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BIRN Vision for Data Pipeline

BIRN Vision for Data Pipeline. Bruce Rosen Shawn Murphy. Data Pipeline Management Goals. Universal ability in BIRN to visualize previous experiments and analyses Able to integrate various different pipeline applications (LONI, Kepler, Taverna) into an analysis

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BIRN Vision for Data Pipeline

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  1. BIRNVision for Data Pipeline Bruce Rosen Shawn Murphy Biomedical Informatics Research Network

  2. Data Pipeline Management Goals • Universal ability in BIRN to visualize previous experiments and analyses • Able to integrate various different pipeline applications (LONI, Kepler, Taverna) into an analysis • Infinite undo/redo from various points in an analysis • Possible to distribute computing to various sites Biomedical Informatics Research Network

  3. Without Pipeline Management Data flowing Synopsis at BIRN AHM 2005 Toga et. al. – LONI ongoing success story Murphy et. al. – Kepler image registration algorithm Kolasny – Kepler statistics package Ozyurt et. at. – jBPM Gerig - Imagine Biomedical Informatics Research Network

  4. Database of XML Workflows Supported by Murphy et. al. workflow analysis paper LONI Pipeline XML Kepler MoML Taverna XScufl Data flowing A program Custom Interfaces Universal ability in BIRN to visualize previous experiments and analyses Workflow DB Organized by: human subject – protocol - investigator Biomedical Informatics Research Network

  5. Able to send XML Workflow back to Application Able to integrate various different pipeline applications (LONI, Kepler, Taverna) into an analysis Data flowing A program Custom Interfaces Ontology Workflow DB Consent Discovery Security Focused manipulation of Workflow XML in a template Biomedical Informatics Research Network

  6. Able to Inspect Intermediate Results and Redirect Sequences Infinite undo/redo from various points in an analysis Data flowing A program Custom Interfaces Ontology Workflow DB Consent Discovery Security Biomedical Informatics Research Network

  7. Focus on Promoting Web services Possible to distribute computing to various sites Services: Soap/Http interfaces Data flowing A program Custom Interfaces Ontology Workflow DB Consent Discovery Security Biomedical Informatics Research Network

  8. clinical trials Scalable to Other Domains Services: HL7 MSH|^/&|736401….. PID|102|3231285.…. Soap/Http interfaces Data flowing Text files A program Custom Interfaces XML <Patient1> <image>.…. database Ontology Workflow DB Consent Discovery Security Biomedical Informatics Research Network

  9. BIRNVision for Data Pipeline Bruce Rosen Shawn Murphy Biomedical Informatics Research Network

  10. SNOMED CODE SN8745 PA5683 SN8745 SN8745 Ontology Workflow DB Consent Discovery Security Full Pipeline Management Vision • Utilize Pipeline Management to meta-coordinate web services patient id 0000004 ProgID AA3.3 subject id 4 ProgID CA2.3 ProgID CN2.3 ProgID XN0.9 subject id 4 ProgID SN5.4 ProgID CX2.3 account # 347 ProgID PN5.1 ProgID TH3.0 Biomedical Informatics Research Network

  11. Overall Implementation Principles • Framework focuses upon allowing application development work to take place in a maximally decoupled fashion. • Supporting Linux and Microsoft Windows • Open source architecture Biomedical Informatics Research Network

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