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					         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 2000     V. 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 2000     V. 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 2000        V. 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 2000     V. 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 2000   V. 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 2000      V. 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 2000   V. 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 2000      V. Breton Milan WP6 DataGRID meeting
       Testing CORBA/Globus
     interface with AppLab(EBI)
• AppLab is a
  Bioinformatic
  platform
  – Using OMG                                       Command file
                                                       location
                                                   Application name
    Biomolecular
                                    CORBA, BSA
    Sequence Analysis
    standards
                                     Graphical          GRID
  – Client and server                interface

    exchange objects on a
    CORBA bus                         Client


 11 Decembre 2000   V. 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 2000    V. Breton Milan WP6 DataGRID meeting
                        EXISTING              CUSTOMIZED
                       ALGORITHMS             ALGORITHMS




LABORATORY                   PLUG AND PLAY
 Biologist 1                                                           ALGORITHM
     …                                                                 DEVELOPPER
 Biologist N                          DATA
                                    WAREHOUSE
 DATA MART



       OCCASIONAL                                                   PLUG AND PLAY
          USER                                                      ADMINISTRATOR

                                  EXTERNAL
                                  DATABASES               R. Médina, LIMOS,
                                                          Université Blaise Pascal
    11 Decembre 2000         V. Breton Milan WP6 DataGRID meeting

				
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