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Distributed execution of aggregated multi domain workflows using an agent framework

Zhiming Zhao, Adam Belloum, Cees de Laat, Pieter Adriaans, Bob Hertzberger
2007 2007 IEEE Congress on Services (Services 2007)  
In this paper, we present our work in the context of Dutch Virtual Laboratory for e-Science (VL-e) project.  ...  In e-Science, meaningful experiment processes and workflow engines emerge as important scientific resources.  ...  Acknowledgment This work was carried out in the context of the Virtual Laboratory for e-Science project (www.vl-e.nl). Part of this  ... 
doi:10.1109/services.2007.30 dblp:conf/IEEEscc/ZhaoBLAH07 fatcat:t6de36zisfcb5csa6ccehokcoi

Provenance Support for Medical Research [chapter]

Richard McClatchey, Jetendr Shamdasani, Andrew Branson, Kamran Munir
2015 Lecture Notes in Computer Science  
This Analysis Base provides an integrated medical data analysis environment to exploit neuroscience workflows, large image datasets and algorithms for scientific analyses.  ...  The VL was developed for neuroscientists involved in Alzheimer's studies but has been designed to be reusable across other medical research communities.  ... 
doi:10.1007/978-3-319-16462-5_37 fatcat:4obwergob5a37kfmjyld5xin4u

Problem Solving Environment for Medical Image Analysis

Ketan C. Maheshwari, Silvia D. Olabarriaga, Charl P. Botha, Jeroen G. Snel, Johan Alkemade, Adam Belloum
2007 Computer-Based Medical Systems (CBMS), Proceedings of the IEEE Symposium on  
for e-Sciences Project.  ...  The development of Medical Image Analysis (MIA) applications that can successfully be applied in clinical practice is difficult for several reasons, one of them being the large amount and variety of resources  ...  This work was carried out in the context of the VL-e project, which is supported by a BSIK grant from the Dutch Ministry of Education, Culture and Science (OC&W) and is part of the ICT innovation program  ... 
doi:10.1109/cbms.2007.87 dblp:conf/cbms/MaheshwariOBSAB07 fatcat:tld527iyq5copbjplpdpveonky

A SOA and Knowledge-based Telemonitoring Framework: Design, Modeling, and Deployment

Weiping Zhang, Kerstin Thurow, Regina Stoll
2013 International Journal of Online Engineering (iJOE)  
Telemonitoring systems have proven to greatly reduce medical costs while improving the quality of medical care.  ...  b) User defined rules may also be added in the reasoning process, e.g.: ! (? patient, hasBloodPressureValue, vl ), GE(?vl, 170), ( ? patient, hasHeartRateValue, vl), LE(?vl, 40) -> ( ?  ...  This system integrates applications and devices like medical sensors, smart phones and data-store centers to provide health care services.  ... 
doi:10.3991/ijoe.v9i6.3312 fatcat:s4bf2znh4bahfgd2kaaz5pordm

10 Steps to Strategically Build and Implement your Enterprise Imaging System: HIMSS-SIIM Collaborative White Paper

Henri Primo, Matthew Bishop, Louis Lannum, Dawn Cram, Abe Nader, Roger Boodoo
2019 Journal of digital imaging  
The first step is to define and access all images used for medical decision-making.  ...  Then, it is recommended that one must understand the specialties and their clinical workflow challenges as related to imaging.  ...  Departments such as, but not limited to, dentistry, pathology, dermatology, wound care, GI endoscopy, surgery, and others use VL in their care workflow in addition to X-ray, MR, or US.  ... 
doi:10.1007/s10278-019-00236-w pmid:31177360 pmcid:PMC6646642 fatcat:ny7nnzhyqbe7blinhvfyhksabq

Initial steps towards a production platform for DNA sequence analysis on the grid

Angela CM Luyf, Barbera DC van Schaik, Michel de Vries, Frank Baas, Antoine HC van Kampen, Silvia D Olabarriaga
2010 BMC Bioinformatics  
Results: In this study we reused a platform that was developed in the VL-e project for the analysis of medical images.  ...  All workflows and executables are available for the members of the Dutch Life Science Grid and the VL-e Medical virtual organizations All components are open source and can be transported to other grid  ...  We also thank Martin Stam and Mark Santcroos for support in the e-BioInfra server; Piter de Boer, Kamel Boulebiar and Spiros Koulouzis for the design and implementation of the VBrowser and its plugins;  ... 
doi:10.1186/1471-2105-11-598 pmid:21156038 pmcid:PMC3018473 fatcat:oy5ex6bwlvfghhmwuyqj6ssqre

Providing traceability for neuroimaging analyses

Richard McClatchey, Andrew Branson, Ashiq Anjum, Peter Bloodsworth, Irfan Habib, Kamran Munir, Jetendr Shamdasani, Kamran Soomro
2013 International Journal of Medical Informatics  
crucial to medical researchers in the pursuance of their research goals.  ...  21st century medical research.  ...  Data or inputs supplied to each workflow task. c. Annotations added to the workflow and individual workflow task. d. Links and dependencies between workflow tasks. e.  ... 
doi:10.1016/j.ijmedinf.2013.05.005 pmid:23763909 fatcat:c3yyjdxqizgp7hlowa32zfthny

A Dynamic Nursing Workflow Management System: A Thailand Hospital Scenario [chapter]

Nantika Prinyapol, Sim Kim Lau, Joshua Poh-Onn Fan
2009 Lecture Notes in Electrical Engineering  
In this paper, we propose the use of dynamic compilation of web services to support workflow management.  ...  Web services related to work practices belong to an organisation will be designed, built and stored in a web services repository.  ...  The communication in the nursing care workflow generally uses paper-based media: doctor passes orders to in-charge nurse, in-charge nurse organizes tasks for each medical nurse, medical nurses obtain drugs  ... 
doi:10.1007/978-90-481-3517-2_37 fatcat:wse6r7y6ufcydmpuivc4scudj4

Simulating Core Floods in Heterogeneous Sandstone and Carbonate Rocks

Nele Wenck, Samuel J. Jackson, Sojwal Manoorkar, Ann Muggeridge, Samuel Krevor
2021 Water Resources Research  
For example, at many 2 CO E storage sites worldwide, carbon dioxide injected underground has migrated away from injection points at much faster rates than had been predicted with reservoir simulations  ...  Details on the c E Ncalculation and the tabulated data are presented in Sections S2 and S9, respectively. VL stands for the viscous-limit relative permeability.  ...  Steady-state experiments were performed with the co-injection of nitrogen and DI water or 2 CO E and brine at high (HR) and low (LR) flow rates to obtain flow parameters in the viscous-limit (VL) and capillary-limit  ... 
doi:10.1029/2021wr030581 fatcat:lclmcgnd3fcn5bbctrobpf6dsa

Gridifying a Diffusion Tensor Imaging Analysis Pipeline

Matthan W.A. Caan, Frans M. Vos, Antoine H.C. van Kampen, Silvia D. Olabarriaga, Lucas J. van Vliet
2010 2010 10th IEEE/ACM International Conference on Cluster, Cloud and Grid Computing  
Diffusion Tensor MRI (DTI) is a rather recent image acquisition modality that can help identify disease processes in nerve bundles in the brain.  ...  Starting with simple jobs submitted from the command-line, we moved towards a workflow-based implementation and finally into a web service that can be accessed via web browsers by end-users.  ...  MOTEUR workflows on the Dutch Grid Later (2008) we ported the coregistration step to the grid using the Virtual Lab for Medical Images [17] developed in the VL-e project.  ... 
doi:10.1109/ccgrid.2010.99 dblp:conf/ccgrid/CaanVKOV10 fatcat:z7nsg7r7fbfonnzmjkccsewoj4

From Forensics to Clinical Research: Expanding the Variant Calling Pipeline for the Precision ID mtDNA Whole Genome Panel

Filipe Cortes-Figueiredo, Filipa S. Carvalho, Ana Catarina Fonseca, Friedemann Paul, José M. Ferro, Sebastian Schönherr, Hansi Weissensteiner, Vanessa A. Morais
2021 International Journal of Molecular Sciences  
Despite a multitude of methods for the sample preparation, sequencing, and data analysis of mitochondrial DNA (mtDNA), the demand for innovation remains, particularly in comparison with nuclear DNA (nDNA  ...  However, its bioinformatic processing occurs in the enterprise Ion Torrent Suite™ Software (TSS), yielding BAM files aligned to an unorthodox version of the revised Cambridge Reference Sequence (rCRS),  ...  Secondly, it outputs a BAM file with the correct rCRS reference, thus allowing for integration into other NGS workflows and greatly facilitating variant annotation.  ... 
doi:10.3390/ijms222112031 pmid:34769461 pmcid:PMC8584537 fatcat:kob5dydy4fburceqf36su4b7jq

Redefining Prevention and Care: A Status-Neutral Approach to HIV

Julie E Myers, Sarah L Braunstein, Qiang Xia, Kathleen Scanlin, Zoe Edelstein, Graham Harriman, Benjamin Tsoi, Adriana Andaluz, Estella Yu, Demetre Daskalakis
2018 Open Forum Infectious Diseases  
Recent biomedical advances inspire hope that an end to the epidemic of HIV is in sight.  ...  Adopting new approaches and paradigms for treatment and prevention in terms of both messaging and programming is a priority to accelerate progress.  ...  Acknowledgments The authors wish to thank Paul Salcuni and Anisha Gandhi for assistance with the estimate of cisgender MSM in NYC and Davida Farhat for assistance with preparation of the manuscript.  ... 
doi:10.1093/ofid/ofy097 pmid:29977957 pmcid:PMC6016418 fatcat:fynegml2tjhlbdnjdcmawhc6vy

Exploring Barriers and Facilitators to the Use of Computerized Clinical Reminders

Jason J. Saleem, Emily S. Patterson, Laura Militello, Marta L. Render, Greg Orshansky, Steven M. Asch
2005 JAMIA Journal of the American Medical Informatics Association  
Facilitators included (1) limiting the number of reminders at a site; (2) strategic location of the computer workstations; (3) integration of reminders into workflow; and (4) the ability to document system  ...  (VA) medical centers.  ...  41 8 11 65 vl.0.22.16 2 48 11 15 37 vl.0.22.16 3 37 9 15 33 vl.0.23.15 4 36 7 14 30 vl.0.23.15 CRs = Clinical reminders; CPRS = Computerized Patient Record System.  ... 
doi:10.1197/jamia.m1777 pmid:15802482 pmcid:PMC1174889 fatcat:tsozsf4j2bfvlimc42sw2gawsi

Distributed Cognition and Process Management Enabling Individualized Translational Research: The NIH Undiagnosed Diseases Program Experience

Amanda E. Links, David Draper, Elizabeth Lee, Jessica Guzman, Zaheer Valivullah, Valerie Maduro, Vlad Lebedev, Maxim Didenko, Garrick Tomlin, Michael Brudno, Marta Girdea, Sergiu Dumitriu (+12 others)
2016 Frontiers in Medicine  
The team, therefore, built the NIH UDP integrated collaboration system (UDPICS) to form virtual collaborative multidisciplinary research networks or communities.  ...  UDPICS supports these communities through integrated process management, ontology-based phenotyping, biospecimen management, cloud-based genomic analysis, and an electronic laboratory notebook.  ...  FUnDIng This work was supported in part by the Common Fund, Office of the Director and the Intramural Research Program of the National Human Genome Research Institute (Z01-HG000215-07,  ... 
doi:10.3389/fmed.2016.00039 pmid:27785453 pmcid:PMC5060938 fatcat:wfom55rpzzhohelp5l2w6yhtte

Integrating the Xpert MTB/RIF Assay into a Diagnostic Workflow for Rapid Detection of Mycobacterium tuberculosis in a Low-Prevalence Area

V. Deggim, A. Somoskovi, A. Voit, E. C. Bottger, G. V. Bloemberg
2013 Journal of Clinical Microbiology  
The Institute of Medical Microbiology (University of Zurich) is a tertiary care diagnostic center that receives clinical specimens 7 days/week for AFB microscopy to urgently confirm or rule out TB in newly  ...  e Phenotypic drug susceptibility testing for rifampin using the critical concentration of 1 g/ml.  ...  ACKNOWLEDGMENTS This work was supported in part by the University of Zurich and the BAG (Federal Office of Public Health, Switzerland). We have no conflicts of interest to disclose.  ... 
doi:10.1128/jcm.00151-13 pmid:23616455 pmcid:PMC3697699 fatcat:nio4acfp7za73ogkeh5sb2mf44
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