biomedical informatics research network birn workflow portal

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

Biomedical Informatics Research NetworkBiomedical Informatics Research Network

Vision presented Oct 2005 Vision presented Oct 2005

Ontology

Consent

Discovery

Data flowing

Custom Interfaces A program

Workflow DB

Security

Biomedical Informatics Research NetworkBiomedical Informatics Research Network

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.

Biomedical Informatics Research NetworkBiomedical Informatics Research Network

Biomedical Informatics Research NetworkBiomedical Informatics Research Network

Biomedical Informatics Research NetworkBiomedical Informatics Research Network

Biomedical Informatics Research NetworkBiomedical Informatics Research Network

Biomedical Informatics Research NetworkBiomedical Informatics Research Network

Biomedical Informatics Research NetworkBiomedical Informatics Research Network

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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Biomedical Informatics Research NetworkBiomedical Informatics Research Network

Biomedical Informatics Research NetworkBiomedical Informatics Research Network

Biomedical Informatics Research NetworkBiomedical Informatics Research Network

Biomedical Informatics Research NetworkBiomedical Informatics Research Network

Biomedical Informatics Research NetworkBiomedical Informatics Research Network

Biomedical Informatics Research NetworkBiomedical Informatics Research Network

Future GoalsFuture Goals

Needed for March mBIRN AHMNeeded for March mBIRN AHM

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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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