1. EGEE-III INFSO-RI Enabling Grids for E-sciencE www.eu-egee.org EGEE08 conference, Istambul Life sciences cluster perspective on EGI V. Breton, CNRS On behalf of EGEE-III life sciences cluster

2. Enabling Grids for E-sciencE EGEE-III INFSO-RI EGEE-EGI transition workshop Community status Life sciences community uses actively grid infrastructures –Dedicated grids (Décrypthon) –EGEE (Biomed VO represents ~ 6% of total CPU in 2008)  First paper accepted in Nature (Genetics) –Multidisciplinary regional grids  Examples: COMETA, AuverGrid But only a few real “end”-users –Technology under adoption by bioinformatics and medical imaging communities –Much less impact on biologists and physicians Grid infrastructures well identified by key European initiatives –Virtual Physiological Human –ELIXIR, LifeWatch design studies Need for a strong international grid infrastructure to enlarge the user community and maintain a world leadership New

3. Enabling Grids for E-sciencE EGEE-III INFSO-RI EGEE-EGI transition workshop Survey results (I/IV) Personal knowledge on grids None Limited Satisfactory Broad Use of grids in the laboratories None Limited Growing routinely

4. Enabling Grids for E-sciencE EGEE-III INFSO-RI EGEE-EGI transition workshop Survey results (II/IV) Personal need of supercomputer resources Personal need of cluster or grid resources Unknown Small Limited Significant Large 1TFlop Unknown Small Limited Significant Large 10CPUyears

5. Enabling Grids for E-sciencE EGEE-III INFSO-RI EGEE-EGI transition workshop Survey results (III/IV) Planning of computing needs Planning of storage needs All Biology Health Chemo- informatics All Biology Health Chemo- informatics Very stable during the year Very unstable with peaks Easy to plan weeks in advance Hard to plan Very stable during the year Very unstable with peaks Easy to plan weeks in advance Hard to plan

6. Enabling Grids for E-sciencE EGEE-III INFSO-RI EGEE-EGI transition workshop Survey results (IV/IV) Security on the input and output data All Biology Health Chemo- informatics No constraints Access control Encryption Anonymization User interface to grid resources Command lines Web portal dedicated interfaces

7. Enabling Grids for E-sciencE EGEE-III INFSO-RI EGEE-EGI transition workshop Survey: conclusions The life sciences community has homogeneous needs –Except for security, all sub-communities have very comparable answers The life sciences community needs to access both cluster grids and supercomputers –Comparable needs expressed for both infrastructures –on demand computing: significant fraction of the computing needs are difficult to plan in advance Significant adoption of grids by the research community –To be counterweighted by the targeted audience Security –90% of the applications in biology require only access control –Only 50% for health applications, the other 50% requiring medical data anonymization

8. Enabling Grids for E-sciencE EGEE-III INFSO-RI EGEE-EGI transition workshop EGI: specific thoughts for the life science SSCs Adoption of the grid infrastructures is still in its infancy –It is critical that the biomed VO is continuously operated for the pioneers already using the grid The life science community is very heterogeneous –Many sub-communities with similar requirements (see survey) –About 8 ESFRI design studies are related to life sciences  BBSRC: biobanking  ELIXIR: molecular biology  LIFEWATCH: biodiversity  … –Need to properly interface them to EGI

9. Six ESFRI projects in biomolecular science area www.elixir-europe.org Upgrade Of European Bioinformatics Infrastructure ELIXIR www.ecrin.org Infrastructures For Clinical Trials And Biotherapy ECRIN www.biobanks.eu European Biobanking And Biomolecular Resources BBMRI www.eatris.eu/ The European Advanced Translational Research Infrastructure EATRIS www.infrafrontier.eu Infrastructure for Phenomefrontier and Archivefrontier Infrafrontier www.instruct-fp7.eu Integrated Structural Biology Infrastructure INSTRUCT BBMRI (Biobanking) INSTRUCT (Structural biology) ELIXIR Infrafrontier (Model Organisms) ECRIN (Clinical Trials)(Translational Research) EATRIS (Life Science Information) Target ID Hit Lead Lead OptPreclinicalPhase IPhase II Phase IIITarget Val ResearchDiscoveryDevelopment Credit: S. Sansonne (EBI)

10. Enabling Grids for E-sciencE EGEE-III INFSO-RI EGEE-EGI transition workshop Why the grid for biomolecular sciences? algorithm 1 Input data algorithm 2 Output Database 1 Database 2 Database storage, curation and update Access to grid computing resources The grid is about federating distributed resources The grid is about sharing tools and resources in a secured way The grid is about leaving the data where they are produced

11. Enabling Grids for E-sciencE EGEE-III INFSO-RI EGEE-EGI transition workshop Life sciences requirements Identified needs –Access to grids of clusters and to supercomputers –Stability and Sustainability –Friendly user interfaces –Standard access to services  One single API, whatever the middleware –Security of medical data Importance of international standards –Integration of resources into european infrastructures and european initiatives  ESFRIs  Virtual Physiological Human –Which standards ?  Open Grid Forum  Web services

12. Enabling Grids for E-sciencE EGEE-III INFSO-RI EGEE-EGI transition workshop Comments on science gateways within life sciences Development of international gateways is the duty of the research communities using it –Example: VPH, Elixir,… –Need for well defined standard interfaces to EGI –Interest for templates –Interest/necessity to share some tools (workflow engines) and technologies (web services, semantic annotation) There is a need for one SSC “mapping” the biomed VO –Use case for the other gateways –Catch all for new users and emerging user groups –Development to start very early in the project to be able to distribute it to the communities –Several SSCs can point to the same VO Need for training and user support –Money ?

13. Enabling Grids for E-sciencE EGEE-III INFSO-RI EGEE-EGI transition workshop Possible picture Life Sciences SSC (Biomed VO) Start day: 6/9/09 Catch all Drug discovery Bioinformatics Medical imaging ELIXIR SSC (Use of biomed VO for computing) Elixir VO for storage and computing Start day: 1/6/10 LifeWatch SSC (Use of biomed VO for computing) LifeWatch VO for storage and computing Start day: 1/6/11

14. Enabling Grids for E-sciencE EGEE-III INFSO-RI EGEE-EGI transition workshop Questions How should the biomed community get organized? –Should there be one life sciences SSC or one per ESFRI? –If any, should biomed SSC be funded by EGI, the NGIs or the community?