Download Biological applications in testbed 0

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
Biomolecular
Sequence Analysis
standards
– Client and server
exchange objects on a
CORBA bus
11 Decembre 2000
Command file
location
Application name
CORBA, BSA
Graphical
interface
GRID
Client
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
ALGORITHMS
LABORATORY
Biologist 1
…
Biologist N
CUSTOMIZED
ALGORITHMS
PLUG AND PLAY
ALGORITHM
DEVELOPPER
DATA
WAREHOUSE
DATA MART
OCCASIONAL
USER
PLUG AND PLAY
ADMINISTRATOR
EXTERNAL
DATABASES
11 Decembre 2000
R. Médina, LIMOS,
Université Blaise Pascal
V. Breton Milan WP6 DataGRID meeting