BIRN Vision for Data Pipeline
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Biomedical Informatics Research Biomedical Informatics Research Network Network BIRN BIRN Vision for Data Vision for Data Pipeline Pipeline Bruce Rosen Bruce Rosen Shawn Murphy Shawn Murphy
description
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 - PowerPoint PPT Presentation
Transcript of BIRN Vision for Data Pipeline
Biomedical Informatics Research NetworkBiomedical Informatics Research Network
BIRNBIRNVision for Data PipelineVision for Data Pipeline
Bruce RosenBruce Rosen
Shawn MurphyShawn Murphy
Biomedical Informatics Research NetworkBiomedical Informatics Research Network
Data Pipeline Management GoalsData 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 NetworkBiomedical Informatics Research Network
Without Pipeline Management Without Pipeline Management
Data flowing
Synopsis at BIRN AHM 2005Toga et. al. – LONI ongoing success storyMurphy et. al. – Kepler image registration algorithmKolasny – Kepler statistics packageOzyurt et. at. – jBPMGerig - Imagine
Biomedical Informatics Research NetworkBiomedical Informatics Research Network
Database of XML Workflows Database of XML Workflows
Data flowing
Custom Interfaces A program
Workflow DB
Organized by:human subject – protocol - investigator
LONI Pipeline XMLKepler MoMLTaverna XScufl
Universal ability in BIRN to visualize previous experiments and analyses
Supported by Murphy et. al. workflow analysis paper
Biomedical Informatics Research NetworkBiomedical Informatics Research Network
Able to send XML Workflow back Able to send XML Workflow back to Applicationto Application
Ontology
Consent
Discovery
Data flowing
Custom Interfaces A program
Workflow DB
Security
Focused manipulation of Workflow XML in a template
HEADER
ACTORS
LINKS
Able to integrate various different pipeline applications (LONI, Kepler, Taverna) into an analysis
Biomedical Informatics Research NetworkBiomedical Informatics Research Network
Able to Inspect Intermediate Able to Inspect Intermediate Results and Redirect Sequences Results and Redirect Sequences
Ontology
Consent
Discovery
Data flowing
Custom Interfaces A program
Workflow DB
Security
Infinite undo/redo from various points in an analysis
Biomedical Informatics Research NetworkBiomedical Informatics Research Network
Focus on Promoting Web servicesFocus on Promoting Web services
Ontology
Consent
Discovery
Services:
Data flowing
Custom Interfaces
Soap/Http interfaces
A program
Workflow DB
Security
Possible to distribute computing to various sites
Biomedical Informatics Research NetworkBiomedical Informatics Research Network
Scalable to Other Domains Scalable to Other Domains
Services:
Data flowing
Custom Interfaces
Soap/Http interfaces
A program
HL7 MSH|^/&|736401….. PID|102|3231285.….
Text filesText files
XML <Patient1> <image>.….
database
clinicaltrials
Gene expression in APOE 4 Allele
Alzheimer's
Seizures
ER visits
Clinic visits
Outcomes calculated every week
Trauma
Surgery
Multiple sclerosis
Gene expression in APOE 4 Allele
Alzheimer's
Seizures
ER visits
Clinic visits
Outcomes calculated every week
Trauma
Surgery
Multiple sclerosis
Gene expression in APOE 4 Allele
Alzheimer's
Seizures
ER visits
Clinic visits
Outcomes calculated every week
Trauma
Surgery
Multiple sclerosis
Ontology
Consent
DiscoveryWorkflow DB
Security
Biomedical Informatics Research NetworkBiomedical Informatics Research Network
BIRNBIRNVision for Data PipelineVision for Data Pipeline
Bruce RosenBruce Rosen
Shawn MurphyShawn Murphy
Biomedical Informatics Research NetworkBiomedical Informatics Research Network
Full Pipeline Management VisionFull Pipeline Management Vision
• Utilize Pipeline Management to meta-coordinate web services
ProgID CA2.3
SN8745
PA5683
SN8745
SN8745
SNOMED CODE
patient id 0000004
account # 347
subject id 4
subject id 4
ProgID CX2.3
ProgID PN5.1 ProgID TH3.0
ProgID SN5.4
ProgID AA3.3
ProgID CN2.3 ProgID XN0.9
Gene expression in APOE 4 Allele
Alzheimer's
Seizures
ER visits
Clinic visits
Outcomes calculated every week
Trauma
Surgery
Multiple sclerosis
Gene expression in APOE 4 Allele
Alzheimer's
Seizures
ER visits
Clinic visits
Outcomes calculated every week
Trauma
Surgery
Multiple sclerosis
OntologyConsent
Discovery Workflow DBSecurity
Biomedical Informatics Research NetworkBiomedical Informatics Research Network
Overall Implementation PrinciplesOverall 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
