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NA4 Biomedical Applications Christophe Blanchet NA4 Biomed deputy CNRS IBCP, Lyon, France

NA4 Biomedical Applications Christophe Blanchet NA4 Biomed deputy CNRS IBCP, Lyon, France. EGEE-Fr 1st meeting, june 11 2004. www.eu-egee.org. EGEE is a project funded by the European Union under contract IST-2003-508833. Contents. NA4 Biomed Activity NA4 Biomed structure

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NA4 Biomedical Applications Christophe Blanchet NA4 Biomed deputy CNRS IBCP, Lyon, France

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  1. NA4 Biomedical ApplicationsChristophe BlanchetNA4 Biomed deputyCNRS IBCP, Lyon, France EGEE-Fr 1st meeting, june 11 2004 www.eu-egee.org EGEE is a project funded by the European Union under contract IST-2003-508833

  2. Contents • NA4 Biomed Activity • NA4 Biomed structure • Participation to project boards: • AWG, MWSG, PTF, … • Tasks and milestones • Applications NA4 Biomedical Applications, EGEE-Fr 1rst meeting, June 11 2004 - 2

  3. NA4 manager: V. Breton NA4 covers 3 application domains High Energy Physics (CERN – F. Harris) Biomedical applications (CNRS – J. Montagnat) Generic applications (INFN – R. Barbera) NA4 Structure Management group, monthly meetings Application Working Group (cross-domains) 12 FTE allocated (4 per application domain): Relationship to other work packages JRA1: middleware (requirements and testing) JRA2: quality (evaluation criteria) JRA3: security (requirements) SA1: testbed operation (VO, deployment agenda, resources) NA3: training (customer) NA4 - Applicationsidentification and support NA4 Biomedical Applications, EGEE-Fr 1rst meeting, June 11 2004 - 3

  4. Working group area Medical image processing – J. Montagnat Bioinformatics – C. Blanchet Objectives Identify an applications portfolio Early deployment of some applications Provide early feedback to middleware and operations Define a common application interface Migrate new applications to the EGEE infrastructure Ensure EGEE meets the needs of the biomedical domain Roadmap 4 deliverables (PM3, PM6, PM9-PM15-PM21, PM24) 4 milestones 8 tasks 4 FTEs 2 FTEs in France: LPC (Clermont-Ferrand), CREATIS (Lyon), IBCP (Lyon) 2 FTEs in Spain: UPV (Valencia), CNB/CSIC (Madrid) NA4 Biomedical Activities NA4 Biomedical Applications, EGEE-Fr 1rst meeting, June 11 2004 - 4

  5. NA4 Biomedical network • Web site • http://www.eu-egee.org/ • -> NA4 -> biomedical • hosted in INFN, http://egee-na4.ct.infn.it/biomed/index.php • Mailing list • project-eu-egee-na4-biomed-applications@cern.ch • Administrators: J. Montagnat • Meetings • NA4 global meetings during EGEE conferences • NA4biomed-1, April 2004, Cork • Meetings every 2 months: • NA4biomed-2, 8th June 2004, Lyon. • Next one: NA4biomed-3 in Madrid on the 2nd week of October. • Monthly phone/videoconferencing if needed. NA4 Biomedical Applications, EGEE-Fr 1rst meeting, June 11 2004 - 5

  6. Members FTEs: Y. Legré (LPC), A. Merino (CNB), TBC (CREATIS), TBC (IBCP), TBC (UPV) Unfunded project members: L. Maigne (LPC), I. Blanquer (UPV), F. Bellet (CREATIS), P. Calvat (CC-IN2P3) Test team: R. Metery, E. Fede Objectives Connected team of technical people Intermediate between applications and middleware developpers Equivalent of ARDA (HEP) for biomedical applications Roadmap Instantiated today! Volunteers?... To Complete the team as soon as people are hired Task1: Open a mailing list and any suitable communication means (chat...) Task2: Define VOs and negociate with LCG an access to the testbed Task3: Install, test & provide feedback on LCG2 middleware NA4 biomed meetings Biomedical Technical Team NA4 Biomedical Applications, EGEE-Fr 1rst meeting, June 11 2004 - 6

  7. Biomed Participations to EGEE groups • Applications • AWG: phone conference and meetings • NA4 open meeting (15-16 june 2004, Catania) • Security: meeting MWSG (16-17 june 2004, CERN) • Middleware: JRA1-NA4 meeting (15 june 2004, CERN) • Project Technical Forum: PTF • Quality insurance: JRA2 phone conference NA4 Biomedical Applications, EGEE-Fr 1rst meeting, June 11 2004 - 7

  8. AWG Application Working Group • Representatives • 2 persons per application domain • J. Montagnat and I. Blanquer for Biomed • Role • Homogenisation of NA4 subgroups (requirements, interface...) • To take part to NA4 deliverables writting • To work on first deliverables and milestones immediatly • Work plan • Weekly phone conferences NA4 Biomedical Applications, EGEE-Fr 1rst meeting, June 11 2004 - 8

  9. MWSG MiddleWare Security Group • Representative for NA4biomed • C. Blanchet • Role of MWSG • To ensure all requirements from NA4, SA1 and JRA1 are handled (received-prioritized-handled-followed up) in an efficient way, ensuring that the optimal priorities are set and followed. • To communicate the prioritized list to JRA3 for action.` • Participation NA4biomed to MWSG • To collect NA4 Biomedical requirements from applications • To provide and explain NA4 Biomedical requirements • Work plan • Monthly workshop • MWSG-1, 5-6 may 2004, CERN (C Blanchet) • MWSG-2, 16-17 may 2004, CERN (C Blanchet, J Montagnat) NA4 Biomedical Applications, EGEE-Fr 1rst meeting, June 11 2004 - 9

  10. Deliverables and milestones • Deliverables: reports • DNA4.1 M3 Definition of common application interface and planning • DNA4.2 M6 Target application sector strategy -> 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 (https://edms.cern.ch/file/474424/4) • 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, EGEE-Fr 1rst meeting, June 11 2004 - 10

  11. First year tasks • Task NA4.1 Initial definition of requirements (PM0-1) (https://edms.cern.ch/file/474424/4) • Task NA4.2 Basic foundation of common application interface and associated roadmap (PM0-3: DNA4.1) • Task NA4.3 Definition of the strategy for application integration and deployment (PM0-6: DNA4.2) • Task NA4.4 Migration of the first pilot applications to the EGEE infrastructure (PM0-12: MNA4.2) • Task NA4.5 Deployment of first generic applications (PM0-12: DNA4.3) • Task NA4.6 Management of NA4 (PM1-12) • Task NA4.7 Testsuite (PM0-12) • Task NA4.8 Industry forum (PM0-12) NA4 Biomedical Applications, EGEE-Fr 1rst meeting, June 11 2004 - 11

  12. Application selection • Three types of application • Pilots: 2-3 applications (day 0), GATE-GPSA-CDSS, evaluate testbed and early feedback • Internal: from project partners, to be deployed on EGEE • External: from other projects, to go through a selection procedure • External applications selection • decision left to NA4 management and EGEE PEB • Candidates are expected to follow EGEE training and to agree with EGEE policy • 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 awareness of the community and coordination role of the application NA4 Biomedical Applications, EGEE-Fr 1rst meeting, June 11 2004 - 12

  13. NA4 first deliverable • Definition of common application interface and planning • Application requirements • Interface definition • Planning • Agenda • To be written at PM3 • List of participants • Review and comment on AWG document, study other relevant documents • Work on interface expectation • Synchronisation with other NA4 application groups • Document assembling for PEB • ... NA4 Biomedical Applications, EGEE-Fr 1rst meeting, June 11 2004 - 13

  14. Biomedical Participation to Infrastructure • VO biomed: • Deployed at ROC Fr by the CC IN2P3 • and at CNAF • First members registered • Biomedical tests of deployment of LCG-2 • CNRS Creatis: install of CE-SE-UI on 2 CPU (10 CPU) • CNRS IBCP: install of UI, CE-SE to be done (~10 CPU) • CNRS LPC: install of CE SE UI (150 CPU) • CNRS LAL: 40 CPU will be certified during june 2004 • UPV: Install of CE SE UI RB MDS DBII; 30-40 CPU • CNB: nac NA4 Biomedical Applications, EGEE-Fr 1rst meeting, June 11 2004 - 14

  15. Conclusions • Biomedical executive structure installed • Application Working Group representatives • to work on MNA4.1 and DNA4.1 • Technical Working Group initiated • Mailing list and web site updated • Representative to project boards: • MWSG, PEB, PTF, … • To install and test EGEE middleware (LCG-2) • To deploy pilots and provide feedback • Pilot applications: GATE (LPC), GPS@ (IBCP), CDSS (UPV) • To study external application candidates • Increase involvment of clinical and research end users NA4 Biomedical Applications, EGEE-Fr 1rst meeting, June 11 2004 - 15

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