infso-ri-508833 enabling grids for e-science wisdom mini-workshop vincent breton (cnrs-in2p3, lpc...

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INFSO-RI-508833 Enabling Grids for E-sciencE www.eu-egee.org WISDOM mini-workshop Vincent Breton (CNRS-IN2P3, LPC Clermont-Ferrand) ISGC 2007 March 28th, 2007

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Page 1: INFSO-RI-508833 Enabling Grids for E-sciencE  WISDOM mini-workshop Vincent Breton (CNRS-IN2P3, LPC Clermont-Ferrand) ISGC 2007 March 28th,

INFSO-RI-508833

Enabling Grids for E-sciencE

www.eu-egee.org

WISDOM mini-workshop

Vincent Breton (CNRS-IN2P3, LPC Clermont-Ferrand)

ISGC 2007

March 28th, 2007

Page 2: INFSO-RI-508833 Enabling Grids for E-sciencE  WISDOM mini-workshop Vincent Breton (CNRS-IN2P3, LPC Clermont-Ferrand) ISGC 2007 March 28th,

WISDOM workshop – March 29th, 2007 – V. Breton 2

Enabling Grids for E-sciencE

INFSO-RI-508833

Mini-workshop program

• Introduction (V.B.)

• Analysis of the first data challenge on avian flu (Y-T Wu, Academia Sinica)

• Short term perspective: second data challenge on avian flu

• Other perspectives – Knowledge repository for avian flu– New data challenges on neglected diseases

Page 3: INFSO-RI-508833 Enabling Grids for E-sciencE  WISDOM mini-workshop Vincent Breton (CNRS-IN2P3, LPC Clermont-Ferrand) ISGC 2007 March 28th,

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Content

• Brief presentation of the collaboration– Status– Membership

• Status of the different data challenges– First data challenge on avian flu – First data challenge on malaria– Second data challenge on malaria

Page 4: INFSO-RI-508833 Enabling Grids for E-sciencE  WISDOM mini-workshop Vincent Breton (CNRS-IN2P3, LPC Clermont-Ferrand) ISGC 2007 March 28th,

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INFSO-RI-508833

WISDOM

• Goal: contribute to develop new drugs for neglected and emerging diseases with a particular focus on malaria and avian flu

• Specificity: extensively rely on emerging information technologies to provide new tools and environments for drug discovery and development.

• Initial focus: screening

• Web site: http://wisdom.healthgrid.org

Page 5: INFSO-RI-508833 Enabling Grids for E-sciencE  WISDOM mini-workshop Vincent Breton (CNRS-IN2P3, LPC Clermont-Ferrand) ISGC 2007 March 28th,

WISDOM workshop – March 29th, 2007 – V. Breton 5

Enabling Grids for E-sciencE

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WISDOM collaboration

7 partners, 4 associated laboratories providing targets and/or in vitro facilities

Univ. Los Andes:Biological

targets, Malaria biology

LPC Clermont-Ferrand:

Biomedical grid

SCAI Fraunhofer:Knowledge extraction,

Chemoinformatics

Univ. Modena:Biological targets,

Molecular Dynamics

ITB CNR:Bioinformatics,

Molecular modelling

Univ. Pretoria:Bioinformatics, Malaria biology

Academica Sinica:

Grid user interfaceBiological targets

In vitro testing

HealthGrid:Biomedical grid, Dissemination

CEA, Acamba project:

Biological targets, Chemogenomics

Chonnam nat. univ.:

In vitro testing

Asian partnersNon Asian partnersAssociated labs

Mahidol UniversityBangkok, Thailand:

In vitro testing

New

Page 6: INFSO-RI-508833 Enabling Grids for E-sciencE  WISDOM mini-workshop Vincent Breton (CNRS-IN2P3, LPC Clermont-Ferrand) ISGC 2007 March 28th,

WISDOM workshop – March 29th, 2007 – V. Breton 6

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INFSO-RI-508833

IT development activities

• Groups involved: ASGC, CNRS and ITB-CNR• Development of a full grid-enabled virtual screening

procedure (EGEE, Embrace, BioinfoGRID)– Docking + post-docking analysis– Molecular Dynamics + post-MD analysis

• Development of a production environment (EGEE, Embrace, BioinfoGRID)– Secure storage of biochemical information in a database– WISDOM client using web service technology– Improved monitoring features– To do: workflow

Page 7: INFSO-RI-508833 Enabling Grids for E-sciencE  WISDOM mini-workshop Vincent Breton (CNRS-IN2P3, LPC Clermont-Ferrand) ISGC 2007 March 28th,

WISDOM workshop – March 29th, 2007 – V. Breton 7

Enabling Grids for E-sciencE

INFSO-RI-508833

Status of WISDOM-I data challenge on malaria

• Reminder– One target: plasmepsins II and IV– Docking software: FlexX– Compound library: ChemBridge (500.000 compounds)

• Docking results completely analyzed (SCAI Fraunhofer)– Best 25000 compounds selected

• Reranking of the selected compounds using MD (Univ. Modena, CNRS)– Best 200 compounds just selected

• In vitro screening to start next month at Chonnam National University

Page 8: INFSO-RI-508833 Enabling Grids for E-sciencE  WISDOM mini-workshop Vincent Breton (CNRS-IN2P3, LPC Clermont-Ferrand) ISGC 2007 March 28th,

WISDOM workshop – March 29th, 2007 – V. Breton 8

Enabling Grids for E-sciencE

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Status of WISDOM-II data challenge on malaria

• Reminder– 4 targets: GST, tubulin, DHFR Pl. falciparum and vivax– Docking software: FlexX– Compound library: ZINC

• Data challenge finished on Jan 31st– > 400 CPU years– Collection of data produced under way

• Analysis to start soon– Tubulin: CEA Grenoble– GST: Univ. Pretoria– DHFR: Univ. Los Andes and Univ. Modena

Page 9: INFSO-RI-508833 Enabling Grids for E-sciencE  WISDOM mini-workshop Vincent Breton (CNRS-IN2P3, LPC Clermont-Ferrand) ISGC 2007 March 28th,

WISDOM workshop – March 29th, 2007 – V. Breton 9

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Second data challenge on avian flu: brainstorming

• Focus: – Target(s)– Docking software– Compound library

§ Issues encountered with first data challenge

• Production environment– New WISDOM environment– Docking workflow

• Amount of resources needed

• Timing

Page 10: INFSO-RI-508833 Enabling Grids for E-sciencE  WISDOM mini-workshop Vincent Breton (CNRS-IN2P3, LPC Clermont-Ferrand) ISGC 2007 March 28th,

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Other issues for discussion

• Relationship with PRAGMA– KISTI volunteering to develop API’s to deploy WISDOM on

PRAGMA testbed– PRAGMA announced last week an initiative on avian flu

§ Focus on building a knowledge repository§ Interest to collaborate ?

• Perspectives on neglected diseases– Invitation to contribute to TDR initiative for the computational

prioritization of candidate targets for neglected tropical diseases http://genoma.unsam.edu.ar/portfolio/

– Offer from WHO/TDR Drug Target Portfolio initiative to recommend targets for the next data challenge on neglected diseases