EGEE (EU IST-2003-508833 project) – Networking Activities 4: biomedical applications

NA4 Biomedical Activities

Johan Montagnat

First EGEE MeetingCork, April 19th, 2004

NA4 Biomedical Applications, First EGEE meeting, Cork , April 18th, 2004 - 2

NA4 Biomedical Activities

• Working group area• Medical image processing – J. Montagnat (CREATIS, CNRS-Inserm)

• Bioinformatics – C. Blanchet (IBCP, CNRS)

• Objectives: demonstrate the interest of grids for real scale biomedical applications• Ensure that EGEE meets the needs of the biomedical domain

• Identify an applications portofolio

• Early deployment of some applications, provide early feedback to middleware and operations

• Migrate new applications to the EGEE infrastructure

• Define a common application interface

• Make the community aware of grid technologies and the need for deploying resources

• Establish contact with clinicians (dissemination and end users assesment)

NA4 Biomedical Applications, First EGEE meeting, Cork , April 18th, 2004 - 3

Internal/external communication

• Web site• http://www.eu-egee.org/

-> NA4 -> biomedical

• Webmaster: Y. Legré

• Mailing list• project-eu-egee-na4-biomed-applications@cern.ch

• Administrators: V. Breton, J. Montagnat

• Meetings• NA4 global meetings during conferences

• Biomedical meetings every 2 months: next one in Lyon on the 8th of June

• Monthly phone/videoconferencing if needed

NA4 Biomedical Applications, First EGEE meeting, Cork , April 18th, 2004 - 4

Participation to the Application Working Group

• Representatives• J. Montagnat (CNRS) and I. Blanquer (UPV)

• Role• Homogeneisation of NA4 subgroups (requirements, interface...)

• To take part to NA4 deliverables writting

• To work on first deliverables and milestones immediatly

• Work plan• Weekly phone conference (wednesday or thursday afternoon)

NA4 Biomedical Applications, First EGEE meeting, Cork , April 18th, 2004 - 5

Biomedical Technical Team

• Members• Biomedical FTEs: Y. Legré (LPC), A. Merino (CNB), TBC (CREATIS), TBC

(IBCP), TBC (UPV)

• Unfunded project members: J. Montagnat (CREATIS), L. Maigne (LPC), I. Blanquer (UPV), others TBC

• Objectives• Equivalent of ARDA (HEP) for biomedical applications

• Connected team of technical people

• Intermediate between applications and middleware developpers

• To face the lack of iteam in EGEE

• Roadmap• Task1: Open a mailing list and any suitable communication means (chat...)

• Task2: Define VOs, get access to LCG2 middleware and make application testing, provide feedback

• Task3: Install middleware, test and provide feedback again

NA4 Biomedical Applications, First EGEE meeting, Cork , April 18th, 2004 - 6

Deliverables and milestones

• Deliverables: reports• DNA4.1 M3 Definition of common application interface and planning

• DNA4.2 M6 Applications deployment strategy

• DNA4.3 M9 application migration process, revised at M15 and M21

• DNA4.4 M24 Final report of applications identification and support activity

• Milestones• MNA4.1 M1 Definition of requirements from applications and first

version of associated testsuite -> reference documents collection on the web site (AWG, WP10 deliverables, mammogrid requirements...)

• MNA4.2 M6 First applications migrated to the EGEE infrastructure

• MNA4.3 M12 First external review of applications identification and support with feedback

• MNA4.4 M24 Second external review

NA4 Biomedical Applications, First EGEE meeting, Cork , April 18th, 2004 - 7

Applications to deploy

• Three types of application• Pilots: 2-3 applications starting at day 0, used to evaluate testbed and return

early feedback

• Internal: from project partners, to be deployed on EGEE

• External: from other projects, to go through a selection procedure

• External applications evaluation procedure• Acceptation left to NA4 management and PEB

• Selection criteria• Application scientific interest

• Grid-added value for the application and added value for EGEE to support this application

• Resources (human and computational) provided

• Grid awarness of the community and coordination role of the application

NA4 Biomedical Applications, First EGEE meeting, Cork , April 18th, 2004 - 8

Day 0 pilot applications

• GATE (LPC)• Radiotherapy planning

• Experimented on INFN LCG2 middleware

• GPS@ (IBCP)• Bioinformatics portal

• Experimented on DataGrid middleware

• To be tested on LCG2

• CDSS (UPV)• Clinical decision support system

• Experimented on inner grid (gridsystems)

• To be ported on LCG2 within one month

NA4 Biomedical Applications, First EGEE meeting, Cork , April 18th, 2004 - 9

Questions

• To SA1: Access to EGEE testbed• Need an immediate access to LCG2 middleware

• How to set up biomedical VOs and how to get access to LCG2 resources for testing?

• How to get access to EGEE middleware once available?

• To JRA1: Middleware – biomedical applications interaction• NA4 to provide requirements and feedback to middleware developpers...

• ...but deliverables are not an efficient communication mean!

• How to replace DataGrid ITeam/ATF

• To JRA3: Security requirements integration

NA4 Biomedical Applications, First EGEE meeting, Cork , April 18th, 2004 - 10

Conclusions

• Biomedical applications working group main objective• demonstrate the interest of grids for real scale biomedical applications

• Work on first deliverable to start immediatly

• 3 Pilot applications identified• GATE, GPS@, CDSS

• First interaction with external applications

• Executive structure set up• Application Working Group representatives nominated

• Technical Working Group initiated

• Next meeting in Lyon, June 8th

• Ready to go: where can we start testing?