1. EU 2nd Year Review – 04 Feb. 2003 – WP10 status report – n° 1 WP10 Status Report Vincent Breton (WP10 manager) breton@clermont.in2p3.fr Presentation address https://agenda.cern.ch/age?a021814https://agenda.cern.ch/age?a021814

2. EU 2nd Year Review – 04 Feb. 2003 – WP10 status report – n° 2 DataGrid, prototype of a biomedical grid u DataGrid has three ambitious goals : n Develop a middleware n Deploy a testbed n Have large scale applications running on this testbed u The biomedical work package faces three challenges n Make the middleware meet biomedical specific requirements n Deploy grid nodes in biomedical laboratories n Run biomedical applications

3. EU 2nd Year Review – 04 Feb. 2003 – WP10 status report – n° 3 Conclusion of last year review u Key achievements n We have shown the relevance of the grid concept for biomedical applications (see demo) n We have established a fruitful dialog with s Biology and medical imaging (25 laboratories involved) s The other applications and middleware work packages of DataGrid n The group has found cohesion and coherence despite the various backgrounds of the actors (biologists, computer scientists, physicists) u Key challenges for the lifetime of the DataGrid project n Deploy a true biomedical testbed involving genomics, bio-informatics and medical imaging laboratories n Run the applications described in D10.2 to demonstrate the use of a grid in genomics and medical imaging

4. EU 2nd Year Review – 04 Feb. 2003 – WP10 status report – n° 4 Difficulties in addressing the key challenges u Delay in testbed1 release (Aug. 2002) n Complexity of deployment of a biomedical testbed u Scalability/Robustness problems on testbed1 n Replica Manager scalability issues n Scalability issues when stressing the Res. Broker n Testbed instability related to info. service u Need to make a very large scale test this year n Competition for testbed resources - HEP applications are often the highest priority u Support for MPI-based job submission is vital for some applications u Programmable APIs to access middleware services u Support by the Storage Element for medical databases u Ports to RH7 and 8 needed Strong expectations on EDG 2.0 components

5. EU 2nd Year Review – 04 Feb. 2003 – WP10 status report – n° 5 Successes addressing the key challenges u Four groups able to deploy their applications on EDG testbed s Implementation of a web portal for phylogenetics s Comparison of genomes of parasite and bacteria s Management of medical images (see WP10’s demo tomorrow) s Search for primers u Interaction with the middleware packages s Feedback on our job submission problems s Discussion on metadata management (spitfire) s On-going discussion through the architecture group (ATF) on biomedical data integration and related security issues

6. EU 2nd Year Review – 04 Feb. 2003 – WP10 status report – n° 6 Status of WP10 applications u Bio-informatics n Phylogenetics : BBE Lyon (T. Sylvestre) n Search for primers : Centrale Paris (K. Kurata) n Statistical genetics : CNG Evry (N. Margetic) n Bio-informatics web portal : IBCP (C. Blanchet) n Parasitology : LBP Clermont, Univ B. Pascal (N. Jacq) n Data-mining on DNA chips : Karolinska (R. Médina, R. Martinez) n Geometrical protein comparison : Univ. Padova (C. Ferrari) u Medical imaging n MR image simulation : CREATIS (H. Benoit-Cattin) n Medical data and metadata management : CREATIS (J. Montagnat) n Mammographies analysis ERIC/Lyon 2 (S. Miguet, T. Tweed) n Simulation platform for PET/SPECT based on Geant4 : GATE collaboration (L. Maigne) Applications deployed Applications tested on EDG Applications under preparation

7. EU 2nd Year Review – 04 Feb. 2003 – WP10 status report – n° 7 Addressing the key challenges… u More successes… n More than 15 WP10 users trained n Several system administrators initiated to the installation procedure of a grid node n First evaluation of performance Credit : T. Silvestre BBE complexity Elapsed time (mn) Phylogenetics (fastDNAm algorithm)

8. EU 2nd Year Review – 04 Feb. 2003 – WP10 status report – n° 8 A major success in 2002 : dissemination u Active participation to the creation of the HealthGrid cluster of EC projects u WP10 actively involved in the European HealthGrid conference (co-organized by CNRS, CERN, EMBnet and the help of the European Community) in Lyon (January 2003). More than 200 participants. u Three demos shown at HealthGrid, more than 10 papers submitted (4 accepted) to workshops and conferences

9. EU 2nd Year Review – 04 Feb. 2003 – WP10 status report – n° 9 Laboratories involved in WP10 … Dublin Hinxton(EBI) Montpellier Moscow Kosice Lyon Uppsala Stockholm (Karolinska) Madrid(CNB) Clermont Lausanne(EPFL,SIB) CERN Evry(CNG) Padova Saclay (CEA) Laboratories testing EDG Middleware Other labs.

10. EU 2nd Year Review – 04 Feb. 2003 – WP10 status report – n° 10 Pending problems u No EDG nodes installed in biomedical laboratories n Delays in EDG 1.2 middleware releases n Middleware is RH6.2 based, RH7.3 happening now, no RH8 release yet foreseen n Complexity of the configuration, despite a tutorial for system engineers n User/site administration support is needed n WP10 human resources limited to 2 funded engineers u Need more synergy between the applications working groups n It is time to revive a cross-application workgroup

11. EU 2nd Year Review – 04 Feb. 2003 – WP10 status report – n° 11 Work program for 2003 u March 2003 : deliverable D10.3 « Report on the first bio- testbed release » u Production (large scale) test in phylogenetics u Deployment of all 7 applications described in D10.2. Applications still to be deployed : n data mining on DNA chips (MPI support needed) n GPSA : web portal for protein structure analysis (EDG interface) n MRI simulator (MPI support needed) u Installation of EDG nodes in biomedical laboratories n We must be able to deploy and maintain our own production platform n To make the community aware of the need for a computing infrastructure n First « WP10 » node expected at LPC Clermont-Ferrand in February