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A demonstration of the use of Datagrid testbed and services for the biomedical community

A demonstration of the use of Datagrid testbed and services for the biomedical community. Biomedical applications work package V. Breton, Y Legré (CNRS/IN2P3) R. Météry (CS) Credits : C. Blanchet, T. Contamine, S. Gadras, M. Joubert, A.Minne, J. Montagnat. The Visual DataGrid Blast.

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A demonstration of the use of Datagrid testbed and services for the biomedical community

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  1. A demonstration of the use of Datagrid testbed and services for the biomedical community Biomedical applications work package V. Breton, Y Legré (CNRS/IN2P3) R. Météry (CS) Credits : C. Blanchet, T. Contamine, S. Gadras, M. Joubert, A.Minne, J. Montagnat

  2. The Visual DataGrid Blast • A graphical interface to enter query sequences and select the reference database • A script to execute the BLAST algorithm on the grid • A graphical interface to analyze results

  3. When/Where do biologists use BLAST ? • (When ?) The first step for analysing new sequences: to compare DNA or protein sequences to other ones: stored in personal or public databases • (Where ?) in a laboratory with an updated version of the genomics and post-genomics data banks • Requires equipment to store databases and run algorithms • Requires manpower for system & network maintenance and frequent update of databases • Most biologists use “integrated” web portals for their genomics comparative analysis: no need to worry about the biological file format and the method arguments

  4. Web portals for biologists under growing pressure • Biologist enters sequences through web interface • Pipelined execution of bio-informatics algorithms • Genomics comparative analysis • Phylogenetics • 2D, 3D molecular structure of proteins… • The algorithms are executed on a local cluster • Big labs have big clusters … • But growing pressure • More and more biologists • compare larger and larger sequences (whole genomes)… • to more and more genomes… • with fancier and fancier algorithms !!

  5. Input Sandbox : Input sequences UI JDL BLAST Output Sandbox : BLAST result Resource Broker Information Service Job Submit Event Job Submission Service Job Status Logging & Bookkeeping Computing Element StorageElement Executing BLAST on the grid Replica Catalog DB DB Credit : Fabio Hernandez

  6. dedzedzdzedezdzecdscsdcscdssdcsdcdscbscdsbcbjbf dedzedzdzedezdzecdscsdcscdssdcsdcdscbscdsbcbjbf dedzedzdzedezdzecdscsdcscdssdcsdcdscbscdsbcbjbf Seq1 > dedzedzdzedezdzecdscsdcscdssdcsdcdscbscdsbcbjbdfndfjvbndfbnbnfbjnbjxbnxbjk:nxbf BLAST BLAST BLAST BLAST DB DB dedzedzdzedezdzecdscsdcscdssdcsdcdscbscdsbcbjbf dedzedzdzedezdzecdscsdcscdssdcsdcdscbscdsbcbjbf dedzedzdzedezdzecdscsdcscdssdcsdcdscbscdsbcbjbf Seq2 > dedzedzdzedezdzecdscsdcscdssdcsdcdscbscdsbcbjbdfndfjvbndfbnbnfbjnbjxbnxbjk:nxbf dedzedzdzedezdzecdscsdcscdssdcsdcdscbscdsbcbjbf dedzedzdzedezdzecdscsdcscdssdcsdcdscbscdsbcbjbf dedzedzdzedezdzecdscsdcscdssdcsdcdscbscdsbcbjbf dedzedzdzedezdzecdscsdcscdssdcsdcdscbscdsbcbjbf dedzedzdzedezdzecdscsdcscdssdcsdcdscbscdsbcbjbf Seqn > dedzedzdzedezdzecdscsdcscdssdcsdcdscbscdsbcbjbdfndfjvbndfbnbnfbjnbjxbnxbjk:nxbf DB dedzedzdzedezdzecdscsdcscdssdcsdcdscbscdsbcbjbf dedzedzdzedezdzecdscsdcscdssdcsdcdscbscdsbcbjbf dedzedzdzedezdzecdscsdcscdssdcsdcdscbscdsbcbjbf dedzedzdzedezdzecdscsdcscdssdcsdcdscbscdsbcbjbf dedzedzdzedezdzecdscsdcscdssdcsdcdscbscdsbcbjbf dedzedzdzedezdzecdscsdcscdssdcsdcdscbscdsbcbjbf dedzedzdzedezdzecdscsdcscdssdcsdcdscbscdsbcbjbf dedzedzdzedezdzecdscsdcscdssdcsdcdscbscdsbcbjbf dedzedzdzedezdzecdscsdcscdssdcsdcdscbscdsbcbjbf dedzedzdzedezdzecdscsdcscdssdcsdcdscbscdsbcbjbf dedzedzdzedezdzecdscsdcscdssdcsdcdscbscdsbcbjbf dedzedzdzedezdzecdscsdcscdssdcsdcdscbscdsbcbjbf dedzedzdzedezdzecdscsdcscdssdcsdcdscbscdsbcbjbf dedzedzdzedezdzecdscsdcscdssdcsdcdscbscdsbcbjbf dedzedzdzedezdzecdscsdcscdssdcsdcdscbscdsbcbjbf dedzedzdzedezdzecdscsdcscdssdcsdcdscbscdsbcbjbf dedzedzdzedezdzecdscsdcscdssdcsdcdscbscdsbcbjbf dedzedzdzedezdzecdscsdcscdssdcsdcdscbscdsbcbjbf dedzedzdzedezdzecdscsdcscdssdcsdcdscbscdsbcbjbf dedzedzdzedezdzecdscsdcscdssdcsdcdscbscdsbcbjbf dedzedzdzedezdzecdscsdcscdssdcsdcdscbscdsbcbjbf dedzedzdzedezdzecdscsdcscdssdcsdcdscbscdsbcbjbf dedzedzdzedezdzecdscsdcscdssdcsdcdscbscdsbcbjbf dedzedzdzedezdzecdscsdcscdssdcsdcdscbscdsbcbjbf dedzedzdzedezdzecdscsdcscdssdcsdcdscbscdsbcbjbf dedzedzdzedezdzecdscsdcscdssdcsdcdscbscdsbcbjbf dedzedzdzedezdzecdscsdcscdssdcsdcdscbscdsbcbjbf dedzedzdzedezdzecdscsdcscdssdcsdcdscbscdsbcbjbf dedzedzdzedezdzecdscsdcscdssdcsdcdscbscdsbcbjbf dedzedzdzedezdzecdscsdcscdssdcsdcdscbscdsbcbjbf dedzedzdzedezdzecdscsdcscdssdcsdcdscbscdsbcbjbf dedzedzdzedezdzecdscsdcscdssdcsdcdscbscdsbcbjbf dedzedzdzedezdzecdscsdcscdssdcsdcdscbscdsbcbjbf dedzedzdzedezdzecdscsdcscdssdcsdcdscbscdsbcbjbf dedzedzdzedezdzecdscsdcscdssdcsdcdscbscdsbcbjbf dedzedzdzedezdzecdscsdcscdssdcsdcdscbscdsbcbjbf dedzedzdzedezdzecdscsdcscdssdcsdcdscbscdsbcbjbf dedzedzdzedezdzecdscsdcscdssdcsdcdscbscdsbcbjbf dedzedzdzedezdzecdscsdcscdssdcsdcdscbscdsbcbjbf dedzedzdzedezdzecdscsdcscdssdcsdcdscbscdsbcbjbf DB Actual demonstration Computing element Input file Seq1 > dcscdssdcsdcdsc bscdsbcbjbfvbfvbvfbvbvbhvbhsvbhdvbhfdbvfd Seq2 > bvdfvfdvhbdfvb bhvdsvbhvbhdvrefghefgdscgdfgcsdycgdkcsqkc … Seqn > bvdfvfdvhbdfvb bhvdsvbhvbhdvrefghefgdscgdfgcsdycgdkcsqkchdsqhfduhdhdhqedezhhezldhezhfehflezfzejfv UI Computing element RESULT dedzedzdzedezdzecdscsdcscdssdcsdcdscbscdsbcbjbfvbfvbvfbvbvbhvbhsvbhdvbhfdbvfdbvdfvfdvhbdfvbhdbhvdsvbhvbhdvrefghefgdscgdfgcsdycgdkcsqkcqhdsqhfduhdhdhqedezhdhezldhezhfehflezfzeflehfhezfhehfezhflezhflhfhfelhfehflzlhfzdjazslzdhfhfdfezhfehfizhflqfhduhsdslchlkchudcscscdscdscdscsddzdzeqvnvqvnq! Vqlvkndlkvnldwdfbwdfbdbd wdfbfbndblnblkdnblkdbdfbwfdbfn Computing element

  7. The Grid impact on computing • Swissprot vs Swissprot (100000 sequences) • Running time on one CPU : 228 hours • Tests at Institut de Biologie et Chimie des Protéines (quadripro) : ~49 hours • Tests on DataGrid (cc-in2p3) : 3 hours • Impacts : • Reduced pressure on local computing • Ability to handle very large jobs

  8. Swissprot (Geneva) The grid impact on data handling • DataGrid will allow mirroring of databases • An alternative to the current costly replication mechanism • Allowing web portals on the grid to access updated databases Trembl(EBI) Biomedical Replica Catalog

  9. This demo illustrates how grids can bring a revolution to genomics • Grids expand the performances of genomics web portals • Distributed execution of bio-informatics algorithms, • Even the ones requiring huge amount of CPU • Maintenance of up-to-date biological databases over the network • Grids open new perspectives in large scale genomics analysis • Complete genome annotation • Cross-genomes analysis • Data mining on distributed databases • Pipelining of huge automatic bio-informatics analysis • …

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