INFSO-RI-508833 Enabling Grids for E-sciencE WISDOM mini-workshop Vincent Breton (CNRS-IN2P3, LPC...
-
Upload
marjory-floyd -
Category
Documents
-
view
220 -
download
2
Transcript of INFSO-RI-508833 Enabling Grids for E-sciencE WISDOM mini-workshop Vincent Breton (CNRS-IN2P3, LPC...
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
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
WISDOM workshop – March 29th, 2007 – V. Breton 3
Enabling Grids for E-sciencE
INFSO-RI-508833
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
WISDOM workshop – March 29th, 2007 – V. Breton 4
Enabling Grids for E-sciencE
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
WISDOM workshop – March 29th, 2007 – V. Breton 5
Enabling Grids for E-sciencE
INFSO-RI-508833
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
WISDOM workshop – March 29th, 2007 – V. Breton 6
Enabling Grids for E-sciencE
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
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
WISDOM workshop – March 29th, 2007 – V. Breton 8
Enabling Grids for E-sciencE
INFSO-RI-508833
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
WISDOM workshop – March 29th, 2007 – V. Breton 9
Enabling Grids for E-sciencE
INFSO-RI-508833
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
WISDOM workshop – March 29th, 2007 – V. Breton 10
Enabling Grids for E-sciencE
INFSO-RI-508833
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