Transcript WISDOM_WORKSHOP-Vincent_03292007

Enabling Grids for E-sciencE
WISDOM mini-workshop
Vincent Breton (CNRS-IN2P3, LPC Clermont-Ferrand)
ISGC 2007
March 28th, 2007
www.eu-egee.org
INFSO-RI-508833
Mini-workshop program
Enabling Grids for E-sciencE
• 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
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Content
Enabling Grids for E-sciencE
• 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
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WISDOM
Enabling Grids for E-sciencE
• 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
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WISDOM collaboration
Enabling Grids for E-sciencE
LPC Clermont-Ferrand:
Biomedical grid
SCAI Fraunhofer:
Knowledge extraction,
Chemoinformatics
CEA, Acamba project:
Biological targets,
Chemogenomics
Univ. Modena:
Biological targets,
Molecular Dynamics
HealthGrid:
Biomedical grid,
Dissemination
ITB CNR:
Bioinformatics,
Molecular modelling
Univ. Los Andes:
Biological targets,
Malaria biology
Univ. Pretoria:
Bioinformatics,
Malaria biology
Mahidol University
Bangkok, Thailand:New
In vitro testing
Chonnam nat. univ.:
In vitro testing
Academica Sinica:
Grid user interface
Biological targets
In vitro testing
Asian partners
Non Asian partners
Associated labs
7 partners, 4 associated laboratories providing targets
and/or in vitro facilities
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IT development activities
Enabling Grids for E-sciencE
• 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)
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Secure storage of biochemical information in a database
WISDOM client using web service technology
Improved monitoring features
To do: workflow
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Status of WISDOM-I data challenge
on malaria
Enabling Grids for E-sciencE
• 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
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Status of WISDOM-II data challenge
on malaria
Enabling Grids for E-sciencE
• 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
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Second data challenge on avian flu:
brainstorming
Enabling Grids for E-sciencE
• 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
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Other issues for discussion
Enabling Grids for E-sciencE
• 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
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