Biomedical Informatics Research NetworkBiomedical Informatics Research Network
BIRNBIRNWorkflow PortalWorkflow Portal
Biomedical Informatics Research NetworkBiomedical Informatics Research Network
GoalsGoals
• Allow mBIRN software to be consumed by both inside and outside groups on a consistent computing platform
• Able to integrate various different pipeline applications (LONI, Kepler, jBPM) into an analysis
• Infinite undo/redo from various points in an analysis; able to recalculate and compare results
• Possible to distribute computing to various sites by promoting web services
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Vision presented Oct 2005 Vision presented Oct 2005
Ontology
Consent
Discovery
Data flowing
Custom Interfaces A program
Workflow DB
Security
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Creation of Workflow PortalCreation of Workflow PortalStarted October 2005Started October 2005
• Allows processing of standard workflows through main BIRN portal.
• Stabilizes many aspects of the environment used in a calculation.
• Allows publication of proprietary algorithms.• Requires de-identification during a calculation.• Results flow into standard database model for
retrieval.
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ArchitectureArchitecture
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BIRN InfrastructureBIRN Infrastructure
Authentication Services (GAMA) Data Grid (SRB)
BIRN-CC Development Environment
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SRB(File Repository)
SRB Client BIRN Portalor
upload download
Web Server
RequestForm
Kepler
LONI
WF
driver (client)
jBPM
WF
driver (server)
Status ofRequest
Check onStatus
and Continue
GAMA authentication server
Tomcat Server
GridSphere
WF portlet
Interfa
ce
SRB Client
Interfa
ce
DB
Resting
FinalReport
start task status
Biomedical Informatics Research NetworkBiomedical Informatics Research Network
SRB(File Repository)
SRB Client BIRN Portalor
upload download
Web ServerKepler
LONI
WF
driver (client)
jBPM
WF
driver (server)
GAMA authentication server
Tomcat Server
GridSphere
WF portlet
Interfa
ce
SRB Client
Interfa
ce
DB
Initialize
RequestForm
Status ofRequest
Check onStatus
and Continue
FinalReport
start task status
Biomedical Informatics Research NetworkBiomedical Informatics Research Network
RequestForm
Status ofRequest
Check onStatus
and Continue
FinalReport
SRB(File Repository)
SRB Client BIRN Portalor
upload download
Web ServerKepler
LONI
WF
driver (client)
jBPM
WF
driver (server)
GAMA authentication server
Tomcat Server
GridSphere
WF portlet
Interfa
ce
SRB Client
Interfa
ce
DB
Starting
start task status
Biomedical Informatics Research NetworkBiomedical Informatics Research Network
SRB(File Repository)
SRB Client BIRN Portalor
upload download
Web ServerKepler
LONI
WF
driver (client)
jBPM
WF
driver (server)
GAMA authentication server
Tomcat Server
GridSphere
WF portlet
Interfa
ce
SRB Client
Interfa
ce
DB
Running
RequestForm
Status ofRequest
Check onStatus
and Continue
FinalReport
start task status
Biomedical Informatics Research NetworkBiomedical Informatics Research Network
SRB(File Repository)
SRB Client BIRN Portalor
upload download
Web ServerKepler
LONI
WF
driver (client)
jBPM
WF
driver (server)
GAMA authentication server
Tomcat Server
GridSphere
WF portlet
Interfa
ce
SRB Client
Interfa
ce
DB
Checking
RequestForm
Status ofRequest
Check onStatus
and Continue
FinalReport
start task status
Biomedical Informatics Research NetworkBiomedical Informatics Research Network
SRB(File Repository)
SRB Client BIRN Portalor
upload download
Web ServerKepler
LONI
WF
driver (client)
jBPM
WF
driver (server)
GAMA authentication server
Tomcat Server
GridSphere
WF portlet
Interfa
ce
SRB Client
Interfa
ce
DB
Finished
RequestForm
Status ofRequest
Check onStatus
and Continue
FinalReport
start task status
Biomedical Informatics Research NetworkBiomedical Informatics Research Network
Workbench DevelopementWorkbench Developement
• Web portal unable to accommodate:– Robust up/downloading of images with de-
identification– Deployment of workflows to jBPM– Cooperative development– Robust displays of study results and
calculations
Biomedical Informatics Research NetworkBiomedical Informatics Research Network
SRB(File Repository)
SRB Client
BIRN Portalor
upload download
Web Server Kepler
LONI
WF
driver (client)
jBPM
WF
driver (server)
GAMA
Tomcat Server
GridSphere
WF portlet
Interfa
ce
SRB Client
Interfa
ce
DB
RequestForm
Status ofRequest
Check onStatus
FinalReport
start task status
BIRN Workflow Workbench
Allows direct creation of jBPM workflowsDisplays and control workflow progressAllow robust uploading to SRBScalable to include results analysis with NCBC softwareEclipse plug-ins
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Future GoalsFuture Goals
Needed for March mBIRN AHMNeeded for March mBIRN AHM
Biomedical Informatics Research NetworkBiomedical Informatics Research Network
Complete the “productionizing” of Complete the “productionizing” of the Portal workflow applicationthe Portal workflow application
• Improve flow with the SRB – flow to the SRB both through the portal and through Jargon API.
• Improve functioning with GAMA authentication• File management enhancements – a client plug-in in the Workbench
that allows FTP-like interactions with the SRB with a robust file management UI
• Improve error handling and reporting – harden internal operation of workflow software.
• Incorporate view in Workbench for start, parameter entry, and status views to provide complete workbench solution
• Complete the support for Data Provenance with latest data provenance specifications.
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Workbench will be completed as Workbench will be completed as Eclipse plug-insEclipse plug-ins
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Store and show results from Store and show results from workflow processesworkflow processes
• Finalize and provide documentation on method XML wrapper uses to expose database updates
• Finalize and provide manual for creating workflow ontologies
• Finalize and provide documentation on how to store results in the workflows database
• Render the results for a limited set of results• Visualize results and download to BIRN
infrastructure• Show results by research subject
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Future GoalsFuture Goals
To come after others achievedTo come after others achieved
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Next 2 years if March Goals Next 2 years if March Goals AchievedAchieved
• Streamline and possibly redefine BIRND-UP functionality so that images can be de-identified without user interaction
• Formalize web services so they can be evoked from the infrastructure of XNAT and HID
• Release workflow for gradient distortion correction algorithm that requires proprietary spherical harmonic information
• Work towards complete support of ADNI calculations ???
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BIRNBIRNWorkflow PortalWorkflow Portal
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