[PDF] GPSA - Grid Protein Sequence Analysis

View - Download GPSA - Grid Protein Sequence Analysis

Previous PDF

Next PDF

INFSO-RI-508833

Enabling Grids for E-sciencE

www.eu-egee.org GPSA

Grid Protein Sequence Analysis

Christophe Blanchet

CNRS IBCP

EGEE conference 2, Den Haag, 24 nov 2004

GPSA genomic grid portal demo - Christophe.Blanchet@ibcp.fr 2

Enabling Grids for E-sciencE

INFSO-RI-508833

Contents

•Bioinformatic context •NPS@: genomic web portal •GPS@: genomic grid portal •GPS@ demo GPSA genomic grid portal demo - Christophe.Blanchet@ibcp.fr 3

Enabling Grids for E-sciencE

INFSO-RI-508833

Complete genome projects

Complete genomes: 1220 projects (nov.

2004)

Finished ones (published): 207

In progress : 506 Prokaryotes, 418

Eukaryotes

Size of genomic data

yH sapiens: 3.000 Mb (24) yS. cerevisae: 120 Mb, yA. thaliana: 116 Mb Geno mes Geno mes Geno mes Geno mes Geno mes Geno mes Geno mes Gen o mes Gen o mes Gen o mes Gen o mes Gen o mes Gen o mes Gen o mes Gen o mes Gen o mes Gen o mes Gen o mes Gen o mes Gen o mes Gen o mes Gen o mes Geno mes Geno mes Geno mes Geno mes Geno mes Geno mes Geno mes Geno mes Geno mes Geno mes Geno mes Geno mes •Large scale Bioinformatics

Ratio of 1000 between raw and annoted data

Updating data and analyses (in automatic way)

GPSA genomic grid portal demo - Christophe.Blanchet@ibcp.fr 4

Enabling Grids for E-sciencE

INFSO-RI-508833

World-used methods for

protein sequence analysis •Pairwise alignment: similarity -BLAST, FASTA, SSEARCH •Pattern scanning: -ScanProsite, PattInProt •Multiple alignment -Clustal W, MultAlin •Secondary structure prediction -GOR, Predator, PHD, SIMPA, SOPMA, HNN,... •Misc. -Physico-chemical profiles transmembran section, .... GPSA genomic grid portal demo - Christophe.Blanchet@ibcp.fr 5

Enabling Grids for E-sciencE

INFSO-RI-508833

Bioinformatic algorithm model

Algorithm

DBs

Results

subDB

Parameters

Nucleic acids,

Proteins,

Signatures,

3D structures,

Bibliography,

Similarity

Alignment

Secondary pred

3D model

Sequence, pattern,...

Data Data Data GPSA genomic grid portal demo - Christophe.Blanchet@ibcp.fr 6

Enabling Grids for E-sciencE

INFSO-RI-508833

TOC •Bioinformatic context •NPS@: genomic web portal •GPS@: genomic grid portal •GPS@ demo GPSA genomic grid portal demo - Christophe.Blanchet@ibcp.fr 7

Enabling Grids for E-sciencE

INFSO-RI-508833

Genomic web portal : NPS@

•http://npsa-pbil.ibcp.fr/ •online since 1998 ; NPS@ release 3 •34 integrated methods for protein sequence analysis •Hypertext cross-links to 11 international biological databanks •Online up-to-date biological databanks •1-click download of NPS@ results in biological softwares: MPSA, AnTheProt, Clustal X, RasMol, ... •International references: Expasy, University of

California, InfoBioGen,...

_" NPS@: Network Protein Sequence Analysis » Combet C., Blanchet C., Geourjon C. et Deléage G.

Tibs, 2000, 25, 147-150.

GPSA genomic grid portal demo - Christophe.Blanchet@ibcp.fr 8

Enabling Grids for E-sciencE

INFSO-RI-508833

133801

547366

1169926

1953285

2876852

5295521

4062544

0

1000000

2000000

3000000

4000000

5000000

6000000

1998199920002001200220032004

NPSA hits

•More than 5 millions analyses since 1998 •More than 3000 analyses/day

America

27%
Asia 11%

Europe

35%

France

24%

Africa

1%

Oceania

2%

Courtesy of C. Combet

GPSA genomic grid portal demo - Christophe.Blanchet@ibcp.fr 9

Enabling Grids for E-sciencE

INFSO-RI-508833

TOC •Bioinformatic context •NPS@: genomic web portal •GPS@: genomic grid portal •GPS@ demo GPSA genomic grid portal demo - Christophe.Blanchet@ibcp.fr 10

Enabling Grids for E-sciencE

INFSO-RI-508833

GPSA-Grid Protein Sequence Analysis

•EGEE - Enabling Grids for E-Science in Europe. •NA4 activity - Biomedical Applications •GPSA -One of the 3 biomed pilot applications (available at day 0) -GPS@ will be an integrated grid portal devoted to molecular bioinformatics. -GPSA is a porting experiment of the NPSA (Network Protein Sequence Analysis) services onto the EGEE grid. The current version is under development and deployed on LCG2. -http://gpsa.ibcp.fr/ GPSA genomic grid portal demo - Christophe.Blanchet@ibcp.fr 11

Enabling Grids for E-sciencE

INFSO-RI-508833

GPSA: grid benefits

•NPS@ - network Protein Sequence Analysis -Production web portal hosting proteins databases and algorithmes for sequences analysis. -Online since 1998. Hosted by a cluster of 14 CPUs -Currently, strong restrictions in terms of databanks and algorithmes due to limited resources. -Therefore the number of users connecting to the portal and the size of the data sets are restricted by the server but they will have to process. •GPSA: bringing the EGEE grid services to the NPSA genomic portal -The same user community will be eager to transparently use the grid version of the same service once available. -Providing biologists with more and larger databanks -Providing biologists with more bioinformatic methods and connections between them (ClustalW and PSSP) -Allowing analysis of larger datasets GPSA genomic grid portal demo - Christophe.Blanchet@ibcp.fr 12

Enabling Grids for E-sciencE

INFSO-RI-508833

GPSA: welcome

GPSA genomic grid portal demo - Christophe.Blanchet@ibcp.fr 13

Enabling Grids for E-sciencE

INFSO-RI-508833

GPSA : Portal Architecture

GPSA bio Portal bioGateway to GRID

XML files

describing

Genomic

Resources

DataGRID

EGEE

Biologist

HTTP bio Resources

International Dbs

Relevant Applications

Integration

EGEE UI

Genomics-ui.ibcp.fr

EGEE CE - SE

WMS - RMS

GPSA UI

http://gpsa.ibcp.fr GPSA

Resources

GPSA genomic grid portal demo - Christophe.Blanchet@ibcp.fr 14

Enabling Grids for E-sciencE

INFSO-RI-508833

Bioinformatic Resources on EGEE

(Nov 2004) •Protein analysis application -Similarity:Ssearch -Multiple Alignment:ClustalW -Functionnal site and signatures:PattInProt -Prot Secondary Pred:Predator, Gor4, Simpa96 •Data -Sequence Bank:SWISSPROT -Pattern and profile bank:PROSITE GPSA genomic grid portal demo - Christophe.Blanchet@ibcp.fr 15

Enabling Grids for E-sciencE

INFSO-RI-508833

Bioinformatic resources on EGEE

Perspective (Feb 2005)

•Deploying more protein databanks (using RMS) •Integrating gridified databanks -in progress into GPSA -to be done into NPS@ •Deploying bioinformatic algorithms (using ESM) -Tested with ClustalW and SSEARCH algorithms (in LAL site) •Integrating more bioinformatic algorithms -Currently 4 in GPSA (chosen as models for the others) -Currently 1 into NPS@ GPSA genomic grid portal demo - Christophe.Blanchet@ibcp.fr 16

Enabling Grids for E-sciencE

INFSO-RI-508833

Demo Time

CNRS IBCP

Institute of Biology and

Chemistry of Proteins

Lyon, France

quotesdbs_dbs44.pdfusesText_44

[PDF] exposition geneve 2017

[PDF] exposition geneve aujourd'hui

[PDF] votre dossier va être vérifié par l'espace campus france.

[PDF] expositions temporaires genève 2017

[PDF] musee geneve

[PDF] musée rath genève exposition

[PDF] express english national stereotypes

[PDF] kwyk hack

[PDF] great expectations themes

[PDF] kwik

[PDF] les grandes espérances pdf

[PDF] great expectations film

[PDF] ecoledirecte

[PDF] great expectations book

[PDF] immunité humorale et cellulaire cours