Transcript Murphy_workflow_AHM

BIRN
Workflow Portal
Shawn Murphy
Michael Mendis
Biomedical Informatics Research Network
Goals
• 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, FIPS, 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
Biomedical Informatics Research Network
BIRN Infrastructure
BIRN-CC Development Environment
Authentication Services (GAMA)
Data Grid (SRB)
Biomedical Informatics Research Network
Final hardening of the Portal
workflow application
• Provide complete workflow management solution in the Workbench
– Improve functioning with GAMA authentication server
– Improve flow with the SRB through client plug-in in the Workbench that
allows interactions with the SRB with a robust file management UI
– Incorporate view in Workbench for start, parameter entry, and status
views to provide complete workbench solution
– Package all pieces as Eclipse plug-ins
• Improve error handling and reporting within internal operation of
workflow software.
• Make ROCKs build
• Complete the support for data provenance as currently specified
• Add ontology of workflows to BIRNLex
• Finalize and provide documentation for:
– creating the application wrapper
– creating additions to the workflow ontology
– storing results in the workflows database
Biomedical Informatics Research Network
• Release workflow for gradient distortion
correction algorithm that requires
proprietary spherical harmonic information
• Assure that LONI pipelines can be run
through the workflow portal
Biomedical Informatics Research Network
BIRN Workflow Workbench
Allows direct creation of jBPM workflows
Displays and control workflow progress
Allow robust uploading to SRB
Scalable to include results analysis with NCBC software
Eclipse plug-ins
SRB Client
GAMA
SRB Client
jBPM
Interface Interface
GridSphere
WF portlet
WF driver (server)
Tomcat Server
WF driver (client)
Web Server
SRB
(File Repository)
FIPS
LONI
DB
upload
download
or BIRN Portal
Request Status of Check on
Form
Request
Status
start
Biomedical Informatics Research Network
task status
Final
Report
Biomedical Informatics Research Network
Biomedical Informatics Research Network
Integration with Upload Goals
• Upload of image files (only) to SRB built
into current BIRN Workflow manager.
• Server-sided clinical data management
may be modeled after NIH NCBC project.
Biomedical Informatics Research Network
Biomedical Informatics Research Network
Biomedical Informatics Research Network
Biomedical Informatics Research Network
Biomedical Informatics Research Network
Biomedical Informatics Research Network
Biomedical Informatics Research Network
Biomedical Informatics Research Network
BIRN
Workflow Portal
Biomedical Informatics Research Network
Biomedical Informatics Research Network