systems. Communication and information exchange between healthcare professionals plays a pivotal role in developing smooth workflow within and between healthcare organizations. The study in this

  5. Development of an integrated genome informatics, data management and workflow infrastructure: A toolbox for the study of complex disease genetics

    Directory of Open Access Journals (Sweden)

    Burren Oliver S

    2004-01-01

    Full Text Available Abstract The genetic dissection of complex disease remains a significant challenge. Sample-tracking and the recording, processing and storage of high-throughput laboratory data with public domain data, require integration of databases, genome informatics and genetic analyses in an easily updated and scaleable format. To find genes involved in multifactorial diseases such as type 1 diabetes (T1D, chromosome regions are defined based on functional candidate gene content, linkage information from humans and animal model mapping information. For each region, genomic information is extracted from Ensembl, converted and loaded into ACeDB for manual gene annotation. Homology information is examined using ACeDB tools and the gene structure verified. Manually curated genes are extracted from ACeDB and read into the feature database, which holds relevant local genomic feature data and an audit trail of laboratory investigations. Public domain information, manually curated genes, polymorphisms, primers, linkage and association analyses, with links to our genotyping database, are shown in Gbrowse. This system scales to include genetic, statistical, quality control (QC and biological data such as expression analyses of RNA or protein, all linked from a genomics integrative display. Our system is applicable to any genetic study of complex disease, of either large or small scale.

  6. [Predicting individual risk of high healthcare cost to identify complex chronic patients].

    Science.gov (United States)

    Coderch, Jordi; Sánchez-Pérez, Inma; Ibern, Pere; Carreras, Marc; Pérez-Berruezo, Xavier; Inoriza, José M

    2014-01-01

    To develop a predictive model for the risk of high consumption of healthcare resources, and assess the ability of the model to identify complex chronic patients. A cross-sectional study was performed within a healthcare management organization by using individual data from 2 consecutive years (88,795 people). The dependent variable consisted of healthcare costs above the 95th percentile (P95), including all services provided by the organization and pharmaceutical consumption outside of the institution. The predictive variables were age, sex, morbidity-based on clinical risk groups (CRG)-and selected data from previous utilization (use of hospitalization, use of high-cost drugs in ambulatory care, pharmaceutical expenditure). A univariate descriptive analysis was performed. We constructed a logistic regression model with a 95% confidence level and analyzed sensitivity, specificity, positive predictive values (PPV), and the area under the ROC curve (AUC). Individuals incurring costs >P95 accumulated 44% of total healthcare costs and were concentrated in ACRG3 (aggregated CRG level 3) categories related to multiple chronic diseases. All variables were statistically significant except for sex. The model had a sensitivity of 48.4% (CI: 46.9%-49.8%), specificity of 97.2% (CI: 97.0%-97.3%), PPV of 46.5% (CI: 45.0%-47.9%), and an AUC of 0.897 (CI: 0.892 to 0.902). High consumption of healthcare resources is associated with complex chronic morbidity. A model based on age, morbidity, and prior utilization is able to predict high-cost risk and identify a target population requiring proactive care. Copyright © 2013 SESPAS. Published by Elsevier Espana. All rights reserved.

  7. Problematisations of Complexity: On the Notion and Production of Diverse Complexities in Healthcare Interventions and Evaluations

    NARCIS (Netherlands)

    T. Broer (Tineke); R.A. Bal (Roland); Pickersgill, M. (Martyn)

    2017-01-01

    textabstractWithin the literature on the evaluation of health (policy) interventions, complexity is a much-debated issue. In particular, many claim that so-called ‘complex interventions’ pose different challenges to evaluation studies than apparently ‘simple interventions’ do. Distinct ways of doing

  8. A Mixed-Methods Research Framework for Healthcare Process Improvement.

    Science.gov (United States)

    Bastian, Nathaniel D; Munoz, David; Ventura, Marta

    2016-01-01

    The healthcare system in the United States is spiraling out of control due to ever-increasing costs without significant improvements in quality, access to care, satisfaction, and efficiency. Efficient workflow is paramount to improving healthcare value while maintaining the utmost standards of patient care and provider satisfaction in high stress environments. This article provides healthcare managers and quality engineers with a practical healthcare process improvement framework to assess, measure and improve clinical workflow processes. The proposed mixed-methods research framework integrates qualitative and quantitative tools to foster the improvement of processes and workflow in a systematic way. The framework consists of three distinct phases: 1) stakeholder analysis, 2a) survey design, 2b) time-motion study, and 3) process improvement. The proposed framework is applied to the pediatric intensive care unit of the Penn State Hershey Children's Hospital. The implementation of this methodology led to identification and categorization of different workflow tasks and activities into both value-added and non-value added in an effort to provide more valuable and higher quality patient care. Based upon the lessons learned from the case study, the three-phase methodology provides a better, broader, leaner, and holistic assessment of clinical workflow. The proposed framework can be implemented in various healthcare settings to support continuous improvement efforts in which complexity is a daily element that impacts workflow. We proffer a general methodology for process improvement in a healthcare setting, providing decision makers and stakeholders with a useful framework to help their organizations improve efficiency. Published by Elsevier Inc.

  9. Workflow in Almaraz NPP

    International Nuclear Information System (INIS)

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

    2000-01-01

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

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

    NARCIS (Netherlands)

    Zeng, R.; He, X.; Aalst, van der W.M.P.

    2011-01-01

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

  11. Agreement Workflow Tool (AWT)

    Data.gov (United States)

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

  12. The complex interface between economy and healthcare: An introductory overview for clinicians.

    Science.gov (United States)

    Ottolini, Federica Liliana; Buggio, Laura; Somigliana, Edgardo; Vercellini, Paolo

    2016-12-01

    In a period of generalized economic crisis, it seems particularly appropriate to try to manage a continuing growing sector such as healthcare in the best possible way. The crucial aim of optimization of available healthcare resources is obtaining the maximum possible benefit with the minimum expenditure. This has important social implications, whether individual citizens or tax-funded national health services eventually have to pay the bill. The keyword here is efficiency, which means either, maximizing the benefit from a fixed sum of money, or minimizing the resources required for a defined benefit. In order to achieve these objectives, economic evaluation is a helpful tool. Five different types of economic evaluation exist in the health-care field: cost-minimization, cost-benefit, cost-consequences, cost-effectiveness and cost-utility analysis. The objective of this narrative review is to provide an overview of the principal methods used for economic evaluation in healthcare. Economic evaluation represents a starting point for the allocation of resources, the decision of the valuable investments and the division of budgets across different health programs. Moreover, economic evaluation allows the comparison of different procedures in terms of quality of life and life expectancy, bearing in mind that cost-effectiveness is only one of multiple facets in the decision making-process. Economic evaluation is important to critically evaluate clinical interventions and ensure that we are implementing the most cost-effective management protocols. Clinicians are called to fulfill the complex task of optimizing the use of resources, and, at the same time, improving the quality of healthcare assistance. Copyright © 2016 European Federation of Internal Medicine. Published by Elsevier B.V. All rights reserved.

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

    CERN Document Server

    Tan, Wei

    2013-01-01

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

  14. Complexity metrics for workflow nets

    NARCIS (Netherlands)

    Lassen, K.B.; Aalst, van der W.M.P.

    2009-01-01

    Process modeling languages such as EPCs, BPMN, flow charts, UML activity diagrams, Petri nets, etc., are used to model business processes and to configure process-aware information systems. It is known that users have problems understanding these diagrams. In fact, even process engineers and system

  15. Complexity Metrics for Workflow Nets

    DEFF Research Database (Denmark)

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

    2009-01-01

    Process modeling languages such as EPCs, BPMN, flow charts, UML activity diagrams, Petri nets, etc.\\ are used to model business processes and to configure process-aware information systems. It is known that users have problems understanding these diagrams. In fact, even process engineers and system...

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

    Science.gov (United States)

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

    2015-11-01

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

  17. Predictive Analytics In Healthcare: Medications as a Predictor of Medical Complexity.

    Science.gov (United States)

    Higdon, Roger; Stewart, Elizabeth; Roach, Jared C; Dombrowski, Caroline; Stanberry, Larissa; Clifton, Holly; Kolker, Natali; van Belle, Gerald; Del Beccaro, Mark A; Kolker, Eugene

    2013-12-01

    Children with special healthcare needs (CSHCN) require health and related services that exceed those required by most hospitalized children. A small but growing and important subset of the CSHCN group includes medically complex children (MCCs). MCCs typically have comorbidities and disproportionately consume healthcare resources. To enable strategic planning for the needs of MCCs, simple screens to identify potential MCCs rapidly in a hospital setting are needed. We assessed whether the number of medications used and the class of those medications correlated with MCC status. Retrospective analysis of medication data from the inpatients at Seattle Children's Hospital found that the numbers of inpatient and outpatient medications significantly correlated with MCC status. Numerous variables based on counts of medications, use of individual medications, and use of combinations of medications were considered, resulting in a simple model based on three different counts of medications: outpatient and inpatient drug classes and individual inpatient drug names. The combined model was used to rank the patient population for medical complexity. As a result, simple, objective admission screens for predicting the complexity of patients based on the number and type of medications were implemented.

  18. Developing Tacit Knowledge of Complex Systems: The Value of Early Empirical Inquiry in Healthcare Design

    Directory of Open Access Journals (Sweden)

    Chantal Trudel

    2016-09-01

    Full Text Available Infection prevention and control has been the subject of much study in medical and epidemiological research and a variety of best practice guidelines have been developed to support healthcare workers and related stakeholders. Yet, despite the availability of information, managing healthcare-associated infections remains a challenge because the relevant explicit knowledge is not being adequately developed and mobilized as tacit knowledge for use "on the front lines". Some researchers have called for a human factors perspective to help address challenges in designing for infection prevention and control, but relatively few studies have been conducted to date. Researchers also suggest that empirical inquiry is needed to better inform the design process, and particularly the design of complex systems where attention to detailed processes and interactions can support the success of an intervention. A human factors approach can help designers develop a deeper understanding of work processes, technology considerations, as well as physiological, psychological, cultural, and organizational factors. The need is particularly pressing in low-resource healthcare environments where funds, time, and human resources may be scarce and strategic design decisions based on evidence are needed to support meaningful and effective changes. With this in mind, a human factors study was conducted in an existing neonatal intensive care unit to identify the influence of product and environment design on infection prevention and control and to inform recommendations for improvement. In this case study, we illustrate how the application of an empirical, methodical approach can help design professionals and stakeholders develop tacit knowledge of complex systems – knowledge that can be used to better inform design priorities, the design process, decision making, and the allocation of resources to help maximize improvements.

  19. Radiology information system: a workflow-based approach

    International Nuclear Information System (INIS)

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

    2009-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-11-15

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

  1. Querying Workflow Logs

    Directory of Open Access Journals (Sweden)

    Yan Tang

    2018-01-01

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

  2. Responsive web design workflow

    OpenAIRE

    LAAK, TIMO

    2013-01-01

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

  3. Integrated workflows for spiking neuronal network simulations

    Directory of Open Access Journals (Sweden)

    Ján eAntolík

    2013-12-01

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

  4. Critical Incident Stress Management (CISM) in complex systems: cultural adaptation and safety impacts in healthcare.

    Science.gov (United States)

    Müller-Leonhardt, Alice; Mitchell, Shannon G; Vogt, Joachim; Schürmann, Tim

    2014-07-01

    In complex systems, such as hospitals or air traffic control operations, critical incidents (CIs) are unavoidable. These incidents can not only become critical for victims but also for professionals working at the "sharp end" who may have to deal with critical incident stress (CIS) reactions that may be severe and impede emotional, physical, cognitive and social functioning. These CIS reactions may occur not only under exceptional conditions but also during every-day work and become an important safety issue. In contrast to air traffic management (ATM) operations in Europe, which have readily adopted critical incident stress management (CISM), most hospitals have not yet implemented comprehensive peer support programs. This survey was conducted in 2010 at the only European general hospital setting which implemented CISM program since 2004. The aim of the article is to describe possible contribution of CISM in hospital settings framed from the perspective of organizational safety and individual health for healthcare professionals. Findings affirm that daily work related incidents also can become critical for healthcare professionals. Program efficiency appears to be influenced by the professional culture, as well as organizational structure and policies. Overall, findings demonstrate that the adaptation of the CISM program in general hospitals takes time but, once established, it may serve as a mechanism for changing professional culture, thereby permitting the framing of even small incidents or near misses as an opportunity to provide valuable feedback to the system. Copyright © 2014 Elsevier Ltd. All rights reserved.

  5. [Complexity of social and healthcare coordination in addictions and the role of the nurse].

    Science.gov (United States)

    Molina Fernández, Antonio Jesús; González Riera, Javier; Montero Bancalero, Francisco José; Gómez-Salgado, Juan

    2016-01-01

    The present article discusses the psychosocial impact of basic and advanced concepts, such as social support and prevention, as well as to establish a link between theoretical models related to the social sphere on one side, and the health aspects on the other. This work is based on the context of the influence on health shared by community psychology and social psychology. Starting from the historical background of current approaches, a review is presented of those first actions focused on the care plan and they are framed in a reaction model to the drug problem, which progressed to the current healthcare network model, through the creation of Spanish National Action Plan on Drugs. The complexity of the problem is then broken down into the following key elements: Multifactorial Model of Drugs and Addictions, importance of prevention, and social support. Subsequently, a description is presented on the different levels of the healthcare network, with their different resources. This is also illustrated using a coordination protocol. Finally, it features the nursing approach to drugs, with its contributions, particularly as regards the coordination of resources, and aspects that must be developed for improvement in this area. Copyright © 2015 Elsevier España, S.L.U. All rights reserved.

  6. Application of simplified Complexity Theory concepts for healthcare social systems to explain the implementation of evidence into practice.

    Science.gov (United States)

    Chandler, Jacqueline; Rycroft-Malone, Jo; Hawkes, Claire; Noyes, Jane

    2016-02-01

    To examine the application of core concepts from Complexity Theory to explain the findings from a process evaluation undertaken in a trial evaluating implementation strategies for recommendations about reducing surgical fasting times. The proliferation of evidence-based guidance requires a greater focus on its implementation. Theory is required to explain the complex processes across the multiple healthcare organizational levels. This social healthcare context involves the interaction between professionals, patients and the organizational systems in care delivery. Complexity Theory may provide an explanatory framework to explain the complexities inherent in implementation in social healthcare contexts. A secondary thematic analysis of qualitative process evaluation data informed by Complexity Theory. Seminal texts applying Complexity Theory to the social context were annotated, key concepts extracted and core Complexity Theory concepts identified. These core concepts were applied as a theoretical lens to provide an explanation of themes from a process evaluation of a trial evaluating the implementation of strategies to reduce surgical fasting times. Sampled substantive texts provided a representative spread of theoretical development and application of Complexity Theory from late 1990's-2013 in social science, healthcare, management and philosophy. Five Complexity Theory core concepts extracted were 'self-organization', 'interaction', 'emergence', 'system history' and 'temporality'. Application of these concepts suggests routine surgical fasting practice is habituated in the social healthcare system and therefore it cannot easily be reversed. A reduction to fasting times requires an incentivised new approach to emerge in the surgical system's priority of completing the operating list. The application of Complexity Theory provides a useful explanation for resistance to change fasting practice. Its utility in implementation research warrants further attention and

  7. Leadership and leadership development in healthcare settings - a simplistic solution to complex problems?

    Science.gov (United States)

    McDonald, Ruth

    2014-10-01

    There is a trend in health systems around the world to place great emphasis on and faith in improving 'leadership'. Leadership has been defined in many ways and the elitist implications of traditional notions of leadership sit uncomfortably with modern healthcare organisations. The concept of distributed leadership incorporates inclusivity, collectiveness and collaboration, with the result that, to some extent, all staff, not just those in senior management roles, are viewed as leaders. Leadership development programmes are intended to equip individuals to improve leadership skills, but we know little about their effectiveness. Furthermore, the content of these programmes varies widely and the fact that many lack a sense of how they fit with individual or organisational goals raises questions about how they are intended to achieve their aims. It is important to avoid simplistic assumptions about the ability of improved leadership to solve complex problems. It is also important to evaluate leadership development programmes in ways that go beyond descriptive accounts.

  8. A Hybrid Methodology for Modeling Risk of Adverse Events in Complex Health-Care Settings.

    Science.gov (United States)

    Kazemi, Reza; Mosleh, Ali; Dierks, Meghan

    2017-03-01

    In spite of increased attention to quality and efforts to provide safe medical care, adverse events (AEs) are still frequent in clinical practice. Reports from various sources indicate that a substantial number of hospitalized patients suffer treatment-caused injuries while in the hospital. While risk cannot be entirely eliminated from health-care activities, an important goal is to develop effective and durable mitigation strategies to render the system "safer." In order to do this, though, we must develop models that comprehensively and realistically characterize the risk. In the health-care domain, this can be extremely challenging due to the wide variability in the way that health-care processes and interventions are executed and also due to the dynamic nature of risk in this particular domain. In this study, we have developed a generic methodology for evaluating dynamic changes in AE risk in acute care hospitals as a function of organizational and nonorganizational factors, using a combination of modeling formalisms. First, a system dynamics (SD) framework is used to demonstrate how organizational-level and policy-level contributions to risk evolve over time, and how policies and decisions may affect the general system-level contribution to AE risk. It also captures the feedback of organizational factors and decisions over time and the nonlinearities in these feedback effects. SD is a popular approach to understanding the behavior of complex social and economic systems. It is a simulation-based, differential equation modeling tool that is widely used in situations where the formal model is complex and an analytical solution is very difficult to obtain. Second, a Bayesian belief network (BBN) framework is used to represent patient-level factors and also physician-level decisions and factors in the management of an individual patient, which contribute to the risk of hospital-acquired AE. BBNs are networks of probabilities that can capture probabilistic relations

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

    Science.gov (United States)

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

    2012-01-01

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

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

    Science.gov (United States)

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

    2012-05-04

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

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

    Directory of Open Access Journals (Sweden)

    Abouelhoda Mohamed

    2012-05-01

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

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

    Science.gov (United States)

    2012-01-01

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

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

    Science.gov (United States)

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

    2013-06-01

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

  14. Convergent Innovation in Emerging Healthcare Technology Ecosystems: Addressing Complexity and Integration

    Directory of Open Access Journals (Sweden)

    Mark A. Phillips

    2017-09-01

    Full Text Available Precision Medicine and Digital Health are emerging areas in healthcare, and they are underpinned by convergent or cross-industry innovation. However, convergence results in greater uncertainty and complexity in terms of technologies, value networks, and organization. There has been limited empirical research on emerging and convergent ecosystems, especially in addressing the issue of integration. This research identifies how organizations innovate in emerging and convergent ecosystems, specifically, how they address the challenge of integration. We base our research on empirical analyses using a series of longitudinal case studies employing a combination of case interviews, field observations, and documents. Our findings identify a need to embrace the complexity by adopting a variety of approaches that balance “credibility-seeking” and “advantage-seeking” behaviours, to navigate, negotiate, and nurture both the innovation and ecosystem, in addition to a combination of “analysis” and “synthesis” actions to manage aspects of integration. We contribute to the convergent innovation agenda and provide practical approaches for innovators in this domain.

  15. Healthcare Utilization and Spending for Constipation in Children With Versus Without Complex Chronic Conditions.

    Science.gov (United States)

    Stephens, John R; Steiner, Michael J; DeJong, Neal; Rodean, Jonathan; Hall, Matt; Richardson, Troy; Berry, Jay G

    2017-01-01

    The aim of the study was to examine the prevalence of diagnosis and treatment for constipation among children receiving Medicaid and to compare healthcare utilization and spending for constipation among children based on number of complex chronic conditions (CCCs). Retrospective cohort study of 4.9 million children ages 1 to 17 years enrolled in Medicaid from 2009 to 2011 in 10 states in the Truven Marketscan Database. Constipation was identified using International Classification of Disease, 9th revision codes for constipation (564.0x), intestinal impaction (560.3x), or encopresis (307.7). Outpatient and inpatient utilization and spending for constipation were assessed. CCC status was identified using validated methodology. A total of 267,188 children (5.4%) were diagnosed with constipation. Total constipation spending was $79.5 million. Outpatient constipation spending was $66.8 million (84.1%) during 406,814 visits, mean spending $120/visit. Among children with constipation, 1363 (0.5%) received inpatient treatment, accounting for $12.2 million (15.4%) of constipation spending, mean spending $7815/hospitalization. Of children hospitalized for constipation, 552 (40.5%) did not have an outpatient visit for constipation before admission. Approximately 6.8% of children in the study had ≥1 CCC; these children accounted for 33.5% of total constipation spending, 70.3% of inpatient constipation spending, and 19.8% of emergency department constipation spending. Constipation prevalence was 11.0% for children with 1 CCC, 16.6% with 2 CCCs, and 27.1% with ≥3 CCCs. Although the majority of pediatric constipation treatment occurs in the outpatient setting, inpatient care accounts for a sizable percentage of spending. Children with CCCs have a higher prevalence of constipation and account for a disproportionate amount of constipation healthcare utilization and spending.

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

    Science.gov (United States)

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

    2013-11-01

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

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

    Directory of Open Access Journals (Sweden)

    Issac Praveen

    2005-03-01

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

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

    DEFF Research Database (Denmark)

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

    2009-01-01

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

  19. Implementation of a web-based national child health-care programme in a local context: A complex facilitator role.

    Science.gov (United States)

    Tell, Johanna; Olander, Ewy; Anderberg, Peter; Berglund, Johan Sanmartin

    2018-02-01

    The aim of this study was to investigate child health-care coordinators' experiences of being a facilitator for the implementation of a new national child health-care programme in the form of a web-based national guide. The study was based on eight remote, online focus groups, using Skype for Business. A qualitative content analysis was performed. The analysis generated three categories: adapt to a local context, transition challenges and led by strong incentives. There were eight subcategories. In the latent analysis, the theme 'Being a facilitator: a complex role' was formed to express the child health-care coordinators' experiences. Facilitating a national guideline or decision support in a local context is a complex task that requires an advocating and mediating role. For successful implementation, guidelines and decision support, such as a web-based guide and the new child health-care programme, must match professional consensus and needs and be seen as relevant by all. Participation in the development and a strong bottom-up approach was important, making the web-based guide and the programme relevant to whom it is intended to serve, and for successful implementation. The study contributes valuable knowledge when planning to implement a national web-based decision support and policy programme in a local health-care context.

  20. Workflow management: an overview

    NARCIS (Netherlands)

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

    2010-01-01

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

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

    DEFF Research Database (Denmark)

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

    2007-01-01

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

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

    Science.gov (United States)

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

    2011-04-10

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

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

    Science.gov (United States)

    2011-01-01

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

  4. Ferret Workflow Anomaly Detection System

    National Research Council Canada - National Science Library

    Smith, Timothy J; Bryant, Stephany

    2005-01-01

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

  5. Managing expectations: cognitive authority and experienced control in complex healthcare processes.

    Science.gov (United States)

    Hunt, Katherine J; May, Carl R

    2017-07-05

    Balancing the normative expectations of others (accountabilities) against the personal and distributed resources available to meet them (capacity) is a ubiquitous feature of social relations in many settings. This is an important problem in the management of long-term conditions, because of widespread problems of non-adherence to treatment regimens. Using long-term conditions as an example, we set out middle range theory of this balancing work. A middle-range theory was constructed four stages. First, a qualitative elicitation study of men with heart failure was used to develop general propositions about patient and care giver experience, and about the ways that the organisation and delivery of care affected this. Second, these propositions were developed and confirmed through a systematic review of qualitative research literature. Third, theoretical propositions and constructs were built, refined and presented as a logic model associated with two main theoretical propositions. Finally, a construct validation exercise was undertaken, in which construct definitions informed reanalysis of a set of systematic reviews of studies of patient and caregiver experiences of heart failure that had been included in an earlier meta-review. Cognitive Authority Theory identifies, characterises and explains negotiation processes in in which people manage their relations with the expectations of normative systems - like those encountered in the management of long-term conditions. Here, their cognitive authority is the product of an assessment of competence, trustworthiness and credibility made about a person by other participants in a healthcare process; and their experienced control is a function of the degree to which they successfully manage the external process-specific limiting factors that make it difficult to otherwise perform in their role. Cognitive Authority Theory assists in explaining how participants in complex social processes manage important relational aspects of

  6. A new generation of healthcare buildings in South Africa: complexities and opportunities for greening

    CSIR Research Space (South Africa)

    De Jager, Peta

    2012-07-01

    Full Text Available , efficient, healing environment desirable for healthcare delivery. In South Africa there has been a commitment to transform the healthcare sector through the introduction of the national health insurance system which is to be unfolded over a 14 year period...

  7. Integrating configuration workflows with project management system

    International Nuclear Information System (INIS)

    Nilsen, Dimitri; Weber, Pavel

    2014-01-01

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

  8. Data intensive ATLAS workflows in the Cloud

    CERN Document Server

    Rzehorz, Gerhard Ferdinand; The ATLAS collaboration

    2018-01-01

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

  9. Quantitative analysis of probabilistic BPMN workflows

    DEFF Research Database (Denmark)

    Herbert, Luke Thomas; Sharp, Robin

    2012-01-01

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

  10. Automation of Flexible Migration Workflows

    Directory of Open Access Journals (Sweden)

    Dirk von Suchodoletz

    2011-03-01

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

  11. Using complexity theory to develop a student-directed interprofessional learning activity for 1220 healthcare students.

    Science.gov (United States)

    Jorm, Christine; Nisbet, Gillian; Roberts, Chris; Gordon, Christopher; Gentilcore, Stacey; Chen, Timothy F

    2016-08-08

    More and better interprofessional practice is predicated to be necessary to deliver good care to the patients of the future. However, universities struggle to create authentic learning activities that enable students to experience the dynamic interprofessional interactions common in healthcare and that can accommodate large interprofessional student cohorts. We investigated a large-scale mandatory interprofessional learning (IPL) activity for health professional students designed to promote social learning. A mixed methods research approach determined feasibility, acceptability and the extent to which student IPL outcomes were met. We developed an IPL activity founded in complexity theory to prepare students for future practice by engaging them in a self-directed (self-organised) learning activity with a diverse team, whose assessable products would be emergent creations. Complicated but authentic clinical cases (n = 12) were developed to challenge student teams (n = 5 or 6). Assessment consisted of a written management plan (academically marked) and a five-minute video (peer marked) designed to assess creative collaboration as well as provide evidence of integrated collective knowledge; the cohesive patient-centred management plan. All students (including the disciplines of diagnostic radiology, exercise physiology, medicine, nursing, occupational therapy, pharmacy, physiotherapy and speech pathology), completed all tasks successfully. Of the 26 % of students who completed the evaluation survey, 70 % agreed or strongly agreed that the IPL activity was worthwhile, and 87 % agreed or strongly agreed that their case study was relevant. Thematic analysis found overarching themes of engagement and collaboration-in-action suggesting that the IPL activity enabled students to achieve the intended learning objectives. Students recognised the contribution of others and described negotiation, collaboration and creation of new collective knowledge after working

  12. Workflow optimization beyond RIS and PACS

    International Nuclear Information System (INIS)

    Treitl, M.; Wirth, S.; Lucke, A.; Nissen-Meyer, S.; Trumm, C.; Rieger, J.; Pfeifer, K.-J.; Reiser, M.; Villain, S.

    2005-01-01

    Technological progress and the rising cost pressure on the healthcare system have led to a drastic change in the work environment of radiologists today. The pervasive demand for workflow optimization and increased efficiency of its activities raises the question of whether by employment of electronic systems, such as RIS and PACS, the potentials of digital technology are sufficiently used to fulfil this demand. This report describes the tasks and structures in radiology departments, which so far are only insufficiently supported by commercially available electronic systems but are nevertheless substantial. We developed and employed a web-based, integrated workplace system, which simplifies many daily tasks of departmental organization and administration apart from well-established tasks of documentation. Furthermore, we analyzed the effects exerted on departmental workflow by employment of this system for 3 years. (orig.) [de

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

    DEFF Research Database (Denmark)

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

    2007-01-01

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

  14. Insightful Workflow For Grid Computing

    Energy Technology Data Exchange (ETDEWEB)

    Dr. Charles Earl

    2008-10-09

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

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

    Science.gov (United States)

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

    2016-01-01

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

  16. Workflow User Interfaces Patterns

    Directory of Open Access Journals (Sweden)

    Jean Vanderdonckt

    2012-03-01

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

  17. Workflow patterns the definitive guide

    CERN Document Server

    Russell, Nick; ter Hofstede, Arthur H M

    2016-01-01

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

  18. Tailoring Healthy Workplace Interventions to Local Healthcare Settings: A Complexity Theory-Informed Workplace of Well-Being Framework.

    Science.gov (United States)

    Brand, Sarah L; Fleming, Lora E; Wyatt, Katrina M

    2015-01-01

    Many healthy workplace interventions have been developed for healthcare settings to address the consistently low scores of healthcare professionals on assessments of mental and physical well-being. Complex healthcare settings present challenges for the scale-up and spread of successful interventions from one setting to another. Despite general agreement regarding the importance of the local setting in affecting intervention success across different settings, there is no consensus on what it is about a local setting that needs to be taken into account to design healthy workplace interventions appropriate for different local settings. Complexity theory principles were used to understand a workplace as a complex adaptive system and to create a framework of eight domains (system characteristics) that affect the emergence of system-level behaviour. This Workplace of Well-being (WoW) framework is responsive and adaptive to local settings and allows a shared understanding of the enablers and barriers to behaviour change by capturing local information for each of the eight domains. We use the results of applying the WoW framework to one workplace, a UK National Health Service ward, to describe the utility of this approach in informing design of setting-appropriate healthy workplace interventions that create workplaces conducive to healthy behaviour change.

  19. Tailoring Healthy Workplace Interventions to Local Healthcare Settings: A Complexity Theory-Informed Workplace of Well-Being Framework

    Directory of Open Access Journals (Sweden)

    Sarah L. Brand

    2015-01-01

    Full Text Available Many healthy workplace interventions have been developed for healthcare settings to address the consistently low scores of healthcare professionals on assessments of mental and physical well-being. Complex healthcare settings present challenges for the scale-up and spread of successful interventions from one setting to another. Despite general agreement regarding the importance of the local setting in affecting intervention success across different settings, there is no consensus on what it is about a local setting that needs to be taken into account to design healthy workplace interventions appropriate for different local settings. Complexity theory principles were used to understand a workplace as a complex adaptive system and to create a framework of eight domains (system characteristics that affect the emergence of system-level behaviour. This Workplace of Well-being (WoW framework is responsive and adaptive to local settings and allows a shared understanding of the enablers and barriers to behaviour change by capturing local information for each of the eight domains. We use the results of applying the WoW framework to one workplace, a UK National Health Service ward, to describe the utility of this approach in informing design of setting-appropriate healthy workplace interventions that create workplaces conducive to healthy behaviour change.

  20. Tailoring Healthy Workplace Interventions to Local Healthcare Settings: A Complexity Theory-Informed Workplace of Well-Being Framework

    Science.gov (United States)

    Brand, Sarah L.; Fleming, Lora E.; Wyatt, Katrina M.

    2015-01-01

    Many healthy workplace interventions have been developed for healthcare settings to address the consistently low scores of healthcare professionals on assessments of mental and physical well-being. Complex healthcare settings present challenges for the scale-up and spread of successful interventions from one setting to another. Despite general agreement regarding the importance of the local setting in affecting intervention success across different settings, there is no consensus on what it is about a local setting that needs to be taken into account to design healthy workplace interventions appropriate for different local settings. Complexity theory principles were used to understand a workplace as a complex adaptive system and to create a framework of eight domains (system characteristics) that affect the emergence of system-level behaviour. This Workplace of Well-being (WoW) framework is responsive and adaptive to local settings and allows a shared understanding of the enablers and barriers to behaviour change by capturing local information for each of the eight domains. We use the results of applying the WoW framework to one workplace, a UK National Health Service ward, to describe the utility of this approach in informing design of setting-appropriate healthy workplace interventions that create workplaces conducive to healthy behaviour change. PMID:26380358

  1. Multi-scalar agent-based complex design systems - the case of CECO (Climatic -Ecologies) Studio; informed generative design systems and performance-driven design workflows

    NARCIS (Netherlands)

    Mostafavi, S.; Yu, S.; Biloria, N.M.

    2014-01-01

    This paper illustrates the application of different types of complex systems for digital form finding and design decision making with underlying methodological and pedagogical aims to emphasize performance-driven design solutions via combining generative methods of complex systems with simulation

  2. Understanding and Visualizing Multitasking and Task Switching Activities: A Time Motion Study to Capture Nursing Workflow.

    Science.gov (United States)

    Yen, Po-Yin; Kelley, Marjorie; Lopetegui, Marcelo; Rosado, Amber L; Migliore, Elaina M; Chipps, Esther M; Buck, Jacalyn

    2016-01-01

    A fundamental understanding of multitasking within nursing workflow is important in today's dynamic and complex healthcare environment. We conducted a time motion study to understand nursing workflow, specifically multitasking and task switching activities. We used TimeCaT, a comprehensive electronic time capture tool, to capture observational data. We established inter-observer reliability prior to data collection. We completed 56 hours of observation of 10 registered nurses. We found, on average, nurses had 124 communications and 208 hands-on tasks per 4-hour block of time. They multitasked (having communication and hands-on tasks simultaneously) 131 times, representing 39.48% of all times; the total multitasking duration ranges from 14.6 minutes to 109 minutes, 44.98 minutes (18.63%) on average. We also reviewed workflow visualization to uncover the multitasking events. Our study design and methods provide a practical and reliable approach to conducting and analyzing time motion studies from both quantitative and qualitative perspectives.

  3. An Approach for Systematic In-the-Loop Simulations for Development and Test of a Complex Mechatronic Embedded System

    NARCIS (Netherlands)

    Soltani Nehzad, Amir; Lukkien, Johan J.; Mak, Rudolf H.; Verhoeven, Richard; van den Heuvel, Martijn M.H.P.; Skavhaug, A.; Guiochet, J.; Schoitsch, E.; Bitsch, F.

    2016-01-01

    Simulations are widely used in the engineering workflow of complex mechatronic embedded systems in various domains, such as healthcare, railway, automotive and aerospace, for analyzing, testing and validating purposes. This paper focuses on the development and test of the control software of complex

  4. A model for understanding diagnostic imaging referrals and complex interaction processes within the bigger picture of a healthcare system

    International Nuclear Information System (INIS)

    Makanjee, Chandra R.; Bergh, Anne-Marie; Hoffmann, Willem A.

    2014-01-01

    Using experiences from the South African public healthcare system with limited resources, this review proposes a model that captures a holistic perspective of diagnostic imaging services embedded in a network of negotiated decision-making processes. Professional interdependency and interprofessional collaboration, cooperation and coordination are built around the central notion of integration in order to achieve a seamless transition through the continuum of various types of services needed to come to a diagnosis. Health-system role players interact with patients who enter the system from the perspective of their life-world. The distribution of diagnostic imaging services – within one setting or at multiple levels of care – demonstrates how fragments of information are filtered, interpreted and transformed at each point of care. The proposed model could contribute to alignment towards a common goal: services providing holistic quality of care within and beyond a complex healthcare system

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

    NARCIS (Netherlands)

    Wombacher, Andreas

    2010-01-01

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

  6. Going beyond the hero in leadership development: the place of healthcare context, complexity and relationships: Comment on "Leadership and leadership development in healthcare settings - a simplistic solution to complex problems?".

    Science.gov (United States)

    Ford, Jackie

    2015-04-01

    There remains a conviction that the torrent of publications and the financial outlay on leadership development will create managers with the skills and characters of perfect leaders, capable of guiding healthcare organisations through the challenges and crises of the 21st century. The focus of much attention continues to be the search for the (illusory) core set of heroic qualities, abilities or competencies that will enable the development of leaders to achieve levels of supreme leadership and organisational performance. This brief commentary adds support to McDonald's (1) call for recognition of the complexity of the undertaking.

  7. Going beyond the Hero in Leadership Development: The Place of Healthcare Context, Complexity and Relationships; Comment on “Leadership and Leadership Development in Healthcare Settings – A Simplistic Solution to Complex Problems?”

    Directory of Open Access Journals (Sweden)

    Jackie Ford

    2015-04-01

    Full Text Available There remains a conviction that the torrent of publications and the financial outlay on leadership development will create managers with the skills and characters of perfect leaders, capable of guiding healthcare organisations through the challenges and crises of the 21st century. The focus of much attention continues to be the search for the (illusory core set of heroic qualities, abilities or competencies that will enable the development of leaders to achieve levels of supreme leadership and organisational performance. This brief commentary adds support to McDonald’s (1 call for recognition of the complexity of the undertaking.

  8. Designing Flexible E-Business Workflow Systems

    OpenAIRE

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

    2010-01-01

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

  9. Parametric Room Acoustic Workflows

    DEFF Research Database (Denmark)

    Parigi, Dario; Svidt, Kjeld; Molin, Erik

    2017-01-01

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

  10. Implementing Oracle Workflow

    CERN Document Server

    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

    Directory of Open Access Journals (Sweden)

    Lars R Christensen

    2017-01-01

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

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

    Science.gov (United States)

    Schweitzer, M; Lasierra, N; Hoerbst, A

    2015-01-01

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

  13. Integrative Workflows for Metagenomic Analysis

    Directory of Open Access Journals (Sweden)

    Efthymios eLadoukakis

    2014-11-01

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

  14. Electronic healthcare information security

    CERN Document Server

    Dube, Kudakwashe; Shoniregun, Charles A

    2010-01-01

    The ever-increasing healthcare expenditure and pressing demand for improved quality and efficiency of patient care services are driving innovation in healthcare information management. The domain of healthcare has become a challenging testing ground for information security due to the complex nature of healthcare information and individual privacy. ""Electronic Healthcare Information Security"" explores the challenges of e-healthcare information and security policy technologies. It evaluates the effectiveness of security and privacy implementation systems for anonymization methods and techniqu

  15. Towards a workflow driven design for mHealth devices within temporary eye clinics in low-income settings.

    Science.gov (United States)

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

    2015-01-01

    Only a small minority of mobile healthcare technologies that have been successful in pilot studies have subsequently been integrated into healthcare systems. Understanding the reasons behind this discrepancy is crucial if such technologies are to be adopted. We believe that the mismatch is due to a breakdown in the relation between technical soundness of the original mobile health (mHealth) device design, and integration into healthcare provision workflows. Quantitative workflow modelling provides an opportunity to test this hypothesis. In this paper we present our current progress in developing a clinical workflow model for mobile eye assessment in low-income settings. We test the model for determining the appropriateness of design parameters of a mHealth device within this workflow, by assessing their impact on the entire clinical workflow performance.

  16. ATLAS Grid Workflow Performance Optimization

    CERN Document Server

    Elmsheuser, Johannes; The ATLAS collaboration

    2018-01-01

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

  17. Privacy-aware workflow management

    NARCIS (Netherlands)

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

    2013-01-01

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

  18. Summer Student Report - AV Workflow

    CERN Document Server

    Abramson, Jessie

    2014-01-01

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

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

    Science.gov (United States)

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

    2016-01-01

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

  20. ERROR HANDLING IN INTEGRATION WORKFLOWS

    Directory of Open Access Journals (Sweden)

    Alexey M. Nazarenko

    2017-01-01

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

  1. Planning bioinformatics workflows using an expert system

    Science.gov (United States)

    Chen, Xiaoling; Chang, Jeffrey T.

    2017-01-01

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

  2. SPECT/CT workflow and imaging protocols

    Energy Technology Data Exchange (ETDEWEB)

    Beckers, Catherine [University Hospital of Liege, Division of Nuclear Medicine and Oncological Imaging, Department of Medical Physics, Liege (Belgium); Hustinx, Roland [University Hospital of Liege, Division of Nuclear Medicine and Oncological Imaging, Department of Medical Physics, Liege (Belgium); Domaine Universitaire du Sart Tilman, Service de Medecine Nucleaire et Imagerie Oncologique, CHU de Liege, Liege (Belgium)

    2014-05-15

    Introducing a hybrid imaging method such as single photon emission computed tomography (SPECT)/CT greatly alters the routine in the nuclear medicine department. It requires designing new workflow processes and the revision of original scheduling process and imaging protocols. In addition, the imaging protocol should be adapted for each individual patient, so that performing CT is fully justified and the CT procedure is fully tailored to address the clinical issue. Such refinements often occur before the procedure is started but may be required at some intermediate stage of the procedure. Furthermore, SPECT/CT leads in many instances to a new partnership with the radiology department. This article presents practical advice and highlights the key clinical elements which need to be considered to help understand the workflow process of SPECT/CT and optimise imaging protocols. The workflow process using SPECT/CT is complex in particular because of its bimodal character, the large spectrum of stakeholders, the multiplicity of their activities at various time points and the need for real-time decision-making. With help from analytical tools developed for quality assessment, the workflow process using SPECT/CT may be separated into related, but independent steps, each with its specific human and material resources to use as inputs or outputs. This helps identify factors that could contribute to failure in routine clinical practice. At each step of the process, practical aspects to optimise imaging procedure and protocols are developed. A decision-making algorithm for justifying each CT indication as well as the appropriateness of each CT protocol is the cornerstone of routine clinical practice using SPECT/CT. In conclusion, implementing hybrid SPECT/CT imaging requires new ways of working. It is highly rewarding from a clinical perspective, but it also proves to be a daily challenge in terms of management. (orig.)

  3. SPECT/CT workflow and imaging protocols

    International Nuclear Information System (INIS)

    Beckers, Catherine; Hustinx, Roland

    2014-01-01

    Introducing a hybrid imaging method such as single photon emission computed tomography (SPECT)/CT greatly alters the routine in the nuclear medicine department. It requires designing new workflow processes and the revision of original scheduling process and imaging protocols. In addition, the imaging protocol should be adapted for each individual patient, so that performing CT is fully justified and the CT procedure is fully tailored to address the clinical issue. Such refinements often occur before the procedure is started but may be required at some intermediate stage of the procedure. Furthermore, SPECT/CT leads in many instances to a new partnership with the radiology department. This article presents practical advice and highlights the key clinical elements which need to be considered to help understand the workflow process of SPECT/CT and optimise imaging protocols. The workflow process using SPECT/CT is complex in particular because of its bimodal character, the large spectrum of stakeholders, the multiplicity of their activities at various time points and the need for real-time decision-making. With help from analytical tools developed for quality assessment, the workflow process using SPECT/CT may be separated into related, but independent steps, each with its specific human and material resources to use as inputs or outputs. This helps identify factors that could contribute to failure in routine clinical practice. At each step of the process, practical aspects to optimise imaging procedure and protocols are developed. A decision-making algorithm for justifying each CT indication as well as the appropriateness of each CT protocol is the cornerstone of routine clinical practice using SPECT/CT. In conclusion, implementing hybrid SPECT/CT imaging requires new ways of working. It is highly rewarding from a clinical perspective, but it also proves to be a daily challenge in terms of management. (orig.)

  4. Simulation As a Method To Support Complex Organizational Transformations in Healthcare

    NARCIS (Netherlands)

    Rothengatter, D.C.F.; Katsma, Christiaan; van Hillegersberg, Jos

    2010-01-01

    In this paper we study the application of simulation as a method to support information system and process design in complex organizational transitions. We apply a combined use of a collaborative workshop approach with the use of a detailed and accurate graphical simulation model in a hospital that

  5. Complexity of health-care needs and interactions in multidisciplinary medical teams

    NARCIS (Netherlands)

    Molleman, E.; Broekhuis, Manda; Stoffels, A.M.R.R.; Jaspers, F.

    By using an information processing and social identity approach, this study examines the relationships between the complexity of the health care needs of a patient and (1) the interactions among physicians during team meetings and (2) how the meeting participants evaluate the discussion. Three

  6. ERP (enterprise resource planning) systems can streamline healthcare business functions.

    Science.gov (United States)

    Jenkins, E K; Christenson, E

    2001-05-01

    Enterprise resource planning (ERP) software applications are designed to facilitate the systemwide integration of complex processes and functions across a large enterprise consisting of many internal and external constituents. Although most currently available ERP applications generally are tailored to the needs of the manufacturing industry, many large healthcare systems are investigating these applications. Due to the significant differences between manufacturing and patient care, ERP-based systems do not easily translate to the healthcare setting. In particular, the lack of clinical standardization impedes the use of ERP systems for clinical integration. Nonetheless, an ERP-based system can help a healthcare organization integrate many functions, including patient scheduling, human resources management, workload forecasting, and management of workflow, that are not directly dependent on clinical decision making.

  7. Agency for Healthcare Research and Quality Evidence-based Practice Center methods for systematically reviewing complex multicomponent health care interventions.

    Science.gov (United States)

    Guise, Jeanne-Marie; Chang, Christine; Viswanathan, Meera; Glick, Susan; Treadwell, Jonathan; Umscheid, Craig A; Whitlock, Evelyn; Fu, Rongwei; Berliner, Elise; Paynter, Robin; Anderson, Johanna; Motu'apuaka, Pua; Trikalinos, Tom

    2014-11-01

    The purpose of this Agency for Healthcare Research and Quality Evidence-based Practice Center methods white paper was to outline approaches to conducting systematic reviews of complex multicomponent health care interventions. We performed a literature scan and conducted semistructured interviews with international experts who conduct research or systematic reviews of complex multicomponent interventions (CMCIs) or organizational leaders who implement CMCIs in health care. Challenges identified include lack of consistent terminology for such interventions (eg, complex, multicomponent, multidimensional, multifactorial); a wide range of approaches used to frame the review, from grouping interventions by common features to using more theoretical approaches; decisions regarding whether and how to quantitatively analyze the interventions, from holistic to individual component analytic approaches; and incomplete and inconsistent reporting of elements critical to understanding the success and impact of multicomponent interventions, such as methods used for implementation the context in which interventions are implemented. We provide a framework for the spectrum of conceptual and analytic approaches to synthesizing studies of multicomponent interventions and an initial list of critical reporting elements for such studies. This information is intended to help systematic reviewers understand the options and tradeoffs available for such reviews. Copyright © 2014 Elsevier Inc. All rights reserved.

  8. CO2 Storage Feasibility: A Workflow for Site Characterisation

    Directory of Open Access Journals (Sweden)

    Nepveu Manuel

    2015-04-01

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

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

    International Nuclear Information System (INIS)

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

    2010-01-01

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

  10. Workflow data patterns

    NARCIS (Netherlands)

    Russell, N.C.; Hofstede, ter A.H.M.; Edmond, D.; Aalst, van der W.M.P.

    2004-01-01

    Workow systems seek to provide an implementation vehicle for complex, recurring business processes. Notwithstanding this common objective, there are a variety of distinct features offered by commercial workow management systems. These differences result in significant variations in the ability of

  11. Data mining workflow templates for intelligent discovery assistance in RapidMiner

    OpenAIRE

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

    2010-01-01

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

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

    Science.gov (United States)

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

    2017-01-01

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

  13. Reenginering of the i4 workflow engine

    OpenAIRE

    Likar, Tilen

    2013-01-01

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

  14. Foreign currency-related translation complexities in cross-border healthcare applications.

    Science.gov (United States)

    Kumar, Anand; Rodrigues, Jean M

    2009-01-01

    International cross-border private hospital chains need to apply the standards for foreign currency translation in order to consolidate the balance sheet and income statements. This not only exposes such chains to exchange rate fluctuations in different ways, but also creates added requirements for enterprise-level IT systems especially when they produce parameters which are used to measure the financial and operational performance of the foreign subsidiary or the parent hospital. Such systems would need to come to terms with the complexities involved in such currency-related translations in order to provide the correct data for performance benchmarking.

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

    Science.gov (United States)

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

    2014-10-01

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

  16. Workflows for microarray data processing in the Kepler environment

    Directory of Open Access Journals (Sweden)

    Stropp Thomas

    2012-05-01

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

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

    Science.gov (United States)

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

    2012-05-17

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

  18. Workflows for microarray data processing in the Kepler environment

    Science.gov (United States)

    2012-01-01

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

  19. Concurrency & Asynchrony in Declarative Workflows

    DEFF Research Database (Denmark)

    Debois, Søren; Hildebrandt, Thomas; Slaats, Tijs

    2015-01-01

    of concurrency in DCR Graphs admits asynchronous execution of declarative workflows both conceptually and by reporting on a prototype implementation of a distributed declarative workflow engine. Both the theoretical development and the implementation is supported by an extended example; moreover, the theoretical....... In this paper, we pro- pose a notion of concurrency for declarative process models, formulated in the context of Dynamic Condition Response (DCR) graphs, and exploiting the so-called “true concurrency” semantics of Labelled Asynchronous Transition Systems. We demonstrate how this semantic underpinning...

  20. Similarity measures for scientific workflows

    OpenAIRE

    Starlinger, Johannes

    2016-01-01

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

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

    NARCIS (Netherlands)

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

    2009-01-01

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

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

    NARCIS (Netherlands)

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

    2009-01-01

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

  3. Office 2010 Workflow Developing Collaborative Solutions

    CERN Document Server

    Mann, David; Enterprises, Creative

    2010-01-01

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

  4. Analysing a Chinese Regional Integrated Healthcare Organisation Reform Failure using a Complex Adaptive System Approach

    Directory of Open Access Journals (Sweden)

    Wenxi Tang

    2017-06-01

    Full Text Available Introduction: China’s organised health system has remained outdated for decades. Current health systems in many less market-oriented countries still adhere to traditional administrative-based directives and linear planning. Furthermore, they neglect the responsiveness and feedback of institutions and professionals, which often results in reform failure in integrated care. Complex adaptive system theory (CAS provides a new perspective and methodology for analysing the health system and policy implementation.  Methods: We observed the typical case of Qianjiang’s Integrated Health Organization Reform (IHO for 2 years to analyse integrated care reforms using CAS theory. Via questionnaires and interviews, we observed 32 medical institutions and 344 professionals. We compared their cooperative behaviours from both organisational and inter-professional levels between 2013 and 2015, and further investigated potential reasons for why medical institutions and professionals did not form an effective IHO. We discovered how interested parties in the policy implementation process influenced reform outcome, and by theoretical induction, proposed a new semi-organised system and corresponding policy analysis flowchart that potentially suits the actual realisation of CAS.  Results: The reform did not achieve its desired effect. The Qianjiang IHO was loosely integrated rather than closely integrated, and the cooperation levels between organisations and professionals were low. This disappointing result was due to low mutual trust among IHO members, with the main contributing factors being insufficient financial incentives and the lack of a common vision.  Discussion and Conclusions: The traditional 'organised health system' is old-fashioned. Rather than being completely organised or adaptive, the health system is currently more similar to a s'emi-organised system'. Medical institutions and professionals operate in a middle ground between complete adherence

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

    NARCIS (Netherlands)

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

    2011-01-01

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

  6. CMS Distributed Computing Workflow Experience

    CERN Document Server

    Haas, Jeffrey David

    2010-01-01

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

  7. New Interactions with Workflow Systems

    NARCIS (Netherlands)

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

    2009-01-01

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

  8. CMS distributed computing workflow experience

    Science.gov (United States)

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

    2011-12-01

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

  9. CMS distributed computing workflow experience

    International Nuclear Information System (INIS)

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

    2011-01-01

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

  10. Design Tools and Workflows for Braided Structures

    DEFF Research Database (Denmark)

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

    2017-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Dreher, M.; Peterka, T.

    2017-07-31

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

  12. Supporting flexible processes with adaptive workflow and case handling

    NARCIS (Netherlands)

    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,

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

    Science.gov (United States)

    Wang, Jing; Yu, ShuXia; Du, YuYue

    2015-01-01

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

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

    Science.gov (United States)

    Wang, Jing; Yu, ShuXia; Du, YuYue

    2015-01-01

    Logic Petri nets (LPNs) can describe and analyze batch processing functions and passing value indeterminacy in cooperative systems. Logic Petri workflow nets (LPWNs) are proposed based on LPNs in this paper. Process mining is regarded as an important bridge between modeling and analysis of data mining and business process. Workflow nets (WF-nets) are the extension to Petri nets (PNs), and have successfully been used to process mining. Some shortcomings cannot be avoided in process mining, such as duplicate tasks, invisible tasks, and the noise of logs. The online shop in electronic commerce in this paper is modeled to prove the equivalence between LPWNs and WF-nets, and advantages of LPWNs are presented. PMID:25821845

  15. Snakemake-a scalable bioinformatics workflow engine

    NARCIS (Netherlands)

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

    2012-01-01

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

  16. Behavioral technique for workflow abstraction and matching

    NARCIS (Netherlands)

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

    2006-01-01

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

  17. A performance study of grid workflow engines

    NARCIS (Netherlands)

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

    2008-01-01

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

  18. wft4galaxy: a workflow testing tool for galaxy.

    Science.gov (United States)

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

    2017-12-01

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

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

    NARCIS (Netherlands)

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

    2013-01-01

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

  20. Climate Data Analytics Workflow Management

    Science.gov (United States)

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

    2016-12-01

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

  1. The OCoN approach to workflow modeling in object-oriented systems

    NARCIS (Netherlands)

    Wirtz, G.; Weske, M.H.; Giese, H.

    2001-01-01

    Workflow management aims at modeling and executing application processes in complex technical and organizational environments. Modern information systems are often based on object-oriented design techniques, for instance, the Unified Modeling Language (UML). These systems consist of application

  2. Evolution of Medication Administration Workflow in Implementing Electronic Health Record System

    Science.gov (United States)

    Huang, Yuan-Han

    2013-01-01

    This study focused on the clinical workflow evolutions when implementing the health information technology (HIT). The study especially emphasized on administrating medication when the electronic health record (EHR) systems were adopted at rural healthcare facilities. Mixed-mode research methods, such as survey, observation, and focus group, were…

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

    Directory of Open Access Journals (Sweden)

    J. van Leeuwen

    2016-06-01

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

  4. Workflows for Full Waveform Inversions

    Science.gov (United States)

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

    2017-04-01

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

  5. Flexible Early Warning Systems with Workflows and Decision Tables

    Science.gov (United States)

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

    2012-04-01

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

  6. The contribution of qualitative research in designing a complex intervention for secondary prevention of coronary heart disease in two different healthcare systems.

    LENUS (Irish Health Repository)

    Corrrigan, Mairead

    2006-01-01

    BACKGROUND: Developing complex interventions for testing in randomised controlled trials is of increasing importance in healthcare planning. There is a need for careful design of interventions for secondary prevention of coronary heart disease (CHD). It has been suggested that integrating qualitative research in the development of a complex intervention may contribute to optimising its design but there is limited evidence of this in practice. This study aims to examine the contribution of qualitative research in developing a complex intervention to improve the provision and uptake of secondary prevention of CHD within primary care in two different healthcare systems. METHODS: In four general practices, one rural and one urban, in Northern Ireland and the Republic of Ireland, patients with CHD were purposively selected. Four focus groups with patients (N = 23) and four with staff (N = 29) informed the development of the intervention by exploring how it could be tailored and integrated with current secondary prevention activities for CHD in the two healthcare settings. Following an exploratory trial the acceptability and feasibility of the intervention were discussed in four focus groups (17 patients) and 10 interviews (staff). The data were analysed using thematic analysis. RESULTS: Integrating qualitative research into the development of the intervention provided depth of information about the varying impact, between the two healthcare systems, of different funding and administrative arrangements, on their provision of secondary prevention and identified similar barriers of time constraints, training needs and poor patient motivation. The findings also highlighted the importance to patients of stress management, the need for which had been underestimated by the researchers. The qualitative evaluation provided depth of detail not found in evaluation questionnaires. It highlighted how the intervention needed to be more practical by minimising administration

  7. The contribution of qualitative research in designing a complex intervention for secondary prevention of coronary heart disease in two different healthcare systems

    Directory of Open Access Journals (Sweden)

    Leathem Claire S

    2006-07-01

    Full Text Available Abstract Background Developing complex interventions for testing in randomised controlled trials is of increasing importance in healthcare planning. There is a need for careful design of interventions for secondary prevention of coronary heart disease (CHD. It has been suggested that integrating qualitative research in the development of a complex intervention may contribute to optimising its design but there is limited evidence of this in practice. This study aims to examine the contribution of qualitative research in developing a complex intervention to improve the provision and uptake of secondary prevention of CHD within primary care in two different healthcare systems. Methods In four general practices, one rural and one urban, in Northern Ireland and the Republic of Ireland, patients with CHD were purposively selected. Four focus groups with patients (N = 23 and four with staff (N = 29 informed the development of the intervention by exploring how it could be tailored and integrated with current secondary prevention activities for CHD in the two healthcare settings. Following an exploratory trial the acceptability and feasibility of the intervention were discussed in four focus groups (17 patients and 10 interviews (staff. The data were analysed using thematic analysis. Results Integrating qualitative research into the development of the intervention provided depth of information about the varying impact, between the two healthcare systems, of different funding and administrative arrangements, on their provision of secondary prevention and identified similar barriers of time constraints, training needs and poor patient motivation. The findings also highlighted the importance to patients of stress management, the need for which had been underestimated by the researchers. The qualitative evaluation provided depth of detail not found in evaluation questionnaires. It highlighted how the intervention needed to be more practical by minimising

  8. The contribution of qualitative research in designing a complex intervention for secondary prevention of coronary heart disease in two different healthcare systems.

    Science.gov (United States)

    Corrrigan, Mairead; Cupples, Margaret E; Smith, Susan M; Byrne, Molly; Leathem, Claire S; Clerkin, Pauline; Murphy, Andrew W

    2006-07-18

    Developing complex interventions for testing in randomised controlled trials is of increasing importance in healthcare planning. There is a need for careful design of interventions for secondary prevention of coronary heart disease (CHD). It has been suggested that integrating qualitative research in the development of a complex intervention may contribute to optimising its design but there is limited evidence of this in practice. This study aims to examine the contribution of qualitative research in developing a complex intervention to improve the provision and uptake of secondary prevention of CHD within primary care in two different healthcare systems. In four general practices, one rural and one urban, in Northern Ireland and the Republic of Ireland, patients with CHD were purposively selected. Four focus groups with patients (N = 23) and four with staff (N = 29) informed the development of the intervention by exploring how it could be tailored and integrated with current secondary prevention activities for CHD in the two healthcare settings. Following an exploratory trial the acceptability and feasibility of the intervention were discussed in four focus groups (17 patients) and 10 interviews (staff). The data were analysed using thematic analysis. Integrating qualitative research into the development of the intervention provided depth of information about the varying impact, between the two healthcare systems, of different funding and administrative arrangements, on their provision of secondary prevention and identified similar barriers of time constraints, training needs and poor patient motivation. The findings also highlighted the importance to patients of stress management, the need for which had been underestimated by the researchers. The qualitative evaluation provided depth of detail not found in evaluation questionnaires. It highlighted how the intervention needed to be more practical by minimising administration, integrating role plays into behaviour

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

    Directory of Open Access Journals (Sweden)

    Vladimir Korkhov

    2007-01-01

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

  10. Integration of services into workflow applications

    CERN Document Server

    Czarnul, Pawel

    2015-01-01

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

  11. Multidetector-row CT: economics and workflow

    International Nuclear Information System (INIS)

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

    2005-01-01

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

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

    NARCIS (Netherlands)

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

    2007-01-01

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

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

    Science.gov (United States)

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

    2016-03-12

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

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

    Science.gov (United States)

    Plale, B.

    2009-05-01

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

  15. Contracts for Cross-Organizational Workflow Management

    NARCIS (Netherlands)

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

    1999-01-01

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

  16. Verifying generalized soundness for workflow nets

    NARCIS (Netherlands)

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

    2007-01-01

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

  17. Implementing bioinformatic workflows within the bioextract server

    Science.gov (United States)

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

  18. Workflow Fault Tree Generation Through Model Checking

    DEFF Research Database (Denmark)

    Herbert, Luke Thomas; Sharp, Robin

    2014-01-01

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

  19. Workflow Patterns for Business Process Modeling

    NARCIS (Netherlands)

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

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

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

    Science.gov (United States)

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

    2013-12-01

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

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

    Directory of Open Access Journals (Sweden)

    Gabriele Pierantoni

    2014-01-01

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

  2. A Formal Framework for Workflow Analysis

    Science.gov (United States)

    Cravo, Glória

    2010-09-01

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

  3. Using Mobile Agents to Implement Workflow System

    Institute of Scientific and Technical Information of China (English)

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

    2004-01-01

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

  4. Dynamic Reusable Workflows for Ocean Science

    Directory of Open Access Journals (Sweden)

    Richard P. Signell

    2016-10-01

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

  5. Dynamic reusable workflows for ocean science

    Science.gov (United States)

    Signell, Richard; Fernandez, Filipe; Wilcox, Kyle

    2016-01-01

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

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

    Science.gov (United States)

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

    2017-07-01

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

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

    Science.gov (United States)

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

    2009-01-01

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

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

    DEFF Research Database (Denmark)

    Herbert, Luke Thomas; Sharp, Robin

    2013-01-01

    We present a framework for modeling and analysis of real-world business workflows. We present a formalized core subset of the business process modeling and notation (BPMN) and then proceed to extend this language with probabilistic nondeterministic branching and general-purpose reward annotations...... the entire BPMN language, allow for more complex annotations and ultimately to automatically synthesize workflows by composing predefined subprocesses, in order to achieve a configuration that is optimal for parameters of interest....

  9. Preventing healthcare-associated infections through human factors engineering.

    Science.gov (United States)

    Jacob, Jesse T; Herwaldt, Loreen A; Durso, Francis T

    2018-05-24

    Human factors engineering (HFE) approaches are increasingly being used in healthcare, but have been applied in relatively limited ways to infection prevention and control (IPC). Previous studies have focused on using selected HFE tools, but newer literature supports a system-based HFE approach to IPC. Cross-contamination and the existence of workarounds suggest that healthcare workers need better support to reduce and simplify steps in delivering care. Simplifying workflow can lead to better understanding of why a process fails and allow for improvements to reduce errors and increase efficiency. Hand hygiene can be improved using visual cues and nudges based on room layout. Using personal protective equipment appropriately appears simple, but exists in a complex interaction with workload, behavior, emotion, and environmental variables including product placement. HFE can help prevent the pathogen transmission through improving environmental cleaning and appropriate use of medical devices. Emerging evidence suggests that HFE can be applied in IPC to reduce healthcare-associated infections. HFE and IPC collaboration can help improve many of the basic best practices including use of hand hygiene and personal protective equipment by healthcare workers during patient care.

  10. ATLAS job transforms: a data driven workflow engine

    International Nuclear Information System (INIS)

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

    2014-01-01

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

  11. Workflow Management in CLARIN-DK

    DEFF Research Database (Denmark)

    Jongejan, Bart

    2013-01-01

    The CLARIN-DK infrastructure is not only a repository of resources, but also a place where users can analyse, annotate, reformat and potentially even translate resources, using tools that are integrated in the infrastructure as web services. In many cases a single tool does not produce the desired...... with the features that describe her goal, because the workflow manager not only executes chains of tools in a workflow, but also takes care of autonomously devising workflows that serve the user’s intention, given the tools that currently are integrated in the infrastructure as web services. To do this...

  12. The Diabetic Retinopathy Screening Workflow

    Science.gov (United States)

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

    2015-01-01

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

  13. Workflow Optimization in Vertebrobasilar Occlusion

    International Nuclear Information System (INIS)

    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. Security aspects in teleradiology workflow

    Science.gov (United States)

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

    2000-05-01

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

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

    Science.gov (United States)

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

    2014-01-01

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

  16. Resilient workflows for computational mechanics platforms

    International Nuclear Information System (INIS)

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

    2010-01-01

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

  17. Resilient workflows for computational mechanics platforms

    Science.gov (United States)

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

    2010-06-01

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

  18. The complex scenario of obesity, diabetes and hypertension in the area of influence of primary healthcare facilities in Mexico.

    Science.gov (United States)

    Alcalde-Rabanal, J E; Orozco-Núñez, E; Espinosa-Henao, O E; Arredondo-López, A; Alcayde-Barranco, L

    2018-01-01

    Among non-communicable chronic diseases (NCCD), diabetes and hypertension are the main cause of adult mortality worldwide. Among the members of the Organization for Economic Cooperation and Development, Mexico is first in prevalence of diabetes and second in obesity. To face this problematic situation of NCCDs the Ministry of Health declared a national epidemiological alert against the overweight, obesity and diabetes. The target of this study is to characterize the status of obesity, diabetes and hypertension in the adult population in the area of influence of primary health facilities located in high social marginality areas. We conducted a cross-sectional observational study and used a convenience sample. A survey was conducted on a population of 18 years old and above in four primary health facilities in four Mexican States. The survey explored sociodemographic characteristics, the presence of chronic diseases, the access to healthcare services, risk factors and life styles. We also applied a complementary questionnaire to 20% of the participants, in order to explore food consumption during the last week and physical activity (International Physical Activity Questionnaire). We based our analysis on descriptive statistics and logistic multivariate regression to analyze factors associated with diabetes and hypertension. 73% (n = 7531, CI 0.72-0.74) percent of the population reported being diabetic, hypertensive and/or overweight. The majority of them receive healthcare in public health services. People over 40 years old, are 11 times more probable of living with diabetes and 8.7 times more probable of living with hypertension. Both conditions affect mostly women, whose main activity is to be a housewife. People who have lunch and dinner out of home are more likely to develop diabetes. People who perform intense physical activity are less likely to live with hypertension. According to the self-report, more than 70% of adult population living in areas with high

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

    Science.gov (United States)

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

    2017-01-01

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

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

    Science.gov (United States)

    Stephan, E.

    2010-12-01

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

  1. Workflow Based Software Development Environment, Phase I

    Data.gov (United States)

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

  2. COSMOS: Python library for massively parallel workflows.

    Science.gov (United States)

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

    2014-10-15

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

  3. Implementing Workflow Reconfiguration in WS-BPEL

    DEFF Research Database (Denmark)

    Mazzara, Manuel; Dragoni, Nicola; Zhou, Mu

    2012-01-01

    This paper investigates the problem of dynamic reconfiguration by means of a workflow-based case study used for discussion. We state the requirements on a system implementing the workflow and its reconfiguration, and we describe the system’s design in BPMN. WS-BPEL, a language that would not natu......This paper investigates the problem of dynamic reconfiguration by means of a workflow-based case study used for discussion. We state the requirements on a system implementing the workflow and its reconfiguration, and we describe the system’s design in BPMN. WS-BPEL, a language that would...... not naturally support dynamic change, is used as a target for implementation. The WS-BPEL recovery framework is here exploited to implement the reconfiguration using principles derived from previous research in process algebra and two mappings from BPMN to WS-BPEL are presented, one automatic and only mostly...

  4. Logical provenance in data-oriented workflows?

    KAUST Repository

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

    2013-01-01

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

  5. A Multilevel Secure Workflow Management System

    National Research Council Canada - National Science Library

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

    1999-01-01

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

  6. Workflow Based Software Development Environment, Phase II

    Data.gov (United States)

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

  7. Multilevel Workflow System in the ATLAS Experiment

    CERN Document Server

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

    2015-01-01

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

  8. Improved compliance by BPM-driven workflow automation.

    Science.gov (United States)

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

    2014-12-01

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

  9. Integrating Process Mining and Cognitive Analysis to Study EHR Workflow.

    Science.gov (United States)

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

    2016-01-01

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

  10. Toyota A3 report: a tool for process improvement in healthcare.

    Science.gov (United States)

    Lee, Te-Shu; Kuo, Mu-Hsing

    2009-01-01

    It is proposed that the A3 problem solving process be used by hospital staff to improve its healthcare workflow. A hypothetical case study is given to demonstrate the applicability and benefits of the methodology. The research results show that A3 is a useful tool for healthcare organizations seeking to continuously improve their healthcare service quality.

  11. Impact of Diabetes E-Consults on Outpatient Clinic Workflow.

    Science.gov (United States)

    Zoll, Brian; Parikh, Pratik J; Gallimore, Jennie; Harrell, Stephen; Burke, Brian

    2015-08-01

    An e-consult is an electronic communication system between clinicians, usually a primary care physician (PCP) and a medical or surgical specialist, regarding general or patient-specific, low complexity questions that would not need an in-person consultation. The objectives of this study were to understand and quantify the impact of the e-consult initiative on outpatient clinic workflow and outcomes. We collected data from 5 different Veterans Affairs (VA) outpatient clinics and interviewed several physicians and staff members. We then developed a simulation model for a primary care team at an outpatient clinic. A detailed experimental study was conducted to determine the effects of factors, such as e-consult demand, view-alert notification arrivals, walk-in patient arrivals, and PCP unavailability, on e-consult cycle time. Statistical tests indicated that 4 factors related to outpatient clinic workflow were significant, and levels within each of the 4 significant factors resulted in statistically different e-consult cycle times. The arrival rate of electronic notifications, along with patient walk-ins, had a considerable effect on cycle time. Splitting the workload of an unavailable PCP among the other PCPs, instead of the current practice of allocating it to a single PCP, increases the system's ability to handle a much larger e-consult demand. The full potential of e-consults can only be realized if the workflow at the outpatient clinics is designed or modified to support this initiative. This study furthers our understanding of how e-consult systems can be analyzed and alternative workflows tested using statistical and simulation modeling to improve care delivery and outcomes. © The Author(s) 2014.

  12. Applications of process improvement techniques to improve workflow in abdominal imaging.

    Science.gov (United States)

    Tamm, Eric Peter

    2016-03-01

    Major changes in the management and funding of healthcare are underway that will markedly change the way radiology studies will be reimbursed. The result will be the need to deliver radiology services in a highly efficient manner while maintaining quality. The science of process improvement provides a practical approach to improve the processes utilized in radiology. This article will address in a step-by-step manner how to implement process improvement techniques to improve workflow in abdominal imaging.

  13. The PBase Scientific Workflow Provenance Repository

    Directory of Open Access Journals (Sweden)

    Víctor Cuevas-Vicenttín

    2014-10-01

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

  14. Multilevel Workflow System in the ATLAS Experiment

    International Nuclear Information System (INIS)

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

    2015-01-01

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

  15. Developing and evaluating the implementation of a complex intervention: using mixed methods to inform the design of a randomised controlled trial of an oral healthcare intervention after stroke

    Directory of Open Access Journals (Sweden)

    St George Bridget

    2011-07-01

    Full Text Available Abstract Background Many interventions delivered within the stroke rehabilitation setting could be considered complex, though some are more complex than others. The degree of complexity might be based on the number of and interactions between levels, components and actions targeted within the intervention. The number of (and variation within participant groups and the contexts in which it is delivered might also reflect the extent of complexity. Similarly, designing the evaluation of a complex intervention can be challenging. Considerations include the necessity for intervention standardisation, the multiplicity of outcome measures employed to capture the impact of a multifaceted intervention and the delivery of the intervention across different clinical settings operating within varying healthcare contexts. Our aim was to develop and evaluate the implementation of a complex, multidimensional oral health care (OHC intervention for people in stroke rehabilitation settings which would inform the development of a randomised controlled trial. Methods After reviewing the evidence for the provision of OHC following stroke, multi-disciplinary experts informed the development of our intervention. Using both quantitative and qualitative methods we evaluated the implementation of the complex OHC intervention across patients, staff and service levels of care. We also adopted a pragmatic approach to patient recruitment, the completion of assessment tools and delivery of OHC, alongside an attention to the context in which it was delivered. Results We demonstrated the feasibility of implementing a complex OHC intervention across three levels of care. The complementary nature of the mixed methods approach to data gathering provided a complete picture of the implementation of the intervention and a detailed understanding of the variations within and interactions between the components of the intervention. Information on the feasibility of the outcome measures

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

    Science.gov (United States)

    McCarthy, Ann

    2006-01-01

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

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

    Science.gov (United States)

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

    2014-03-01

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

  18. Lean healthcare.

    Science.gov (United States)

    Weinstock, Donna

    2008-01-01

    As healthcare organizations look for new and improved ways to reduce costs and still offer quality healthcare, many are turning to the Toyota Production System of doing business. Rather than focusing on cutting personnel and assets, "lean healthcare" looks to improve patient satisfaction through improved actions and processes.

  19. The MPO system for automatic workflow documentation

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-11-15

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

  20. The MPO system for automatic workflow documentation

    International Nuclear Information System (INIS)

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

    2016-01-01

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

  1. Data intensive ATLAS workflows in the Cloud

    CERN Document Server

    Rzehorz, Gerhard Ferdinand; The ATLAS collaboration

    2016-01-01

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

  2. Data intensive ATLAS workflows in the Cloud

    CERN Document Server

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

    2017-01-01

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

  3. Logical provenance in data-oriented workflows?

    KAUST Repository

    Ikeda, R.

    2013-04-01

    We consider the problem of defining, generating, and tracing provenance in data-oriented workflows, in which input data sets are processed by a graph of transformations to produce output results. We first give a new general definition of provenance for general transformations, introducing the notions of correctness, precision, and minimality. We then determine when properties such as correctness and minimality carry over from the individual transformations\\' provenance to the workflow provenance. We describe a simple logical-provenance specification language consisting of attribute mappings and filters. We provide an algorithm for provenance tracing in workflows where logical provenance for each transformation is specified using our language. We consider logical provenance in the relational setting, observing that for a class of Select-Project-Join (SPJ) transformations, logical provenance specifications encode minimal provenance. We have built a prototype system supporting the features and algorithms presented in the paper, and we report a few preliminary experimental results. © 2013 IEEE.

  4. Impact of CGNS on CFD Workflow

    Science.gov (United States)

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

    2004-01-01

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

  5. A virtual radiation therapy workflow training simulation

    International Nuclear Information System (INIS)

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

    2016-01-01

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

  6. Quantitative analysis of probabilistic BPMN workflows

    DEFF Research Database (Denmark)

    Herbert, Luke Thomas; Sharp, Robin

    2012-01-01

    We present a framework for modelling and analysis of realworld business workflows. We present a formalised core subset of the Business Process Modelling and Notation (BPMN) and then proceed to extend this language with probabilistic nondeterministic branching and general-purpose reward annotations...... of events, reward-based properties and best- and worst- case scenarios. We develop a simple example of medical workflow and demonstrate the utility of this analysis in accurate provisioning of drug stocks. Finally, we suggest a path to building upon these techniques to cover the entire BPMN language, allow...

  7. A Prudent Approach to Fair Use Workflow

    Directory of Open Access Journals (Sweden)

    Karey Patterson

    2018-02-01

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

  8. Perti Net-Based Workflow Access Control Model

    Institute of Scientific and Technical Information of China (English)

    陈卓; 骆婷; 石磊; 洪帆

    2004-01-01

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

  9. Extension of specification language for soundness and completeness of service workflow

    Science.gov (United States)

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

    2018-05-01

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

  10. Soundness of Timed-Arc Workflow Nets

    DEFF Research Database (Denmark)

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

    2014-01-01

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

  11. Distributed interoperable workflow support for electronic commerce

    NARCIS (Netherlands)

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

    1998-01-01

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

  12. Using workflow for projects in higher education

    NARCIS (Netherlands)

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

    2000-01-01

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

  13. Workflow Automation: A Collective Case Study

    Science.gov (United States)

    Harlan, Jennifer

    2013-01-01

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

  14. On Secure Workflow Decentralisation on the Internet

    Directory of Open Access Journals (Sweden)

    Petteri Kaskenpalo

    2010-06-01

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

  15. Text mining for the biocuration workflow.

    Science.gov (United States)

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

    2012-01-01

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

  16. Conventions and workflows for using Situs

    International Nuclear Information System (INIS)

    Wriggers, Willy

    2012-01-01

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

  17. Adaptive workflow simulation of emergency response

    NARCIS (Netherlands)

    Bruinsma, Guido Wybe Jan

    2010-01-01

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

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

    International Nuclear Information System (INIS)

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

    2009-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-07-15

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

  20. Healthcare Robotics

    OpenAIRE

    Riek, Laurel D.

    2017-01-01

    Robots have the potential to be a game changer in healthcare: improving health and well-being, filling care gaps, supporting care givers, and aiding health care workers. However, before robots are able to be widely deployed, it is crucial that both the research and industrial communities work together to establish a strong evidence-base for healthcare robotics, and surmount likely adoption barriers. This article presents a broad contextualization of robots in healthcare by identifying key sta...

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2017-07-01

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

  2. Using SensorML to describe scientific workflows in distributed web service environments

    CSIR Research Space (South Africa)

    Van Zyl, TL

    2009-07-01

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

  3. Using SensorML to describe scientific workflows in distributed web service environments

    CSIR Research Space (South Africa)

    Van Zyl, TL

    2009-07-01

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

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

    Directory of Open Access Journals (Sweden)

    Thoraval Samuel

    2005-04-01

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

  5. Performing Workflows in Pervasive Environments Based on Context Specifications

    OpenAIRE

    Xiping Liu; Jianxin Chen

    2010-01-01

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

  6. Workflow Support for Advanced Grid-Enabled Computing

    OpenAIRE

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

    2004-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Cherian Mathew

    2014-12-01

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

  8. On Lifecycle Constraints of Artifact-Centric Workflows

    Science.gov (United States)

    Kucukoguz, Esra; Su, Jianwen

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

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

    NARCIS (Netherlands)

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

    2007-01-01

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

  10. Optimal resource assignment in workflows for maximizing cooperation

    NARCIS (Netherlands)

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

    2013-01-01

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

  11. Database Support for Workflow Management: The WIDE Project

    NARCIS (Netherlands)

    Grefen, P.W.P.J.; Pernici, B; Sánchez, G.; Unknown, [Unknown

    1999-01-01

    Database Support for Workflow Management: The WIDE Project presents the results of the ESPRIT WIDE project on advanced database support for workflow management. The book discusses the state of the art in combining database management and workflow management technology, especially in the areas of

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

    Directory of Open Access Journals (Sweden)

    Shaymaa Elsherbiny

    2018-03-01

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

  13. RMCgui: a new interface for the workflow associated with running Reverse Monte Carlo simulations

    International Nuclear Information System (INIS)

    Dove, Martin T; Rigg, Gary

    2013-01-01

    The Reverse Monte Carlo method enables construction and refinement of large atomic models of materials that are tuned to give best agreement with experimental data such as neutron and x-ray total scattering data, capturing both the average structure and fluctuations. The practical drawback with the current implementations of this approach is the relatively complex workflow required, from setting up the configuration and simulation details through to checking the final outputs and analysing the resultant configurations. In order to make this workflow more accessible to users, we have developed an end-to-end workflow wrapped within a graphical user interface—RMCgui—designed to make the Reverse Monte Carlo more widely accessible. (paper)

  14. Parallel workflow tools to facilitate human brain MRI post-processing

    Directory of Open Access Journals (Sweden)

    Zaixu eCui

    2015-05-01

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

  15. Teaching Workflow Analysis and Lean Thinking via Simulation: A Formative Evaluation

    Science.gov (United States)

    Campbell, Robert James; Gantt, Laura; Congdon, Tamara

    2009-01-01

    This article presents the rationale for the design and development of a video simulation used to teach lean thinking and workflow analysis to health services and health information management students enrolled in a course on the management of health information. The discussion includes a description of the design process, a brief history of the use of simulation in healthcare, and an explanation of how video simulation can be used to generate experiential learning environments. Based on the results of a survey given to 75 students as part of a formative evaluation, the video simulation was judged effective because it allowed students to visualize a real-world process (concrete experience), contemplate the scenes depicted in the video along with the concepts presented in class in a risk-free environment (reflection), develop hypotheses about why problems occurred in the workflow process (abstract conceptualization), and develop solutions to redesign a selected process (active experimentation). PMID:19412533

  16. Responsibilising managers and clinicians, neglecting system health? What kind of healthcare leadership development do we want?: Comment on "Leadership and leadership development in healthcare settings - a simplistic solution to complex problems?".

    Science.gov (United States)

    Martin, Graham P

    2015-01-01

    Responding to Ruth McDonald's editorial on the rise of leadership and leadership development programmes in healthcare, this paper offers three arguments. Firstly, care is needed in evaluating impact of leadership development, since achievement of organisational goals is not necessarily an appropriate measure of good leadership. Secondly, the proliferation of styles of leadership might be understood in part as a means of retaining control over public services while distributing responsibility for their success and failure. Thirdly, it makes a plea for the continued utility of good administrative skills for clinicians and managers, which are likely to become all-the-more important given recent developments in healthcare policy and governance.

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

    Science.gov (United States)

    Ozkaynak, M; Brennan, P

    2013-01-01

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

  18. Autonomic Management of Application Workflows on Hybrid Computing Infrastructure

    Directory of Open Access Journals (Sweden)

    Hyunjoo Kim

    2011-01-01

    Full Text Available In this paper, we present a programming and runtime framework that enables the autonomic management of complex application workflows on hybrid computing infrastructures. The framework is designed to address system and application heterogeneity and dynamics to ensure that application objectives and constraints are satisfied. The need for such autonomic system and application management is becoming critical as computing infrastructures become increasingly heterogeneous, integrating different classes of resources from high-end HPC systems to commodity clusters and clouds. For example, the framework presented in this paper can be used to provision the appropriate mix of resources based on application requirements and constraints. The framework also monitors the system/application state and adapts the application and/or resources to respond to changing requirements or environment. To demonstrate the operation of the framework and to evaluate its ability, we employ a workflow used to characterize an oil reservoir executing on a hybrid infrastructure composed of TeraGrid nodes and Amazon EC2 instances of various types. Specifically, we show how different applications objectives such as acceleration, conservation and resilience can be effectively achieved while satisfying deadline and budget constraints, using an appropriate mix of dynamically provisioned resources. Our evaluations also demonstrate that public clouds can be used to complement and reinforce the scheduling and usage of traditional high performance computing infrastructure.

  19. Grid workflow job execution service 'Pilot'

    Science.gov (United States)

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

    2011-12-01

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

  20. Grid workflow job execution service 'Pilot'

    International Nuclear Information System (INIS)

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

    2011-01-01

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

  1. IDD Archival Hardware Architecture and Workflow

    Energy Technology Data Exchange (ETDEWEB)

    Mendonsa, D; Nekoogar, F; Martz, H

    2008-10-09

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

  2. Schedule-Aware Workflow Management Systems

    Science.gov (United States)

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

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

  3. Routine digital pathology workflow: The Catania experience

    Directory of Open Access Journals (Sweden)

    Filippo Fraggetta

    2017-01-01

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

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

    Science.gov (United States)

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

    2016-08-01

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

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

    Directory of Open Access Journals (Sweden)

    Michael Rosemann

    1998-11-01

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

  6. Healthcare avoidance: a critical review.

    Science.gov (United States)

    Byrne, Sharon K

    2008-01-01

    The purpose of this study is to provide a critical review and synthesis of theoretical and research literature documenting the impact of avoidance on healthcare behaviors, identify the factors that influence healthcare avoidance and delay in the adult population, and propose a direction for future research. The Theory of Reasoned Action, Theory of Planned Behavior, Theory of Care-Seeking Behavior, the Transtheoretical Model, and the Behavioral Model of Health Services Use/Utilization are utilized to elaborate on the context within which individual intention to engage in healthcare behaviors occurs. Research literature on the concept of healthcare avoidance obtained by using computerized searches of CINAHL, MEDLINE, PSYCH INFO, and HAPI databases, from 1995 to 2007, were reviewed. Studies were organized by professional disciplines. Healthcare avoidance is a common and highly variable experience. Multiple administrative, demographic, personal, and provider factors are related to healthcare avoidance, for example, distrust of providers and/or the science community, health beliefs, insurance status, or socioeconomic/income level. Although the concept is recognized by multiple disciplines, limited research studies address its impact on healthcare decision making. More systematic research is needed to determine correlates of healthcare avoidance. Such studies will help investigators identify patients at risk for avoidant behaviors and provide the basis for health-promoting interventions. Methodological challenges include identification of characteristics of individuals and environments that hinder healthcare behaviors, as well as, the complexity of measuring healthcare avoidance. Studies need to systematically explore the influence of avoidance behaviors on specific healthcare populations at risk.

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

    Science.gov (United States)

    Simonis, I.; Vahed, A.

    2008-12-01

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

  8. Barriers to effective, safe communication and workflow between nurses and non-consultant hospital doctors during out-of-hours.

    Science.gov (United States)

    Brady, Anne-Marie; Byrne, Gobnait; Quirke, Mary Brigid; Lynch, Aine; Ennis, Shauna; Bhangu, Jaspreet; Prendergast, Meabh

    2017-11-01

    This study aimed to evaluate the nature and type of communication and workflow arrangements between nurses and doctors out-of-hours (OOH). Effective communication and workflow arrangements between nurses and doctors are essential to minimize risk in hospital settings, particularly in the out-of-hour's period. Timely patient flow is a priority for all healthcare organizations and the quality of communication and workflow arrangements influences patient safety. Qualitative descriptive design and data collection methods included focus groups and individual interviews. A 500 bed tertiary referral acute hospital in Ireland. Junior and senior Non-Consultant Hospital Doctors, staff nurses and nurse managers. Both nurses and doctors acknowledged the importance of good interdisciplinary communication and collaborative working, in sustaining effective workflow and enabling a supportive working environment and patient safety. Indeed, issues of safety and missed care OOH were found to be primarily due to difficulties of communication and workflow. Medical workflow OOH is often dependent on cues and communication to/from nursing. However, communication systems and, in particular the bleep system, considered central to the process of communication between doctors and nurses OOH, can contribute to workflow challenges and increased staff stress. It was reported as commonplace for routine work, that should be completed during normal hours, to fall into OOH when resources were most limited, further compounding risk to patient safety. Enhancement of communication strategies between nurses and doctors has the potential to remove barriers to effective decision-making and patient flow. © The Author 2017. Published by Oxford University Press in association with the International Society for Quality in Health Care. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

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

    Science.gov (United States)

    Zhao, Yong

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

  10. Responsibilising Managers and Clinicians, Neglecting System Health? What Kind of Healthcare Leadership Development Do We Want? Comment on “Leadership and Leadership Development in Healthcare Settings - A Simplistic Solution to Complex Problems?”

    Directory of Open Access Journals (Sweden)

    Graham P. Martin

    2015-01-01

    Full Text Available Responding to Ruth McDonald’s editorial on the rise of leadership and leadership development programmes in healthcare, this paper offers three arguments. Firstly, care is needed in evaluating impact of leadership development, since achievement of organisational goals is not necessarily an appropriate measure of good leadership. Secondly, the proliferation of styles of leadership might be understood in part as a means of retaining control over public services while distributing responsibility for their success and failure. Thirdly, it makes a plea for the continued utility of good administrative skills for clinicians and managers, which are likely to become all-the-more important given recent developments in healthcare policy and governance.

  11. The robust schedule - A link to improved workflow

    DEFF Research Database (Denmark)

    Lindhard, Søren; Wandahl, Søren

    2012-01-01

    -down the contractors, and force them to rigorously adhere to the initial schedule. If delayed the work-pace or manpower has to be increased to observe the schedule. In attempt to improve productivity three independent site-mangers have been interviewed about time-scheduling. Their experiences and opinions have been...... analyzed and weaknesses in existing time scheduling have been found. The findings showed a negative side effect of keeping the schedule to tight. A too tight schedule is inflexible and cannot absorb variability in production. Flexibility is necessary because of the contractors interacting and dependable....... The result is a chaotic, complex and uncontrolled construction site. Furthermore, strict time limits entail the workflow to be optimized under non-optimal conditions. Even though productivity seems to be increasing, productivity per man-hour is decreasing resulting in increased cost. To increase productivity...

  12. Tools and Workflows for Collaborating on Static Website Projects

    Directory of Open Access Journals (Sweden)

    Kaitlin Newson

    2017-10-01

    Full Text Available Static website generators have seen a significant increase in popularity in recent years, offering many advantages over their dynamic counterparts. While these generators were typically used for blogs, they have grown in usage for other web-based projects, including documentation, conference websites, and image collections. However, because of their technical complexity, these tools can be inaccessible to content creators depending on their level of technical skill and comfort with web development technologies. Drawing from experience with a collaborative static website project, this article will provide an overview of static website generators, review different tools available for managing content, and explore workflows and best practices for collaborating with teams on static website projects.

  13. SegMine workflows for semantic microarray data analysis in Orange4WS

    Directory of Open Access Journals (Sweden)

    Kulovesi Kimmo

    2011-10-01

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

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

    Science.gov (United States)

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

    2017-04-01

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

  15. Responsibilising managers and clinicians, neglecting system health? What kind of healthcare leadership development do we want?: Comment on "Leadership and leadership development in healthcare settings - a simplistic solution to complex problems?"

    OpenAIRE

    Martin, Graham P.

    2014-01-01

    Responding to Ruth McDonald’s editorial on the rise of leadership and leadership development programmes in healthcare, this paper offers three arguments. Firstly, care is needed in evaluating impact of leadership development, since achievement of organisational goals is not necessarily an appropriate measure of good leadership. Secondly, the proliferation of styles of leadership might be understood in part as a means of retaining control over public services while distributing responsibility ...

  16. Implementing standards for the interoperability among healthcare providers in the public regionalized Healthcare Information System of the Lombardy Region.

    Science.gov (United States)

    Barbarito, Fulvio; Pinciroli, Francesco; Mason, John; Marceglia, Sara; Mazzola, Luca; Bonacina, Stefano

    2012-08-01

    Information technologies (ITs) have now entered the everyday workflow in a variety of healthcare providers with a certain degree of independence. This independence may be the cause of difficulty in interoperability between information systems and it can be overcome through the implementation and adoption of standards. Here we present the case of the Lombardy Region, in Italy, that has been able, in the last 10 years, to set up the Regional Social and Healthcare Information System, connecting all the healthcare providers within the region, and providing full access to clinical and health-related documents independently from the healthcare organization that generated the document itself. This goal, in a region with almost 10 millions citizens, was achieved through a twofold approach: first, the political and operative push towards the adoption of the Health Level 7 (HL7) standard within single hospitals and, second, providing a technological infrastructure for data sharing based on interoperability specifications recognized at the regional level for messages transmitted from healthcare providers to the central domain. The adoption of such regional interoperability specifications enabled the communication among heterogeneous systems placed in different hospitals in Lombardy. Integrating the Healthcare Enterprise (IHE) integration profiles which refer to HL7 standards are adopted within hospitals for message exchange and for the definition of integration scenarios. The IHE patient administration management (PAM) profile with its different workflows is adopted for patient management, whereas the Scheduled Workflow (SWF), the Laboratory Testing Workflow (LTW), and the Ambulatory Testing Workflow (ATW) are adopted for order management. At present, the system manages 4,700,000 pharmacological e-prescriptions, and 1,700,000 e-prescriptions for laboratory exams per month. It produces, monthly, 490,000 laboratory medical reports, 180,000 radiology medical reports, 180

  17. Data mining applications in healthcare.

    Science.gov (United States)

    Koh, Hian Chye; Tan, Gerald

    2005-01-01

    Data mining has been used intensively and extensively by many organizations. In healthcare, data mining is becoming increasingly popular, if not increasingly essential. Data mining applications can greatly benefit all parties involved in the healthcare industry. For example, data mining can help healthcare insurers detect fraud and abuse, healthcare organizations make customer relationship management decisions, physicians identify effective treatments and best practices, and patients receive better and more affordable healthcare services. The huge amounts of data generated by healthcare transactions are too complex and voluminous to be processed and analyzed by traditional methods. Data mining provides the methodology and technology to transform these mounds of data into useful information for decision making. This article explores data mining applications in healthcare. In particular, it discusses data mining and its applications within healthcare in major areas such as the evaluation of treatment effectiveness, management of healthcare, customer relationship management, and the detection of fraud and abuse. It also gives an illustrative example of a healthcare data mining application involving the identification of risk factors associated with the onset of diabetes. Finally, the article highlights the limitations of data mining and discusses some future directions.

  18. Text mining for the biocuration workflow

    Science.gov (United States)

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

    2012-01-01

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

  19. Electronic resource management systems a workflow approach

    CERN Document Server

    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

  20. Evolutionary optimization of production materials workflow processes

    DEFF Research Database (Denmark)

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

    2014-01-01

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

  1. CMS data and workflow management system

    CERN Document Server

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

    2008-01-01

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

  2. E-health and healthcare enterprise information system leveraging service-oriented architecture.

    Science.gov (United States)

    Hsieh, Sung-Huai; Hsieh, Sheau-Ling; Cheng, Po-Hsun; Lai, Feipei

    2012-04-01

    To present the successful experiences of an integrated, collaborative, distributed, large-scale enterprise healthcare information system over a wired and wireless infrastructure in National Taiwan University Hospital (NTUH). In order to smoothly and sequentially transfer from the complex relations among the old (legacy) systems to the new-generation enterprise healthcare information system, we adopted the multitier framework based on service-oriented architecture to integrate the heterogeneous systems as well as to interoperate among many other components and multiple databases. We also present mechanisms of a logical layer reusability approach and data (message) exchange flow via Health Level 7 (HL7) middleware, DICOM standard, and the Integrating the Healthcare Enterprise workflow. The architecture and protocols of the NTUH enterprise healthcare information system, especially in the Inpatient Information System (IIS), are discussed in detail. The NTUH Inpatient Healthcare Information System is designed and deployed on service-oriented architecture middleware frameworks. The mechanisms of integration as well as interoperability among the components and the multiple databases apply the HL7 standards for data exchanges, which are embedded in XML formats, and Microsoft .NET Web services to integrate heterogeneous platforms. The preliminary performance of the current operation IIS is evaluated and analyzed to verify the efficiency and effectiveness of the designed architecture; it shows reliability and robustness in the highly demanding traffic environment of NTUH. The newly developed NTUH IIS provides an open and flexible environment not only to share medical information easily among other branch hospitals, but also to reduce the cost of maintenance. The HL7 message standard is widely adopted to cover all data exchanges in the system. All services are independent modules that enable the system to be deployed and configured to the highest degree of flexibility

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

    Directory of Open Access Journals (Sweden)

    David K Brown

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

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

    Science.gov (United States)

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

    2015-01-01

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

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

    Science.gov (United States)

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

    2015-01-01

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

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

    Science.gov (United States)

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

    2003-09-01

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

  7. Building and documenting workflows with python-based snakemake

    OpenAIRE

    Köster, Johannes; Rahmann, Sven

    2012-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2017-10-01

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

  9. A Model of Workflow Composition for Emergency Management

    Science.gov (United States)

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

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

  10. Healthcare leadership's diversity paradox.

    Science.gov (United States)

    Silver, Reginald

    2017-02-06

    color in leadership roles that guide healthcare policy and access. This study connects contemporary literature to perspectives of executives in the field and offers practical solutions to improving the representation of people of color in executive healthcare leadership roles. Social implications The recommendations offered as a result of this research effort serve to create awareness of the challenges that people of color face in career attainment. Although the process of increasing the representation of people of color in executive healthcare leadership will be a complex task that will involve a number of players over the course of several years, this study serves to provide a practical roadmap with actionable tactics that can be deployed. Originality/value This paper is an extension of the work that was done by the author during the course of completing the program requirements for the author's doctoral program. The findings were previously discussed in the author's dissertation. The value of these findings is significant because they validate some of the topics in contemporary literature with the perspectives of practicing healthcare executives. This study is also unique from other studies in that it offers a long-term plan to increase the representation of people of color in executive roles by creating an early disposition toward executive level roles and identifies a number of practical steps toward that end.

  11. Comparison of Resource Platform Selection Approaches for Scientific Workflows

    Energy Technology Data Exchange (ETDEWEB)

    Simmhan, Yogesh; Ramakrishnan, Lavanya

    2010-03-05

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

  12. Design, Modelling and Analysis of a Workflow Reconfiguration

    DEFF Research Database (Denmark)

    Mazzara, Manuel; Abouzaid, Faisal; Dragoni, Nicola

    2011-01-01

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

  13. A Strategy for an MLS Workflow Management System

    National Research Council Canada - National Science Library

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

    1999-01-01

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

  14. Deriving DICOM surgical extensions from surgical workflows

    Science.gov (United States)

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

    2007-03-01

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

  15. Workflow-Based Software Development Environment

    Science.gov (United States)

    Izygon, Michel E.

    2013-01-01

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

  16. Workflow management for a cosmology collaboratory

    International Nuclear Information System (INIS)

    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

  17. The Prosthetic Workflow in the Digital Era

    Directory of Open Access Journals (Sweden)

    Lidia Tordiglione

    2016-01-01

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

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

    Science.gov (United States)

    Manson, Amy; Poyade, Matthieu; Rea, Paul

    2015-10-19

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

  19. Healthcare Lean.

    Science.gov (United States)

    Long, John C

    2003-01-01

    Lean Thinking is an integrated approach to designing, doing and improving the work of people that have come together to produce and deliver goods, services and information. Healthcare Lean is based on the Toyota production system and applies concepts and techniques of Lean Thinking to hospitals and physician practices.

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

    Science.gov (United States)

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

    2016-10-25

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

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

    Science.gov (United States)

    Kadima, Hubert; Granado, Bertrand

    2013-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Sonia Yassa

    2013-01-01

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

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

    Science.gov (United States)

    Aranguren, Mikel Egaña; Wilkinson, Mark D

    2015-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Yolanda Gil

    2009-01-01

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

  5. Accelerating the scientific exploration process with scientific workflows

    International Nuclear Information System (INIS)

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

    2006-01-01

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

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

    Science.gov (United States)

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

    2007-03-08

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

  7. Biowep: a workflow enactment portal for bioinformatics applications

    Directory of Open Access Journals (Sweden)

    Romano Paolo

    2007-03-01

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

  8. Towards seamless workflows in agile data science

    Science.gov (United States)

    Klump, J. F.; Robertson, J.

    2017-12-01

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

  9. Managing Library IT Workflow with Bugzilla

    Directory of Open Access Journals (Sweden)

    Nina McHale

    2010-09-01

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

  10. Swabs to genomes: a comprehensive workflow

    Directory of Open Access Journals (Sweden)

    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.

  11. The P2P approach to interorganizational workflows

    NARCIS (Netherlands)

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

    2001-01-01

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

  12. Reasoning about repairability of workflows at design time

    NARCIS (Netherlands)

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

    2009-01-01

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

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

    NARCIS (Netherlands)

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

    2009-01-01

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

  14. Conceptual framework and architecture for service mediating workflow management

    NARCIS (Netherlands)

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

    2003-01-01

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

  15. Building and documenting workflows with python-based snakemake

    NARCIS (Netherlands)

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

    2012-01-01

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

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

    NARCIS (Netherlands)

    Groth, P.T.; Gil, Y

    2009-01-01

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

  17. Modelling and analysis of workflow for lean supply chains

    Science.gov (United States)

    Ma, Jinping; Wang, Kanliang; Xu, Lida

    2011-11-01

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

  18. Two-Layer Transaction Management for Workflow Management Applications

    NARCIS (Netherlands)

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

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

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

    DEFF Research Database (Denmark)

    Parigi, Dario

    2017-01-01

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

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

    NARCIS (Netherlands)

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

    2008-01-01

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

  1. Distributed Global Transaction Support for Workflow Management Applications

    NARCIS (Netherlands)

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

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

  2. A Collaborative Workflow for the Digitization of Unique Materials

    Science.gov (United States)

    Gueguen, Gretchen; Hanlon, Ann M.

    2009-01-01

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

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

    NARCIS (Netherlands)

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

    2006-01-01

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

  4. Workflow automation based on OSI job transfer and manipulation

    NARCIS (Netherlands)

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

    1999-01-01

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

  5. Walking the history of healthcare.

    Science.gov (United States)

    Black, Nick

    2007-12-01

    The history of healthcare is complex, confusing and contested. In Walking London's medical history the story of how health services developed from medieval times to the present day is told through seven walks. The book also aims to help preserve our legacy, as increasingly former healthcare buildings are converted to other uses, and to enhance understanding of the current challenges we face in trying to improve healthcare in the 21st century. Each walk has a theme, ranging from the way hospitals merge or move and the development of primary care to how key healthcare trades became professions and the competition between the church, Crown and City for control of healthcare. While recognising the contributions of the 'great men of medicine', the book takes as much interest in the six ambulance stations built by the London County Council (1915) as the grandest teaching hospitals.

  6. geoKepler Workflow Module for Computationally Scalable and Reproducible Geoprocessing and Modeling

    Science.gov (United States)

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

    2015-12-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Ramakrishnan, Lavanya; Plale, Beth

    2010-04-05

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

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

    Science.gov (United States)

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

    2012-01-01

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

  9. Federated Database Services for Wind Tunnel Experiment Workflows

    Directory of Open Access Journals (Sweden)

    A. Paventhan

    2006-01-01

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

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

    Science.gov (United States)

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

    2017-12-01

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

  11. Interplay between Clinical Guidelines and Organizational Workflow Systems. Experience from the MobiGuide Project.

    Science.gov (United States)

    Shabo, Amnon; Peleg, Mor; Parimbelli, Enea; Quaglini, Silvana; Napolitano, Carlo

    2016-12-07

    Implementing a decision-support system within a healthcare organization requires integration of clinical domain knowledge with resource constraints. Computer-interpretable guidelines (CIG) are excellent instruments for addressing clinical aspects while business process management (BPM) languages and Workflow (Wf) engines manage the logistic organizational constraints. Our objective is the orchestration of all the relevant factors needed for a successful execution of patient's care pathways, especially when spanning the continuum of care, from acute to community or home care. We considered three strategies for integrating CIGs with organizational workflows: extending the CIG or BPM languages and their engines, or creating an interplay between them. We used the interplay approach to implement a set of use cases arising from a CIG implementation in the domain of Atrial Fibrillation. To provide a more scalable and standards-based solution, we explored the use of Cross-Enterprise Document Workflow Integration Profile. We describe our proof-of-concept implementation of five use cases. We utilized the Personal Health Record of the MobiGuide project to implement a loosely-coupled approach between the Activiti BPM engine and the Picard CIG engine. Changes in the PHR were detected by polling. IHE profiles were used to develop workflow documents that orchestrate cross-enterprise execution of cardioversion. Interplay between CIG and BPM engines can support orchestration of care flows within organizational settings.

  12. Population-Wide Genetic Risk Prediction of Complex Diseases: A Pilot Feasibility Study in Macau Population for Precision Public Healthcare Planning

    OpenAIRE

    Tsui, Nancy B. Y.; Cheng, Gregory; Chung, Teresa; Lam, Christopher W. K.; Yee, Anita; Chung, Peter K. C.; Kwan, Tsz-Ki; Ko, Elaine; He, Daihai; Wong, Wing-Tak; Lau, Johnson Y. N.; Lau, Lok Ting; Fok, Manson

    2018-01-01

    The genetic bases of many common diseases have been identified through genome-wide association studies in the past decade. However, the application of this approach on public healthcare planning has not been well established. Using Macau with population of around 650,000 as a basis, we conducted a pilot study to evaluate the feasibility of population genomic research and its potential on public health decisions. By performing genome-wide SNP genotyping of over a thousand Macau individuals, we...

  13. Machine learning in healthcare informatics

    CERN Document Server

    Acharya, U; Dua, Prerna

    2014-01-01

    The book is a unique effort to represent a variety of techniques designed to represent, enhance, and empower multi-disciplinary and multi-institutional machine learning research in healthcare informatics. The book provides a unique compendium of current and emerging machine learning paradigms for healthcare informatics and reflects the diversity, complexity and the depth and breath of this multi-disciplinary area. The integrated, panoramic view of data and machine learning techniques can provide an opportunity for novel clinical insights and discoveries.

  14. Developing and evaluating the implementation of a complex intervention: using mixed methods to inform the design of a randomised controlled trial of an oral healthcare intervention after stroke

    OpenAIRE

    Brady, Marian C; Stott, David J; Norrie, John; Chalmers, Campbell; St George, Bridget; Sweeney, Petrina M; Langhorne, Peter

    2011-01-01

    Abstract Background Many interventions delivered within the stroke rehabilitation setting could be considered complex, though some are more complex than others. The degree of complexity might be based on the number of and interactions between levels, components and actions targeted within the intervention. The number of (and variation within) participant groups and the contexts in which it is delivered might also reflect the extent of complexity. Similarly, designing the evaluation of a compl...

  15. Healthcare service quality: towards a broad definition.

    Science.gov (United States)

    Mosadeghrad, Ali Mohammad

    2013-01-01

    The main purpose of this study is to define healthcare quality to encompass healthcare stakeholder needs and expectations because healthcare quality has varying definitions for clients, professionals, managers, policy makers and payers. This study represents an exploratory effort to understand healthcare quality in an Iranian context. In-depth individual and focus group interviews were conducted with key healthcare stakeholders. Quality healthcare is defined as "consistently delighting the patient by providing efficacious, effective and efficient healthcare services according to the latest clinical guidelines and standards, which meet the patient's needs and satisfies providers". Healthcare quality definitions common to all stakeholders involve offering effective care that contributes to the patient well-being and satisfaction. This study helps us to understand quality healthcare, highlighting its complex nature, which has direct implications for healthcare providers who are encouraged to regularly monitor healthcare quality using the attributes identified in this study. Accordingly, they can initiate continuous quality improvement programmes to maintain high patient-satisfaction levels. This is the first time a comprehensive healthcare quality definition has been developed using various healthcare stakeholder perceptions and expectations.

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

    Science.gov (United States)

    Chung, Jane; Ozkaynak, Mustafa; Demiris, George

    2017-07-01

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

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

    Science.gov (United States)

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

    2016-12-01

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

  18. From Design to Production Control Through the Integration of Engineering Data Management and Workflow Management Systems

    CERN Document Server

    Le Goff, J M; Bityukov, S; Estrella, F; Kovács, Z; Le Flour, T; Lieunard, S; McClatchey, R; Murray, S; Organtini, G; Vialle, J P; Bazan, A; Chevenier, G

    1997-01-01

    At a time when many companies are under pressure to reduce "times-to-market" the management of product information from the early stages of design through assembly to manufacture and production has become increasingly important. Similarly in the construction of high energy physics devices the collection of ( often evolving) engineering data is central to the subsequent physics analysis. Traditionally in industry design engineers have employed Engineering Data Management Systems ( also called Product Data Management Systems) to coordinate and control access to documented versions of product designs. However, these systems provide control only at the collaborative design level and are seldom used beyond design. Workflow management systems, on the other hand, are employed in industry to coordinate and support the more complex and repeatable work processes of the production environment. Commer cial workflow products cannot support the highly dynamic activities found both in the design stages of product developmen...

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

    Science.gov (United States)

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

    2013-02-18

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

  20. [IHE (Integrating the Healthcare Enterprise): a new approach for the improvement of digital communication in healthcare].

    Science.gov (United States)

    Wein, B B

    2003-02-01

    Parallel to the introduction of diagnosis related groups (DRGs) for the reimbursement of hospitals, a marked reduction of financial means within the healthcare system is taking place. Healthcare enterprise information systems will play an increasing role to accommodate the new working conditions by developing reliable and efficient workflow solutions. Interfacing the systems currently in use can meet considerable obstacles. By offering high connectivity, IHE (Integrating the Healthcare Enterprise), which was initiated by concerted actions of users and vendors, ensures improved health care delivery and, furthermore, assists in acquiring new information systems in the future. IHE is not a standard but makes extensive use of existing international standards, such as HL7 and DICOM. National IHE demonstrations confirmed the power of this approach and presented its mission to large groups of users and vendors. The concept continues to grow and for the first time provides groups of various interests cooperative solutions to the problems encountered in collecting and distributing information.

  1. IHE (Integrating the Healthcare Enterprise): A new approach for the improvement of digital communication in healthcare

    International Nuclear Information System (INIS)

    Wein, B.B.

    2003-01-01

    Parallel to the introduction of diagnosis related groups (DRGs) for the reimbursement of hospitals, a marked reduction of financial means within the healthcare system is taking place. Healthcare enterprise information systems will play an increasing role to accommodate the new working conditions by developing reliable and efficient workflow solutions. Interfacing the systems currently in use can meet considerable obstacles. By offering high connectivity, IHE (Integrating the Healthcare Enterprise), which was initiated by concerted actions of users and vendors, ensures improved health care delivery and, furthermore, assists in acquiring new information systems in the future. IHE is not a standard but makes extensive use of existing international standards, such as HL7 and DICOM. National IHE demonstrations confirmed the power of this approach and presented its mission to large groups of users and vendors. The concept continues to grow and for the first time provides groups of various interests cooperative solutions to the problems encountered in collecting and distributing information. (orig.) [de

  2. Distributed Workflow Service Composition Based on CTR Technology

    Science.gov (United States)

    Feng, Zhilin; Ye, Yanming

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

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

    CERN Document Server

    AUTHOR|(CDS)2069172

    2014-01-01

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

  4. What is needed for effective open access workflows?

    CERN Multimedia

    CERN. Geneva

    2017-01-01

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

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

    Science.gov (United States)

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

    2018-01-01

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

  6. EDMS based workflow for Printing Industry

    Directory of Open Access Journals (Sweden)

    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.

  7. Workflow management in large distributed systems

    International Nuclear Information System (INIS)

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

    2011-01-01

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

  8. Workflow management in large distributed systems

    Science.gov (United States)

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

    2011-12-01

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

  9. Designing the future of healthcare.

    Science.gov (United States)

    Fidsa, Gianfranco Zaccai

    2009-01-01

    This paper describes the application of a holistic design process to a variety of problems plaguing current healthcare systems. A design process for addressing complex, multifaceted problems is contrasted with the piecemeal application of technological solutions to specific medical or administrative problems. The goal of this design process is the ideal customer experience, specifically the ideal experience for patients, healthcare providers, and caregivers within a healthcare system. Holistic design is shown to be less expensive and wasteful in the long run because it avoids solving one problem within a complex system at the cost of creating other problems within that system. The article applies this approach to the maintenance of good health throughout life; to the creation of an ideal experience when a person does need medical care; to the maintenance of personal independence as one ages; and to the enjoyment of a comfortable and dignified death. Virginia Mason Medical Center is discussed as an example of a healthcare institution attempting to create ideal patient and caregiver experiences, in this case by applying the principles of the Toyota Production System ("lean manufacturing") to healthcare. The article concludes that healthcare is inherently dedicated to an ideal, that science and technology have brought it closer to that ideal, and that design can bring it closer still.

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

    Directory of Open Access Journals (Sweden)

    Senger Martin

    2006-11-01

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

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

    Science.gov (United States)

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

    2013-12-01

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

  12. A standard-enabled workflow for synthetic biology

    KAUST Repository

    Myers, Chris J.

    2017-06-15

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

  13. A standard-enabled workflow for synthetic biology

    KAUST Repository

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

    2017-01-01

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

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

    Science.gov (United States)

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

    2010-01-01

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

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

    International Nuclear Information System (INIS)

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

    2010-01-01

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

  16. A Community-Driven Workflow Recommendation and Reuse Infrastructure

    Data.gov (United States)

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

  17. modeling workflow management in a distributed computing system

    African Journals Online (AJOL)

    Dr Obe

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

  18. Scientific workflows as productivity tools for drug discovery.

    Science.gov (United States)

    Shon, John; Ohkawa, Hitomi; Hammer, Juergen

    2008-05-01

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

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

    CSIR Research Space (South Africa)

    McFerren, G

    2011-07-01

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

  20. The importance of symbolic and engaged participation in evidence-based quality improvement in a complex integrated healthcare system: response to "The science of stakeholder engagement in research".

    Science.gov (United States)

    Hamilton, Alison B; Yano, Elizabeth M

    2017-09-01

    In this commentary, we respond to the commentary provided by Goodman and Sanders Thompson regarding our paper on multilevel stakeholder engagement in a VA implementation trial of evidence-based quality improvement (EBQI) in women's health primary care. We clarify our overall approach to engagement (comprised of both symbolic and engaged participation, according to the authors' classification rubric), highlighting that symbolic participation is of more import and value than the authors suggest, especially in the context of a hierarchical healthcare system. We contend that the issue of power-and how power matters in stakeholder engagement-needs to be considered in this context rather than in global "community" terms. In response to the authors' call for greater detail, we clarify our planning processes as well as our approach to veteran engagement. We concur with Goodman and Sanders Thompson that the science of stakeholder engagement necessitates a broader understanding of best practices as well as the impact of engagement on implementation outcomes.

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

    DEFF Research Database (Denmark)

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

    2008-01-01

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

  2. Worklist handling in workflow-enabled radiological application systems

    Science.gov (United States)

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

    2000-05-01

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

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

    Science.gov (United States)

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

    2015-01-01

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

  4. Inverse IMRT workflow process at Austin health

    International Nuclear Information System (INIS)

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

    2004-01-01

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

  5. LabelFlow Framework for Annotating Workflow Provenance

    Directory of Open Access Journals (Sweden)

    Pinar Alper

    2018-02-01

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

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

    Science.gov (United States)

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

    2017-06-20

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

  7. Teaching medical students about fair distribution of healthcare resources.

    NARCIS (Netherlands)

    Leget, C.J.W.; Hoedemaekers, R.H.M.V.

    2007-01-01

    Healthcare package decisions are complex. Different judgements about effectiveness, cost-effectiveness and disease burden influence the decision-making process. Moreover, different concepts of justice generate different ideas about fair distribution of healthcare resources. This paper presents a

  8. Highly Reproducible Automated Proteomics Sample Preparation Workflow for Quantitative Mass Spectrometry.

    Science.gov (United States)

    Fu, Qin; Kowalski, Michael P; Mastali, Mitra; Parker, Sarah J; Sobhani, Kimia; van den Broek, Irene; Hunter, Christie L; Van Eyk, Jennifer E

    2018-01-05

    Sample preparation for protein quantification by mass spectrometry requires multiple processing steps including denaturation, reduction, alkylation, protease digestion, and peptide cleanup. Scaling these procedures for the analysis of numerous complex biological samples can be tedious and time-consuming, as there are many liquid transfer steps and timed reactions where technical variations can be introduced and propagated. We established an automated sample preparation workflow with a total processing time for 96 samples of 5 h, including a 2 h incubation with trypsin. Peptide cleanup is accomplished by online diversion during the LC/MS/MS analysis. In a selected reaction monitoring (SRM) assay targeting 6 plasma biomarkers and spiked β-galactosidase, mean intraday and interday cyclic voltammograms (CVs) for 5 serum and 5 plasma samples over 5 days were samples repeated on 3 separate days had total CVs below 20%. Similar results were obtained when the workflow was transferred to a second site: 93% of peptides had CVs below 20%. An automated trypsin digestion workflow yields uniformly processed samples in less than 5 h. Reproducible quantification of peptides was observed across replicates, days, instruments, and laboratory sites, demonstrating the broad applicability of this approach.

  9. Supporting the Construction of Workflows for Biodiversity Problem-Solving Accessing Secure, Distributed Resources

    Directory of Open Access Journals (Sweden)

    J.S. Pahwa

    2006-01-01

    Full Text Available In the Biodiversity World (BDW project we have created a flexible and extensible Web Services-based Grid environment for biodiversity researchers to solve problems in biodiversity and analyse biodiversity patterns. In this environment, heterogeneous and globally distributed biodiversity-related resources such as data sets and analytical tools are made available to be accessed and assembled by users into workflows to perform complex scientific experiments. One such experiment is bioclimatic modelling of the geographical distribution of individual species using climate variables in order to explain past and future climate-related changes in species distribution. Data sources and analytical tools required for such analysis of species distribution are widely dispersed, available on heterogeneous platforms, present data in different formats and lack inherent interoperability. The present BDW system brings all these disparate units together so that the user can combine tools with little thought as to their original availability, data formats and interoperability. The new prototype BDW system architecture not only brings together heterogeneous resources but also enables utilisation of computational resources and provides a secure access to BDW resources via a federated security model. We describe features of the new BDW system and its security model which enable user authentication from a workflow application as part of workflow execution.

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

    Science.gov (United States)

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

    2017-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Esteban Pérez-Wohlfeil

    2016-10-01

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

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

    Directory of Open Access Journals (Sweden)

    Iván Tomás Cotes-Ruiz

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

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

    Science.gov (United States)

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

    2008-08-08

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

  14. Visual Workflows for Oil and Gas Exploration

    KAUST Repository

    Hollt, Thomas

    2013-04-14

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

  15. Automated Processing Workflow for Ambient Seismic Recordings

    Science.gov (United States)

    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

  16. Licensed Healthcare Facilities

    Data.gov (United States)

    California Natural Resource Agency — The Licensed Healthcare Facilities point layer represents the locations of all healthcare facilities licensed by the State of California, Department of Health...

  17. Stakeholders' Perceptions on Shortage of Healthcare Workers in Primary Healthcare in Botswana: Focus Group Discussions.

    Directory of Open Access Journals (Sweden)

    Oathokwa Nkomazana

    Full Text Available An adequate health workforce force is central to universal health coverage and positive public health outcomes. However many African countries have critical shortages of healthcare workers, which are worse in primary healthcare. The aim of this study was to explore the perceptions of healthcare workers, policy makers and the community on the shortage of healthcare workers in Botswana.Fifteen focus group discussions were conducted with three groups of policy makers, six groups of healthcare workers and six groups of community members in rural, urban and remote rural health districts of Botswana. All the participants were 18 years and older. Recruitment was purposive and the framework method was used to inductively analyse the data.There was a perceived shortage of healthcare workers in primary healthcare, which was believed to result from an increased need for health services, inequitable distribution of healthcare workers, migration and too few such workers being trained. Migration was mainly the result of unfavourable personal and family factors, weak and ineffective healthcare and human resources management, low salaries and inadequate incentives for rural and remote area service.Botswana has a perceived shortage of healthcare workers, which is worse in primary healthcare and rural areas, as a result of multiple complex factors. To address the scarcity the country should train adequate numbers of healthcare workers and distribute them equitably to sufficiently resourced healthcare facilities. They should be competently managed and adequately remunerated and the living conditions and rural infrastructure should also be improved.

  18. Improving adherence to the Epic Beacon ambulatory workflow.

    Science.gov (United States)

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

    2017-06-01

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

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

    Science.gov (United States)

    Liu, Rui; Zhang, Xiaoli; Zhang, Hao

    2016-11-01

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

  20. Parent-Driven Campaign Videos: An Analysis of the Motivation and Affect of Videos Created by Parents of Children With Complex Healthcare Needs.

    Science.gov (United States)

    Carter, Bernie; Bray, Lucy; Keating, Paula; Wilkinson, Catherine

    2017-09-15

    Caring for a child with complex health care needs places additional stress and time demands on parents. Parents often turn to their peers to share their experiences, gain support, and lobby for change; increasingly this is done through social media. The WellChild #notanurse_but is a parent-driven campaign that states its aim is to "shine a light" on the care parents, who are not nurses, have to undertake for their child with complex health care needs and to raise decision-makers' awareness of the gaps in service provision and support. This article reports on a study that analyzed the #notanurse_but parent-driven campaign videos. The purpose of the study was to consider the videos in terms of the range, content, context, perspectivity (motivation), and affect (sense of being there) in order to inform the future direction of the campaign. Analysis involved repeated viewing of a subset of 30 purposively selected videos and documenting our analysis on a specifically designed data extraction sheet. Each video was analyzed by a minimum of 2 researchers. All but 2 of the 30 videos were filmed inside the home. A variety of filming techniques were used. Mothers were the main narrators in all but 1 set of videos. The sense of perspectivity was clearly linked to the campaign with the narration pressing home the reality, complexity, and need for vigilance in caring for a child with complex health care needs. Different clinical tasks and routines undertaken as part of the child's care were depicted. Videos also reported on a sense of feeling different than "normal families"; the affect varied among the researchers, ranging from strong to weaker emotional responses.

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

    Science.gov (United States)

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

    2012-01-01

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

  2. Distributing Workflows over a Ubiquitous P2P Network

    Directory of Open Access Journals (Sweden)

    Eddie Al-Shakarchi

    2007-01-01

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

  3. Provenance-based refresh in data-oriented workflows

    KAUST Repository

    Ikeda, Robert; Salihoglu, Semih; Widom, Jennifer

    2011-01-01

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

  4. Application of Workflow Technology for Big Data Analysis Service

    Directory of Open Access Journals (Sweden)

    Bin Zhang

    2018-04-01

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

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

    International Nuclear Information System (INIS)

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

    2013-01-01

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

  6. Artificial Intelligence and Public Healthcare Service Innovation

    DEFF Research Database (Denmark)

    Sun, Tara Qian; Medaglia, Rony

    Public healthcare ecosystems are complex networks of diverse actors that are subject to pressures to innovate, also a result of technological advancements. Artificial Intelligence (AI), in particular, has the potential to transform the way hospitals, doctors, patients, government agencies...

  7. Steering healthcare service delivery: a regulatory perspective.

    Science.gov (United States)

    Prakash, Gyan

    2015-01-01

    The purpose of this paper is to explore regulation in India's healthcare sector and makes recommendations needed for enhancing the healthcare service. The literature was reviewed to understand healthcare's regulatory context. To understand the current healthcare system, qualitative data were collected from state-level officials, public and private hospital staff. A patient survey was performed to assess service quality (QoS). Regulation plays a central role in driving healthcare QoS. India needs to strengthen market and institutional co-production based approaches for steering its healthcare in which delivery processes are complex and pose different challenges. This study assesses current healthcare regulation in an Indian state and presents a framework for studying and strengthening regulation. Agile regulation should be based on service delivery issues (pull approach) rather than monitoring and sanctions based regulatory environment (push approach). Healthcare pitfalls across the world seem to follow similar follies. India's complexity and experience is useful for emerging and developed economies. The author reviewed around 70 publications and synthesised them in healthcare regulatory contexts. Patient's perception of private providers could be a key input towards steering regulation. Identifying gaps across QoS dimensions would be useful in taking corrective measures.

  8. A versatile mathematical work-flow to explore how Cancer Stem Cell fate influences tumor progression.

    Science.gov (United States)

    Fornari, Chiara; Balbo, Gianfranco; Halawani, Sami M; Ba-Rukab, Omar; Ahmad, Ab Rahman; Calogero, Raffaele A; Cordero, Francesca; Beccuti, Marco

    2015-01-01

    effectiveness of the presented work-flow was firstly verified on two well known models and then applied to investigate our extended CSC model. We propose a new work-flow to study in a practical and informative way complex systems, allowing an easy identification, interpretation, and visualization of the key model parameters. Our methodology is useful to investigate possible model behaviors and to establish factors driving model dynamics. Analyzing our new CSC model guided by the proposed work-flow, we found that the deregulation of CSC asymmetric proliferation contributes to cancer initiation, in accordance with several experimental evidences. Specifically, model results indicated that the probability of CSC symmetric proliferation is responsible of a switching-like behavior which discriminates between tumorigenesis and unsustainable tumor growth.

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

    Science.gov (United States)

    Wideman, Catherine; Gallet, Jacqueline

    2006-01-01

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

  10. Dynamic Service Selection in Workflows Using Performance Data

    Directory of Open Access Journals (Sweden)

    David W. Walker

    2007-01-01

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

  11. Task Delegation Based Access Control Models for Workflow Systems

    Science.gov (United States)

    Gaaloul, Khaled; Charoy, François

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

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

    International Nuclear Information System (INIS)

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

    1996-06-01

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

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

    Science.gov (United States)

    Krogel, Jaron T.

    2016-01-01

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

  14. Assessment of the Nurse Medication Administration Workflow Process

    Directory of Open Access Journals (Sweden)

    Nathan Huynh

    2016-01-01

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

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

    International Nuclear Information System (INIS)

    Benjamin, Menashe; Aradi, Yinon; Shreiber, Reuven

    2010-01-01

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

  16. In vitro activity of aminoglycosides against clinical isolates of Acinetobacter baumannii complex and other nonfermentative Gram-negative bacilli causing healthcare-associated bloodstream infections in Taiwan.

    Science.gov (United States)

    Liu, Jyh-You; Wang, Fu-Der; Ho, Mao-Wang; Lee, Chen-Hsiang; Liu, Jien-Wei; Wang, Jann-Tay; Sheng, Wang-Huei; Hseuh, Po-Ren; Chang, Shan-Chwen

    2016-12-01

    Aminoglycosides possess in vitro activity against aerobic and facultative Gram-negative bacilli. However, nationwide surveillance on susceptibility data of Acinetobacter baumannii complex and Pseudomonas aeruginosa to aminoglycosides was limited, and aminoglycoside resistance has emerged in the past decade. We study the in vitro susceptibility of A. baumannii complex and other nonfermentative Gram-negative bacilli (NFGNB) to aminoglycosides. A total of 378 NFGNB blood isolates causing healthcare-associated bloodstream infections during 2008 and 2013 at four medical centers in Taiwan were tested for their susceptibilities to four aminoglycosides using the agar dilution method (gentamicin, amikacin, tobramycin, and isepamicin) and disc diffusion method (isepamicin). A. baumannii was highly resistant to all four aminoglycosides (range of susceptibility, 0-4%), whereas >80% of Acinetobacter nosocomialis and Acinetobacter pittii blood isolates were susceptible to amikacin (susceptibility: 96% and 91%, respectively), tobramycin (susceptibility: 92% and 80%, respectively), and isepamicin (susceptibility: 96% and 80%, respectively). All aminoglycosides except gentamicin possessed good in vitro activity (>94%) against P. aeruginosa. Amikacin has the best in vitro activity against P. aeruginosa (susceptibility, 98%), followed by A. nosocomialis (96%), and A. pittii (91%), whereas tobramycin and isepamicin were less potent against A. pittii (both 80%). Aminoglycoside resistances were prevalent in Stenotrophomonas maltophilia and Burkholderia cepacia complex blood isolates in Taiwan. Genospecies among the A. baumannii complex had heterogeneous susceptibility profiles to aminoglycosides. Aminoglycosides, except gentamicin, remained good in vitro antimicrobial activity against P. aeruginosa. Further in vivo clinical data and continuous resistance monitoring are warranted for clinical practice guidance. Copyright © 2015. Published by Elsevier B.V.

  17. Exformatics Declarative Case Management Workflows as DCR Graphs

    DEFF Research Database (Denmark)

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

    2013-01-01

    Declarative workflow languages have been a growing research subject over the past ten years, but applications of the declarative approach in industry are still uncommon. Over the past two years Exformatics A/S, a Danish provider of Electronic Case Management systems, has been cooperating...... with researchers at IT University of Copenhagen (ITU) to create tools for the declarative workflow language Dynamic Condition Response Graphs (DCR Graphs) and incorporate them into their products and in teaching at ITU. In this paper we give a status report over the work. We start with an informal introduction...

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

    Science.gov (United States)

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

    2008-09-01

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

  19. Dynamic networks: Presentation held at the Workshop "Beyond Workflow Management: Supporting Dynamic Organizational Processes", CSCW 2000. 2. Dezember 2000, Philadelphia

    OpenAIRE

    Fuchs-Kittowski, F.

    2000-01-01

    Complex, dynamic organizational processes, especially problem-solving processes, require that the design and control of the cooperative work process is left to the cooperating persons. In reality of social organizations, a permanent change between extraneous- and self-organization is taking place. By integrating communication tools with application sharing synchronous CSCW systems can support dynamic workflows without restraining the self-organizing social processes of the people involved. .

  20. Healthcare waste management in Asia

    International Nuclear Information System (INIS)

    Prem Ananth, A.; Prashanthini, V.; Visvanathan, C.

    2010-01-01

    The risks associated with healthcare waste and its management has gained attention across the world in various events, local and international forums and summits. However, the need for proper healthcare waste management has been gaining recognition slowly due to the substantial disease burdens associated with poor practices, including exposure to infectious agents and toxic substances. Despite the magnitude of the problem, practices, capacities and policies in many countries in dealing with healthcare waste disposal, especially developing nations, is inadequate and requires intensification. This paper looks upon aspects to drive improvements to the existing healthcare waste management situation. The paper places recommendation based on a 12 country study reflecting the current status. The paper does not advocate for any complex technology but calls for changes in mindset of all concerned stakeholders and identifies five important aspects for serious consideration. Understanding the role of governments and healthcare facilities, the paper also outlines three key areas for prioritized action for both parties - budget support, developing policies and legislation and technology and knowledge management.

  1. Healthcare waste management in Asia.

    Science.gov (United States)

    Ananth, A Prem; Prashanthini, V; Visvanathan, C

    2010-01-01

    The risks associated with healthcare waste and its management has gained attention across the world in various events, local and international forums and summits. However, the need for proper healthcare waste management has been gaining recognition slowly due to the substantial disease burdens associated with poor practices, including exposure to infectious agents and toxic substances. Despite the magnitude of the problem, practices, capacities and policies in many countries in dealing with healthcare waste disposal, especially developing nations, is inadequate and requires intensification. This paper looks upon aspects to drive improvements to the existing healthcare waste management situation. The paper places recommendation based on a 12 country study reflecting the current status. The paper does not advocate for any complex technology but calls for changes in mindset of all concerned stakeholders and identifies five important aspects for serious consideration. Understanding the role of governments and healthcare facilities, the paper also outlines three key areas for prioritized action for both parties - budget support, developing policies and legislation and technology and knowledge management.

  2. A Web-Based Tool for Automatic Data Collection, Curation, and Visualization of Complex Healthcare Survey Studies including Social Network Analysis

    Directory of Open Access Journals (Sweden)

    José Alberto Benítez

    2017-01-01

    Full Text Available There is a great concern nowadays regarding alcohol consumption and drug abuse, especially in young people. Analyzing the social environment where these adolescents are immersed, as well as a series of measures determining the alcohol abuse risk or personal situation and perception using a number of questionnaires like AUDIT, FAS, KIDSCREEN, and others, it is possible to gain insight into the current situation of a given individual regarding his/her consumption behavior. But this analysis, in order to be achieved, requires the use of tools that can ease the process of questionnaire creation, data gathering, curation and representation, and later analysis and visualization to the user. This research presents the design and construction of a web-based platform able to facilitate each of the mentioned processes by integrating the different phases into an intuitive system with a graphical user interface that hides the complexity underlying each of the questionnaires and techniques used and presenting the results in a flexible and visual way, avoiding any manual handling of data during the process. Advantages of this approach are shown and compared to the previous situation where some of the tasks were accomplished by time consuming and error prone manipulations of data.

  3. A Web-Based Tool for Automatic Data Collection, Curation, and Visualization of Complex Healthcare Survey Studies including Social Network Analysis.

    Science.gov (United States)

    Benítez, José Alberto; Labra, José Emilio; Quiroga, Enedina; Martín, Vicente; García, Isaías; Marqués-Sánchez, Pilar; Benavides, Carmen

    2017-01-01

    There is a great concern nowadays regarding alcohol consumption and drug abuse, especially in young people. Analyzing the social environment where these adolescents are immersed, as well as a series of measures determining the alcohol abuse risk or personal situation and perception using a number of questionnaires like AUDIT, FAS, KIDSCREEN, and others, it is possible to gain insight into the current situation of a given individual regarding his/her consumption behavior. But this analysis, in order to be achieved, requires the use of tools that can ease the process of questionnaire creation, data gathering, curation and representation, and later analysis and visualization to the user. This research presents the design and construction of a web-based platform able to facilitate each of the mentioned processes by integrating the different phases into an intuitive system with a graphical user interface that hides the complexity underlying each of the questionnaires and techniques used and presenting the results in a flexible and visual way, avoiding any manual handling of data during the process. Advantages of this approach are shown and compared to the previous situation where some of the tasks were accomplished by time consuming and error prone manipulations of data.

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

    Science.gov (United States)

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

    2017-08-01

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

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

    Directory of Open Access Journals (Sweden)

    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.

  6. A Generalized Email Classification System for Workflow Analysis

    NARCIS (Netherlands)

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

    2017-01-01

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

  7. 3D workflows in orthodontics, maxillofacial surgery and prosthodontics

    NARCIS (Netherlands)

    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

  8. Collaborative e-Science Experiments and Scientific Workflows

    NARCIS (Netherlands)

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

    2011-01-01

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

  9. SHIWA workflow interoperability solutions for neuroimaging data analysis

    NARCIS (Netherlands)

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

    2012-01-01

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

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

    Directory of Open Access Journals (Sweden)

    J.D. Blower

    2006-01-01

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

  11. CrossFlow: integrating workflow management and electronic commerce

    NARCIS (Netherlands)

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

    2001-01-01

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

  12. CrossFlow: Integrating Workflow Management and Electronic Commerce

    NARCIS (Netherlands)

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

    2001-01-01

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

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

    NARCIS (Netherlands)

    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.

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

    Science.gov (United States)

    Geeslin, Matthew G; Gaskin, Cree M

    2016-01-01

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

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

    International Nuclear Information System (INIS)

    Frosali, Simone

    2010-01-01

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

  16. A standard-enabled workflow for synthetic biology.

    Science.gov (United States)

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

    2017-06-15

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

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

    DEFF Research Database (Denmark)

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

    2009-01-01

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

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

    NARCIS (Netherlands)

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

    2017-01-01

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

  19. Closha: bioinformatics workflow system for the analysis of massive sequencing data.

    Science.gov (United States)

    Ko, GunHwan; Kim, Pan-Gyu; Yoon, Jongcheol; Han, Gukhee; Park, Seong-Jin; Song, Wangho; Lee, Byungwook

    2018-02-19

    While next-generation sequencing (NGS) costs have fallen in recent years, the cost and complexity of computation remain substantial obstacles to the use of NGS in bio-medical care and genomic research. The rapidly increasing amounts of data available from the new high-throughput methods have made data processing infeasible without automated pipelines. The integration of data and analytic resources into workflow systems provides a solution to the problem by simplifying the task of data analysis. To address this challenge, we developed a cloud-based workflow management system, Closha, to provide fast and cost-effective analysis of massive genomic data. We implemented complex workflows making optimal use of high-performance computing clusters. Closha allows users to create multi-step analyses using drag and drop functionality and to modify the parameters of pipeline tools. Users can also import the Galaxy pipelines into Closha. Closha is a hybrid system that enables users to use both analysis programs providing traditional tools and MapReduce-based big data analysis programs simultaneously in a single pipeline. Thus, the execution of analytics algorithms can be parallelized, speeding up the whole process. We also developed a high-speed data transmission solution, KoDS, to transmit a large amount of data at a fast rate. KoDS has a file transfer speed of up to 10 times that of normal FTP and HTTP. The computer hardware for Closha is 660 CPU cores and 800 TB of disk storage, enabling 500 jobs to run at the same time. Closha is a scalable, cost-effective, and publicly available web service for large-scale genomic data analysis. Closha supports the reliable and highly scalable execution of sequencing analysis workflows in a fully automated manner. Closha provides a user-friendly interface to all genomic scientists to try to derive accurate results from NGS platform data. The Closha cloud server is freely available for use from http://closha.kobic.re.kr/ .

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

    Science.gov (United States)

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

    2010-12-01

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

  1. Does transitioning from computed radiography (CR) to direct radiography (DR) with portable imaging systems affect workflow efficiency?

    Science.gov (United States)

    Gali, Raja L.; Roth, Christopher G.; Smith, Elizabeth; Dave, Jaydev K.

    2018-03-01

    In digital radiography, computed radiography (CR) technology is based on latent image capture by storage phosphors whereas direct radiography (DR) technology is based either on indirect conversion using a scintillator or direct conversion using a photoconductor. DR-based portable imaging systems may enhance workflow efficiency. The purpose of this work was to investigate changes in workflow efficiency at a tertiary healthcare center after transitioning from CR to DR technology for imaging with portable x-ray units. An IRB exemption was obtained. Data for all inpatient-radiographs acquired with portable x-ray units from July-2014 till June-2015 (period 1) with CR technology (AMX4 or AMX4+ portable unit from GE Healthcare, NX workstation from Agfa Healthcare for digitization), from July-2015 till June-2016 (period 2) with DR technology (Carestream DRX-Revolution x-ray units and DRX-1C image receptors) and from July-2016 till January-2017 (period 3; same DR technology) were extracted using Centricity RIS-IC (GE Healthcare). Duration between the imaging-examination scheduled time and completed time (timesch-com) was calculated and compared using non-parametric tests (between the three time periods with corrections for multiple comparisons; three time periods were used to identify if there were any other potential temporal trends not related to transitioning from CR to DR). IBM's SPSS package was used for statistical analysis. Overall data was obtained from 33131, 32194, and 18015 cases in periods 1, 2 and 3, respectively. Independent-Samples Kruskal-Wallis test revealed a statistically significant difference in timesch-com across the three time periods (χ2(2, n= 83,340) = 2053, p < 0.001). The timesch-com was highest for period 1 i.e., radiographs acquired with CR technology (median: 64 minutes) and it decreased significantly for radiographs acquired with DR technology in periods 2 (median: 49 minutes; p < 0.001) and 3 (median∶ 44 minutes; p < 0.001). Overall

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

    KAUST Repository

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

    2012-01-01

    Panda (for Provenance and Data) is a system that supports the creation and execution of data-oriented workflows, with automatic provenance generation and built-in provenance tracing operations. Workflows in Panda are arbitrary a cyclic graphs

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

    NARCIS (Netherlands)

    Grefen, P.W.P.J.

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

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

    CSIR Research Space (South Africa)

    Mthombeni, Thabo DM

    2011-12-01

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

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

    International Nuclear Information System (INIS)

    Delgado Peris, A.

    2015-01-01

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

  6. Atomic energy in healthcare

    International Nuclear Information System (INIS)

    Gupta, Sudeep; Rangarajan, Venkatesh; Thakur, Meenakshi; Parmar, Vani; Jalali, Rakesh; Ashgar, Ali; Pramesh, C.S.; Shrivastava, Shyam; Badwe, Rajendra

    2013-01-01

    One of the socially important non-power programmes of the DAE is in the beneficial use of radiation and related techniques for healthcare. The diagnosis and therapy aspects of radiation based healthcare are discussed in this article. (author)

  7. Communicating with Healthcare Professionals

    Science.gov (United States)

    ... at follow-up appointments by talking with your healthcare team about your concerns, asking questions and getting ... from the time you spend with all your healthcare providers, not just your doctor. Use the skills ...

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

    OpenAIRE

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

    2014-01-01

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

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

    Science.gov (United States)

    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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-09-15

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

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

    International Nuclear Information System (INIS)

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

    2016-01-01

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

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

    NARCIS (Netherlands)

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

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

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

    NARCIS (Netherlands)

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

    2010-01-01

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

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

    DEFF Research Database (Denmark)

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

    2014-01-01

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

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

    DEFF Research Database (Denmark)

    Herbert, Luke Thomas; Hansen, Zaza Nadja Lee

    2016-01-01

    This article presents a framework for the automated restructuring of stochastic workflows to reduce the impact of faults. The framework allows for the modelling of workflows by means of a formalised subset of the BPMN workflow language. We extend this modelling formalism to describe faults...

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

    Science.gov (United States)

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

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

  17. Healthcare. Executive Summary

    Science.gov (United States)

    Carnevale, Anthony P.; Smith, Nicole; Gulish, Artem; Beach, Bennett H.

    2012-01-01

    This executive summary highlights several findings about healthcare. These are: (1) Healthcare is 18 percent of the U.S. economy, twice as high as in other countries; (2) There are two labor markets in healthcare: high-skill, high-wage professional and technical jobs and low-skill, low-wage support jobs; (3) Demand for postsecondary education in…

  18. Enabling scientific workflows in virtual reality

    Science.gov (United States)

    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.

  19. Changes in the cardiac rehabilitation workflow process needed for the implementation of a self-management system.

    Science.gov (United States)

    Wiggers, Anne-Marieke; Vosbergen, Sandra; Kraaijenhagen, Roderik; Jaspers, Monique; Peek, Niels

    2013-01-01

    E-health interventions are of a growing importance for self-management of chronic conditions. This study aimed to describe the process adaptions that are needed in cardiac rehabilitation (CR) to implement a self-management system, called MyCARDSS. We created a generic workflow model based on interviews and observations at three CR clinics. Subsequently, a workflow model of the ideal situation after implementation of MyCARDSS was created. We found that the implementation will increase the complexity of existing working procedures because 1) not all patients will use MyCARDSS, 2) there is a transfer of tasks and responsibilities from professionals to patients, and 3) information in MyCARDSS needs to be synchronized with the EPR system for professionals.

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

    Directory of Open Access Journals (Sweden)

    Bernd Zipper

    2004-12-01

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

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

    Science.gov (United States)

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

    2015-01-01

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

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

    Science.gov (United States)

    Vrabec, Marko; Dolžan, Erazem

    2016-04-01

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

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

    Science.gov (United States)

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

    2010-06-12

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

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

    Science.gov (United States)

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

    2006-11-06

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

  5. Assessment of current mass spectrometric workflows for the quantification of low abundant proteins and phosphorylation sites

    Directory of Open Access Journals (Sweden)

    Manuel Bauer

    2015-12-01

    Full Text Available The data described here provide a systematic performance evaluation of popular data-dependent (DDA and independent (DIA mass spectrometric (MS workflows currently used in quantitative proteomics. We assessed the limits of identification, quantification and detection for each method by analyzing a dilution series of 20 unmodified and 10 phosphorylated synthetic heavy labeled reference peptides, respectively, covering six orders of magnitude in peptide concentration with and without a complex human cell digest background. We found that all methods performed very similarly in the absence of background proteins, however, when analyzing whole cell lysates, targeted methods were at least 5–10 times more sensitive than directed or DDA methods. In particular, higher stage fragmentation (MS3 of the neutral loss peak using a linear ion trap increased dynamic quantification range of some phosphopeptides up to 100-fold. We illustrate the power of this targeted MS3 approach for phosphopeptide monitoring by successfully quantifying 9 phosphorylation sites of the kinetochore and spindle assembly checkpoint component Mad1 over different cell cycle states from non-enriched pull-down samples. The data are associated to the research article ‘Evaluation of data-dependent and data-independent mass spectrometric workflows for sensitive quantification of proteins and phosphorylation sites׳ (Bauer et al., 2014 [1]. The mass spectrometry and the analysis dataset have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org via the PRIDE partner repository with the dataset identifier PXD000964.

  6. MSM, an Efficient Workflow for Metabolite Identification Using Hybrid Linear Ion Trap Orbitrap Mass Spectrometer

    Science.gov (United States)

    Cho, Robert; Huang, Yingying; Schwartz, Jae C.; Chen, Yan; Carlson, Timothy J.; Ma, Ji

    2012-05-01

    Identification of drug metabolites can often yield important information regarding clearance mechanism, pharmacologic activity, or toxicity for drug candidate molecules. Additionally, the identification of metabolites can provide beneficial structure-activity insight to help guide lead optimization efforts towards molecules with optimal metabolic profiles. There are challenges associated with detecting and identifying metabolites in the presence of complex biological matrices, and new LC-MS technologies have been developed to meet these challenges. In this report, we describe the development of an experimental approach that applies unique features of the hybrid linear ion trap Orbitrap mass spectrometer to streamline in vitro and in vivo metabolite identification experiments. The approach, referred to as MSM, utilizes multiple collision cells, dissociation methods, mass analyzers, and detectors. With multiple scan types and different dissociation modes built into one experimental method, along with flexible post-acquisition analysis options, the MSM workflow offers an attractive option to fast and reliable identification of metabolites in different kinds of in vitro and in vivo samples. The MSM workflow was successfully applied to metabolite identification analysis of verapamil in both in vitro rat hepatocyte incubations and in vivo rat bile samples.

  7. Flexible End2End Workflow Automation of Hit-Discovery Research.

    Science.gov (United States)

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

    2014-08-01

    The article considers a new approach of more complex laboratory automation at the workflow layer. The authors purpose the automation of end2end workflows. The combination of all relevant subprocesses-whether automated or manually performed, independently, and in which organizational unit-results in end2end processes that include all result dependencies. The end2end approach focuses on not only the classical experiments in synthesis or screening, but also on auxiliary processes such as the production and storage of chemicals, cell culturing, and maintenance as well as preparatory activities and analyses of experiments. Furthermore, the connection of control flow and data flow in the same process model leads to reducing of effort of the data transfer between the involved systems, including the necessary data transformations. This end2end laboratory automation can be realized effectively with the modern methods of business process management (BPM). This approach is based on a new standardization of the process-modeling notation Business Process Model and Notation 2.0. In drug discovery, several scientific disciplines act together with manifold modern methods, technologies, and a wide range of automated instruments for the discovery and design of target-based drugs. The article discusses the novel BPM-based automation concept with an implemented example of a high-throughput screening of previously synthesized compound libraries. © 2014 Society for Laboratory Automation and Screening.

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

    Science.gov (United States)

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

    2006-01-01

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

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

    Science.gov (United States)

    Dao, Tien Tuan

    2017-06-01

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

  10. A novel digital workflow to manufacture personalized three-dimensional-printed hollow surgical obturators after maxillectomy.

    Science.gov (United States)

    Kortes, J; Dehnad, H; Kotte, A N T; Fennis, W M M; Rosenberg, A J W P

    2018-04-07

    Partial or complete resection of the maxilla during tumour surgery causes oronasal defects, leading to oral-maxillofacial dysfunction, for which the surgical obturator (SO) is an important treatment option. Traditional manufacturing of SOs is complex, time-consuming, and often results in inadequate fit and function. This technical note describes a novel digital workflow to design and manufacture a three-dimensional (3D)-printed hollow SO. Registered computed tomography and magnetic resonance imaging images are used for gross tumour delineation. The produced RTStruct set is exported as a stereolitography (STL) file and merged with a 3D model of the dental status. Based on these merged files, a personalized and hollow digital SO design is created, and 3D printed. Due to the proper fit of the prefabricated SO, a soft silicone lining material can be used during surgery to adapt the prosthesis to the oronasal defect, instead of putty materials that are not suitable for this purpose. An STL file of this final SO is created during surgery, based on a scan of the relined SO. The digital workflow results in a SO weight reduction, an increased fit, an up-to-date digital SO copy, and overall easier clinical handling. Copyright © 2018 International Association of Oral and Maxillofacial Surgeons. Published by Elsevier Ltd. All rights reserved.

  11. Integrating hospital information systems in healthcare institutions: a mediation architecture.

    Science.gov (United States)

    El Azami, Ikram; Cherkaoui Malki, Mohammed Ouçamah; Tahon, Christian

    2012-10-01

    Many studies have examined the integration of information systems into healthcare institutions, leading to several standards in the healthcare domain (CORBAmed: Common Object Request Broker Architecture in Medicine; HL7: Health Level Seven International; DICOM: Digital Imaging and Communications in Medicine; and IHE: Integrating the Healthcare Enterprise). Due to the existence of a wide diversity of heterogeneous systems, three essential factors are necessary to fully integrate a system: data, functions and workflow. However, most of the previous studies have dealt with only one or two of these factors and this makes the system integration unsatisfactory. In this paper, we propose a flexible, scalable architecture for Hospital Information Systems (HIS). Our main purpose is to provide a practical solution to insure HIS interoperability so that healthcare institutions can communicate without being obliged to change their local information systems and without altering the tasks of the healthcare professionals. Our architecture is a mediation architecture with 3 levels: 1) a database level, 2) a middleware level and 3) a user interface level. The mediation is based on two central components: the Mediator and the Adapter. Using the XML format allows us to establish a structured, secured exchange of healthcare data. The notion of medical ontology is introduced to solve semantic conflicts and to unify the language used for the exchange. Our mediation architecture provides an effective, promising model that promotes the integration of hospital information systems that are autonomous, heterogeneous, semantically interoperable and platform-independent.

  12. Experiences of primary care physicians and staff following lean workflow redesign.

    Science.gov (United States)

    Hung, Dorothy Y; Harrison, Michael I; Truong, Quan; Du, Xue

    2018-04-10

    In response to growing pressures on primary care, leaders have introduced a wide range of workforce and practice innovations, including team redesigns that delegate some physician tasks to nonphysicians. One important question is how such innovations affect care team members, particularly in view of growing dissatisfaction and burnout among healthcare professionals. We examine the work experiences of primary care physicians and staff after implementing Lean-based workflow redesigns. This included co-locating physician and medical assistant dyads, delegating significant responsibilities to nonphysician staff, and mandating greater coordination and communication among all care team members. The redesigns were implemented and scaled in three phases across 46 primary care departments in a large ambulatory care delivery system. We fielded 1164 baseline and 1333 follow-up surveys to physicians and other nonphysician staff (average 73% response rate) to assess workforce engagement (e.g., job satisfaction, motivation), perceptions of the work environment, and job-related burnout. We conducted multivariate regressions to detect changes in experiences after the redesign, adjusting for respondent characteristics and clustering of within-clinic responses. We found that both physicians and nonphysician staff reported higher levels of engagement and teamwork after implementing redesigns. However, they also experienced higher levels of burnout and perceptions of the workplace as stressful. Trends were the same for both occupational groups, but the increased reports of stress were greater among physicians. Additionally, members of all clinics, except for the pilot site that developed the new workflows, reported higher burnout, while perceptions of workplace stress increased in all clinics after the redesign. Our findings partially align with expectations of work redesign as a route to improving physician and staff experiences in delivering care. Although teamwork and engagement

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

    Science.gov (United States)

    Pan, Tianheng

    2018-01-01

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

  14. A framework for streamlining research workflow in neuroscience and psychology

    Directory of Open Access Journals (Sweden)

    Jonas eKubilius

    2014-01-01

    Full Text Available Successful accumulation of knowledge is critically dependent on the ability to verify and replicate every part of scientific conduct. However, such principles are difficult to enact when researchers continue to resort on ad hoc workflows and with poorly maintained code base. In this paper I examine the needs of neuroscience and psychology community, and introduce psychopy_ext, a unifying framework that seamlessly integrates popular experiment building, analysis and manuscript preparation tools by choosing reasonable defaults and implementing relatively rigid patterns of workflow. This structure allows for automation of multiple tasks, such as generated user interfaces, unit testing, control analyses of stimuli, single-command access to descriptive statistics, and publication quality plotting. Taken together, psychopy_ext opens an exciting possibility for faster, more robust code development and collaboration for researchers.

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

    Science.gov (United States)

    Joda, Tim; Zarone, Fernando; Ferrari, Marco

    2017-09-19

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

  16. Staffing and Workflow of a Maturing Institutional Repository

    Directory of Open Access Journals (Sweden)

    Debora L. Madsen

    2013-02-01

    Full Text Available Institutional repositories (IRs have become established components of many academic libraries. As an IR matures it will face the challenge of how to scale up its operations to increase the amount and types of content archived. These challenges involve staffing, systems, workflows, and promotion. In the past eight years, Kansas State University's IR (K-REx has grown from a platform for student theses, dissertations, and reports to also include faculty works. The initial workforce of a single faculty member was expanded as a part of a library-wide reorganization, resulting in a cross-departmental team that is better able to accommodate the expansion of the IR. The resultant need to define staff responsibilities and develop resources to manage the workflows has led to the innovations described here, which may prove useful to the greater library community as other IRs mature.

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

    Science.gov (United States)

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-07-15

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

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

    International Nuclear Information System (INIS)

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

    2015-01-01

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

  20. Collaborative Purchasing of Complex Technologies in Healthcare

    DEFF Research Database (Denmark)

    Gobbi, Chiara; Hsuan, Juliana

    2015-01-01

    implications: – The study can offer hospitals, vendors, governmental and regional institutions a better understanding about the alignment mechanisms for successful implementation of CP and how to avoid pitfalls. Originality/value: – Literature on CP is scarce as there are virtually no contributions that debate...

  1. Perspectives on healthcare leader and leadership development

    OpenAIRE

    Scott, Elaine S.

    2010-01-01

    Elaine S ScottCollege of Nursing, Graduate Nursing Science Department, East Carolina University, Greenville, NC USAAbstract: Healthcare delivery systems are complex entities that must merge the best of administrative and clinical practices into a new model of leadership. But, despite growing recognition that healthcare organizational leaders must partner with clinical leaders to address patient safety, evidence based practice, financial sustainability, and capacity, tensions between the group...

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

    Science.gov (United States)

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

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

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

    Science.gov (United States)

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

    2013-12-01

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

  4. Optimising metadata workflows in a distributed information environment

    OpenAIRE

    Robertson, R. John; Barton, Jane

    2005-01-01

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

  5. Workflow Optimization for Tuning Prostheses with High Input Channel

    Science.gov (United States)

    2017-10-01

    of Specific Aim 1 by driving a commercially available two DoF wrist and single DoF hand. The high -level control system will provide analog signals...AWARD NUMBER: W81XWH-16-1-0767 TITLE: Workflow Optimization for Tuning Prostheses with High Input Channel PRINCIPAL INVESTIGATOR: Daniel Merrill...Unlimited The views, opinions and/or findings contained in this report are those of the author(s) and should not be construed as an official Department

  6. A STRUCTURAL MODEL OF AN EXCAVATOR WORKFLOW CONTROL SYSTEM

    Directory of Open Access Journals (Sweden)

    A. Gurko

    2016-12-01

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

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

    Science.gov (United States)

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

    2008-08-01

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

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

    Science.gov (United States)

    Franke, Stefan; Meixensberger, Jürgen; Neumuth, Thomas

    2015-04-01

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

  9. Developing 3D Imaging Programmes-Workflow and Quality Control

    OpenAIRE

    Hess, M.; Robson, S.; Serpico, M.; Amati, G.; Pridden, I.; Nelson, T.

    2016-01-01

    This article reports on a successful project for 3D imaging research, digital applications, and use of new technologies in the museum. The article will focus on the development and implementation of a viable workflow for the production of high-quality 3D models of museum objects, based on the 3D laser scanning and photogrammetry of selected ancient Egyptian artefacts. The development of a robust protocol for the complete process chain for imaging cultural heritage artefacts, from the acquisit...

  10. Yadage and Packtivity - analysis preservation using parametrized workflows

    Science.gov (United States)

    Cranmer, Kyle; Heinrich, Lukas

    2017-10-01

    Preserving data analyses produced by the collaborations at LHC in a parametrized fashion is crucial in order to maintain reproducibility and re-usability. We argue for a declarative description in terms of individual processing steps - “packtivities” - linked through a dynamic directed acyclic graph (DAG) and present an initial set of JSON schemas for such a description and an implementation - “yadage” - capable of executing workflows of analysis preserved via Linux containers.

  11. Thermal Remote Sensing with Uav-Based Workflows

    Science.gov (United States)

    Boesch, R.

    2017-08-01

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

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

    Science.gov (United States)

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

    2016-06-01

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

  13. AnalyzeThis: An Analysis Workflow-Aware Storage System

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-01-01

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

  14. Reproducible Research Data Analyses using the Common Workflow Language standards

    CERN Multimedia

    CERN. Geneva

    2017-01-01

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

  15. Formalizing an integrative, multidisciplinary cancer therapy discovery workflow

    Science.gov (United States)

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

    2014-01-01

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

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

    Science.gov (United States)

    Zhang, Lina

    2014-04-01

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

  17. An integrated billing application to streamline clinician workflow.

    Science.gov (United States)

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

    2014-01-01

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

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

    Science.gov (United States)

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

    2014-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-05-15

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

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

    Science.gov (United States)

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

    2014-01-01

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

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

    International Nuclear Information System (INIS)

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

    2014-01-01

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

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

    Science.gov (United States)

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

    2012-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Elspeth Haston

    2012-07-01

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

  4. Nationwide Buildings Energy Research enabled through an integrated Data Intensive Scientific Workflow and Advanced Analysis Environment

    Energy Technology Data Exchange (ETDEWEB)

    Kleese van Dam, Kerstin [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Lansing, Carina S. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Elsethagen, Todd O. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Hathaway, John E. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Guillen, Zoe C. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Dirks, James A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Skorski, Daniel C. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Stephan, Eric G. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Gorrissen, Willy J. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Gorton, Ian [Carnegie Mellon Univ., Pittsburgh, PA (United States); Liu, Yan [Concordia Univ., Montreal, QC (Canada)

    2014-01-28

    Modern workflow systems enable scientists to run ensemble simulations at unprecedented scales and levels of complexity, allowing them to study system sizes previously impossible to achieve, due to the inherent resource requirements needed for the modeling work. However as a result of these new capabilities the science teams suddenly also face unprecedented data volumes that they are unable to analyze with their existing tools and methodologies in a timely fashion. In this paper we will describe the ongoing development work to create an integrated data intensive scientific workflow and analysis environment that offers researchers the ability to easily create and execute complex simulation studies and provides them with different scalable methods to analyze the resulting data volumes. The integration of simulation and analysis environments is hereby not only a question of ease of use, but supports fundamental functions in the correlated analysis of simulation input, execution details and derived results for multi-variant, complex studies. To this end the team extended and integrated the existing capabilities of the Velo data management and analysis infrastructure, the MeDICi data intensive workflow system and RHIPE the R for Hadoop version of the well-known statistics package, as well as developing a new visual analytics interface for the result exploitation by multi-domain users. The capabilities of the new environment are demonstrated on a use case that focusses on the Pacific Northwest National Laboratory (PNNL) building energy team, showing how they were able to take their previously local scale simulations to a nationwide level by utilizing data intensive computing techniques not only for their modeling work, but also for the subsequent analysis of their modeling results. As part of the PNNL research initiative PRIMA (Platform for Regional Integrated Modeling and Analysis) the team performed an initial 3 year study of building energy demands for the US Eastern

  5. Safe medication management in specialized home healthcare - an observational study.

    Science.gov (United States)

    Lindblad, Marléne; Flink, Maria; Ekstedt, Mirjam

    2017-08-24

    Medication management is a complex, error-prone process. The aim of this study was to explore what constitutes the complexity of the medication management process (MMP) in specialized home healthcare and how healthcare professionals handle this complexity. The study is theoretically based in resilience engineering. Data were collected during the MMP at three specialized home healthcare units in Sweden using two strategies: observation of workplaces and shadowing RNs in everyday work, including interviews. Transcribed material was analysed using grounded theory. The MMP in home healthcare was dynamic and complex with unclear boundaries of responsibilities, inadequate information systems and fluctuating work conditions. Healthcare professionals adapted their everyday clinical work by sharing responsibility and simultaneously being authoritative and preserving patients' active participation, autonomy and integrity. To promote a safe MMP, healthcare professionals constantly re-prioritized goals, handled gaps in communication and information transmission at a distance by creating new bridging solutions. Trade-offs and workarounds were necessary elements, but also posed a threat to patient safety, as these interim solutions were not systematically evaluated or devised learning strategies. To manage a safe medication process in home healthcare, healthcare professionals need to adapt to fluctuating conditions and create bridging strategies through multiple parallel activities distributed over time, space and actors. The healthcare professionals' strategies could be integrated in continuous learning, while preserving boundaries of safety, instead of being more or less interim solutions. Patients' and family caregivers' as active partners in the MMP may be an underestimated resource for a resilient home healthcare.

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

    Energy Technology Data Exchange (ETDEWEB)

    Gunter, Daniel

    2008-07-31

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

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

    Science.gov (United States)

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

    2017-10-01

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

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

    Directory of Open Access Journals (Sweden)

    Wibisono Adianto

    2008-08-01

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

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

    Science.gov (United States)

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

    2010-11-01

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

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

    Science.gov (United States)

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

    2012-01-01

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

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

    DEFF Research Database (Denmark)

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

    2007-01-01

    code and not easy to use by end-users. Therefore, we provide a mapping from WF-nets to BPEL. This mapping builds on the rich theory of Petri nets and can also be used to map other languages (e.g., UML, EPC, BPMN, etc.) onto BPEL. To evaluate WorkflowNet2BPEL4WS we used more than 100 processes modeled...

  12. The Cadmio XML healthcare record.

    Science.gov (United States)

    Barbera, Francesco; Ferri, Fernando; Ricci, Fabrizio L; Sottile, Pier Angelo

    2002-01-01

    The management of clinical data is a complex task. Patient related information reported in patient folders is a set of heterogeneous and structured data accessed by different users having different goals (in local or geographical networks). XML language provides a mechanism for describing, manipulating, and visualising structured data in web-based applications. XML ensures that the structured data is managed in a uniform and transparent manner independently from the applications and their providers guaranteeing some interoperability. Extracting data from the healthcare record and structuring them according to XML makes the data available through browsers. The MIC/MIE model (Medical Information Category/Medical Information Elements), which allows the definition and management of healthcare records and used in CADMIO, a HISA based project, is described in this paper, using XML for allowing the data to be visualised through web browsers.

  13. Strategic planning in healthcare organizations.

    Science.gov (United States)

    Rodríguez Perera, Francisco de Paula; Peiró, Manel

    2012-08-01

    Strategic planning is a completely valid and useful tool for guiding all types of organizations, including healthcare organizations. The organizational level at which the strategic planning process is relevant depends on the unit's size, its complexity, and the differentiation of the service provided. A cardiology department, a hemodynamic unit, or an electrophysiology unit can be an appropriate level, as long as their plans align with other plans at higher levels. The leader of each unit is the person responsible for promoting the planning process, a core and essential part of his or her role. The process of strategic planning is programmable, systematic, rational, and holistic and integrates the short, medium, and long term, allowing the healthcare organization to focus on relevant and lasting transformations for the future. Copyright © 2012 Sociedad Española de Cardiología. Published by Elsevier Espana. All rights reserved.

  14. Why healthcare providers merge.

    Science.gov (United States)

    Postma, Jeroen; Roos, Anne-Fleur

    2016-04-01

    In many OECD countries, healthcare sectors have become increasingly concentrated as a result of mergers. However, detailed empirical insight into why healthcare providers merge is lacking. Also, we know little about the influence of national healthcare policies on mergers. We fill this gap in the literature by conducting a survey study on mergers among 848 Dutch healthcare executives, of which 35% responded (resulting in a study sample of 239 executives). A total of 65% of the respondents was involved in at least one merger between 2005 and 2012. During this period, Dutch healthcare providers faced a number of policy changes, including increasing competition, more pressure from purchasers, growing financial risks, de-institutionalisation of long-term care and decentralisation of healthcare services to municipalities. Our empirical study shows that healthcare providers predominantly merge to improve the provision of healthcare services and to strengthen their market position. Also efficiency and financial reasons are important drivers of merger activity in healthcare. We find that motives for merger are related to changes in health policies, in particular to the increasing pressure from competitors, insurers and municipalities.

  15. Healthcare financing in Croatia

    Directory of Open Access Journals (Sweden)

    Nevenka Kovač

    2013-12-01

    Full Text Available Healthcare financing system is of crucial importance for the functioning of any healthcare system, especially because there is no country in the world that is able to provide all its residents with access to all the benefits afforded by modern medicine. Lack of resources in general and rising healthcare expenditures are considered a difficult issue to solve in Croatia as well. Since Croatia gained its independence, its healthcare system has undergone a number of reforms, the primary objective of which was to optimize healthcare services to the actual monetary capacity of the Croatian economy. The objectives of the mentioned re - forms were partially achieved. The solutions that have been offered until now, i.e. consolidation measures undertaken in the last 10 years were necessary; however, they have not improved the operating conditions. There is still the issue of the deficit from the previous years, i.e. outstanding payments, the largest in the last decade. Analysis of the performance of healthcare institutions in 2011 shows that the decision makers will have to take up a major challenge of finding a solution to the difficulties the Croatian healthcare system has been struggling with for decades, causing a debt of 7 billion kuna. At the same time, they will need to uphold the basic principles of the Healthcare Act, i.e. to provide access to healthcare and ensure its continuity, comprehensiveness and solidarity, keeping in mind that the National Budget Act and Fiscal Responsibility Act have been adopted.

  16. Information Engineering and Workflow Design in a Clinical Decision Support System for Colorectal Cancer Screening in Iran.

    Science.gov (United States)

    Maserat, Elham; Seied Farajollah, Seiede Sedigheh; Safdari, Reza; Ghazisaeedi, Marjan; Aghdaei, Hamid Asadzadeh; Zali, Mohammad Reza

    2015-01-01

    Colorectal cancer is a major cause of morbidity and mortality throughout the world. Colorectal cancer screening is an optimal way for reducing of morbidity and mortality and a clinical decision support system (CDSS) plays an important role in predicting success of screening processes. DSS is a computer-based information system that improves the delivery of preventive care services. The aim of this article was to detail engineering of information requirements and work flow design of CDSS for a colorectal cancer screening program. In the first stage a screening minimum data set was determined. Developed and developing countries were analyzed for identifying this data set. Then information deficiencies and gaps were determined by check list. The second stage was a qualitative survey with a semi-structured interview as the study tool. A total of 15 users and stakeholders' perspectives about workflow of CDSS were studied. Finally workflow of DSS of control program was designed by standard clinical practice guidelines and perspectives. Screening minimum data set of national colorectal cancer screening program was defined in five sections, including colonoscopy data set, surgery, pathology, genetics and pedigree data set. Deficiencies and information gaps were analyzed. Then we designed a work process standard of screening. Finally workflow of DSS and entry stage were determined. A CDSS facilitates complex decision making for screening and has key roles in designing optimal interactions between colonoscopy, pathology and laboratory departments. Also workflow analysis is useful to identify data reconciliation strategies to address documentation gaps. Following recommendations of CDSS should improve quality of colorectal cancer screening.

  17. Ameliorating the emergency department workflow by involving the observation unit: effects on crowding

    Directory of Open Access Journals (Sweden)

    Primiano Iannone

    2015-06-01

    Full Text Available Crowding adversely affects the performance of emergency departments (EDs by worsening efficiency, timeliness of care, clinical outcomes and patients’ satisfaction. We describe in this study our attempt at improving crowding by modifying the roles and workflow of the ED physicians. The observation unit physician was given the additional duty of prioritizing admissions and managing unclear, complex cases, which were previously under the responsibility of front line emergency physicians. We analyzed two corresponding periods, both before the intervention (9897 ED attendances in 2012 and after the intervention (10,297 attendances in 2013. Most of the crowding indices improved significantly, including timeliness of triage, of first medical contact, access to resus area, and overall length of stay in ED. Also, emergency hospital admissions, average specialist consultations and imaging studies per patient decreased significantly. The observation unit workload increased. There was no significant excess of adverse events.

  18. Who doesn't want to be a leader? Leaders are such wonderful people: Comment on "Leadership and leadership development in healthcare settings - a simplistic solution to complex problems?".

    Science.gov (United States)

    Learmonth, Mark

    2015-01-01

    Leadership, as McDonald (1) argues, is a phenomenon which many people involved in healthcare around the globe put great emphasis on today; some even see the improvement of leadership as a panacea for all the ills of their healthcare system. This brief commentary on her work seeks to supplement the points she makes by emphasising the personal attractions leadership enjoys, at least in the eyes of many of those who exercise power in healthcare. It also endeavours to highlight some of the ironies and absurdities which arise as a result of the conflicts about what terms we should use to describe the "leaders" (or, alternatively perhaps, those who seek to enjoy supremacy) within healthcare.

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

    Science.gov (United States)

    Lucas, G.

    2015-08-01

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

  20. Cloud Bursting with GlideinWMS: Means to satisfy ever increasing computing needs for Scientific Workflows

    International Nuclear Information System (INIS)

    Mhashilkar, Parag; Tiradani, Anthony; Holzman, Burt; Larson, Krista; Sfiligoi, Igor; Rynge, Mats

    2014-01-01

    Scientific communities have been in the forefront of adopting new technologies and methodologies in the computing. Scientific computing has influenced how science is done today, achieving breakthroughs that were impossible to achieve several decades ago. For the past decade several such communities in the Open Science Grid (OSG) and the European Grid Infrastructure (EGI) have been using GlideinWMS to run complex application workflows to effectively share computational resources over the grid. GlideinWMS is a pilot-based workload management system (WMS) that creates on demand, a dynamically sized overlay HTCondor batch system on grid resources. At present, the computational resources shared over the grid are just adequate to sustain the computing needs. We envision that the complexity of the science driven by 'Big Data' will further push the need for computational resources. To fulfill their increasing demands and/or to run specialized workflows, some of the big communities like CMS are investigating the use of cloud computing as Infrastructure-As-A-Service (IAAS) with GlideinWMS as a potential alternative to fill the void. Similarly, communities with no previous access to computing resources can use GlideinWMS to setup up a batch system on the cloud infrastructure. To enable this, the architecture of GlideinWMS has been extended to enable support for interfacing GlideinWMS with different Scientific and commercial cloud providers like HLT, FutureGrid, FermiCloud and Amazon EC2. In this paper, we describe a solution for cloud bursting with GlideinWMS. The paper describes the approach, architectural changes and lessons learned while enabling support for cloud infrastructures in GlideinWMS.