11 Decembre 2000V. Breton Milan WP6 DataGRID meeting Biological applications in testbed 0 Evaluate GRID added value for handling biological data –What are the needs of the biologists for a GRID ? Evaluate Globus on existing bioinformatic tools –Is Globus the middleware to answer these needs ? Propose suitable applications on testbed to develop middleware in connection to biology –3 applications under discussion in WP10 –Explore existing GRID-oriented CORBA tools (NASA,LIFL)

11 Decembre 2000V. Breton Milan WP6 DataGRID meeting Biological data : the challenges Data organization (format, storage) –Need for a coherent format –Exponential growth of the data volume Data accessibility (network, storage) –Saturation of the network (9GB banks download) –Information spread over several databases Data interpretation –Difficulty to mine pertinent information from exponentially growing volume of data Data errors –Wrong sequence/homologies/annotation

11 Decembre 2000V. Breton Milan WP6 DataGRID meeting GRID added value for data accessibility One unique entry to the data bases –No need to consult multiple data bases to have full information –Automated (hidden from user) consulting of databases for the biological object of interest –Possibility to read this collection of information at different level Summarized Detailed Fast access to data User-friendly access to data – Possibility to ask biological questions to data bases

11 Decembre 2000V. Breton Milan WP6 DataGRID meeting GRID added value for data organization Dynamic update of the data bases –Automatic search of the web for new results (litterature) –Background CPU to update biological links (à la Swissprot) before each new release Dissemination of data on the GRID –Coherent representation of data bases –Easy mirroring Integration of new data bases and data types

11 Decembre 2000V. Breton Milan WP6 DataGRID meeting GRID added value for data interpretation Find links between data –Data mining Massive comparison of sequences –I.e comparison of mouse and human genomes –Parallelized blast search Automated enlarged choice of algorithms –I.e what can I do on a protein ?

11 Decembre 2000V. Breton Milan WP6 DataGRID meeting Biological applications in testbed 0 WP10 goals in the testbed –Month 12 : specification for a testbed, selection of a suitable application and planning document –Month 24 : report on the 1st bio-testbed release –Month 36 : final report including report on the 2nd testbed release WP10 deadlines are postponed compared to WP8 3 applications under investigation in WP10 –2 in bioinformatics –1 in medical imaging

11 Decembre 2000V. Breton Milan WP6 DataGRID meeting Testbed applications Short term use cases –Testing Globus environment with Artemis (Sanger) –Testing CORBA-Globus interface with AppLab (EBI) Long term use cases –grid-aware bioinformatic platform (CORBA) –Other projects under investigation

11 Decembre 2000V. Breton Milan WP6 DataGRID meeting Artemis (Sanger) Artemis is a Java viewer to view biological data stored in a database It allows to run algorithms (with PERL scripts) on the data and view results Testbed goal –Modify ARTEMIS to run algorithms on distant data through the GRID –Modify ARTEMIS to run algorithms on distant computers of the GRID

11 Decembre 2000V. Breton Milan WP6 DataGRID meeting Testing CORBA/Globus interface with AppLab(EBI) AppLab is a Bioinformatic platform –Using OMG Biomolecular Sequence Analysis standards –Client and server exchange objects on a CORBA bus

11 Decembre 2000V. Breton Milan WP6 DataGRID meeting Testbed nodes French nodes : –Clermont-Ferrand (Globus deployed) –Marseille (Globus deployed) –CCPN Lyon (Globus deployed) –Montpellier (February 2001) EBI (Globus deployed) Sweden ? Italy ?

11 Decembre 2000V. Breton Milan WP6 DataGRID meeting LABORATORY Biologist 1 … Biologist N ALGORITHM DEVELOPPER DATA MART EXTERNAL DATABASES OCCASIONAL USER CUSTOMIZED ALGORITHMS EXISTING ALGORITHMS PLUG AND PLAY ADMINISTRATOR PLUG AND PLAY DATA WAREHOUSE R. Médina, LIMOS, Université Blaise Pascal