A perspective on life science grids in Europe

1
A perspective on life science grids in Europe

• Vincent Breton (CNRS-IN2P3, LPC Clermont-Ferrand)
• ISGC 2007
• March 28th, 2007

2
Content

• Introduction
• The life science grid ecosystem
• Embrace, BioinfoGRID, 2 contributions to life
  science activities on grids in Europe
• Conclusion

3
Introduction

• In this talk, LIFE SCIENCE bioinformatics and
  molecular biology
• Hurng-Chun Lee addressed already grid-enabled
  drug discovery
• WISDOM workshop tomorrow
• Yannick Legré will address medical research later
  this afternoon

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Needs of the life sciences community

• Biologists need growing capability to handle all
  the data relevant to their research topics
• Design of complex analysis workflows
• Knowledge management
• Bioinformaticians who are developing the IT
  services for the biologists need growing
  resources
• to store, update, curate exponentially growing
  databases
• To run increasingly complex algorithms on this
  growing data set
• To build new databases exploiting the growing
  body of knowledge
• Biologists and bioinformaticians have therefore
  different needs
• Biologists need high level environments and
  little resources
• Bioinformaticians need large resources to develop
  and/or update the services needed by the
  biologist

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The life science community needs both e-science
and grid infrastructures

• E-science focusses at creating new research
  environments for biologists
• Use of the most recent information technologies
  (semantics, ontologies)
• Design of virtual laboratories where the
  biologist can run experiments and manipulate the
  knowledge she/he is familiar with
• Examples MyGrid (UK) and VLe (Netherlands) -gt T.
  Oinn talk
• Grid infrastructures provide ressources needed at
  different levels
• to support bioinformaticians who maintain data
  bases accessed by e-science environments (update,
  curate, store/duplicate)
• To increase resources for e-science environments
  when needed
• To enable specific heavy computing or data
  production projects (Decrypthon)

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The situation in Europe

• Several e-science projects are developing high
  level e-science environments under adoption by
  the biology community
• Grid infrastructures (EGEE, DEISA) are now
  providing robust computing and growing data
  management services
• Two projects are exploring the interface between
  e-science and grid infrastructures for life
  science Embrace and BioinfoGRID

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Introduction

• EMBRACE is a EU-sponsored Network of Excellence
  aimed at enabling bioinformatics research through
  better operability of databases, servers, and
  services

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Example

• You want to predict phosphorylation sites just
  outside
• transmembrane helices in 1329 membrane proteins.
• Yesterday
• 1) Obtain software to predict transmembrane
  helices
• 2) Obtain software to predict phosphorylation
  sites
• 3) Install both programs
• 4) Write software that calls both programs
• 5) Write software that combines outputs and
  presents results.
• Tomorrow
• Import APIs for the two services
• Write software that combines outputs and presents
  results.

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Data

• EMBRACE includes nearly all European
  bioinformaticians with longstanding track-records
  in terms of providing databases, servers, and
  services.
• Data types that they will make available
• DNA sequences,
• protein sequences, macromolecular structures,
  SNPs,
• expression information, alignments,
  untranslated regions,
• structure domains, protein families,
  literature, electron
• micrographs, orthologs, ORFs, genome
  annotation,
• proteomics patterns, GPCRs, protein
  interactions, nucleotid

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Software

• EMBRACE includes nearly all large European
  bioinformatics centers that all will make their
  servers, services, and computational tools
  available using the EMBRACE-GRID.
• Computational facilities that all European
  bioinformaticians will get at
• their finger tips include
• DNA sequence analysis,
• genome annotation, homology searches at
  sequence and
• structure level, structure analysis,
  visualization, protein
• sequence analysis, phylogeny, protein domain
  mapping,
• pattern matching, HMM, neural nets,
  micro-arrays, workflow
• management, text-mining, systems biology,
  database techno

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Contact

• EMBRACE is coordinated by Graham Cameron
• and Kerstin Nyberg at the EBI.
• Peter Rice coordinates the content integration
• Alan Bleasby coordinates the tools integration
• Vincent Breton coordinates technology
  recommendation
• Erik Bongcam Rudloff coordinates the test cases
• Gert Vriend coordinates outreach and education

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Recommendation web service technology
Application
User interface
Application interface
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Embrace grid

• Develop standard web service interfaces to tools
  and data bases
• Provide a workbench (Taverna) to exploit these
  tools and data (-gt T. Oinn talk)
• Support data base providers in accessing grid
  infrastructures for resources and grid services
• Pioneers Swiss Institute of Bioinformatics, CMBI
  (Netherland)
• Creation of an Embrace VO on EGEE
• Develop interfaces between the e-science
  environments and the grid infrastructure
• Issues web service interface to grid services

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Refinement of Protein structures

• Project led by Gert Vriend (CMBI, Niejmegen, NL)
• Goal recalculate the 3D structures of the 40000
  proteins stored in PDB with improved image
  reconstruction algorithm
• Estimated computing need 4 CPU years
• Status under deployment on the Embrace EGEE VO

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BioinfoGRID Objective

• BioinfoGRID project aims at deploying
  bioinformatics applications on existing grid
  infrastructures (EGEE)

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Grid-enabled in silico drug discovery
Grid service customers
Chemist biologist teams
Check point
Check point
Check point
Biology teams
Selected hits
hits
In vitro tests
target
Grid infrastructure
Annotation services
Docking services
MD service
Grid service providers
Chimioinformatics teams
Bioinformatics teams
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Molecular Dynamics (MD) simulation on the grid

• Choice of Amber as MD software
• MMPBSA procedure developed by G. Rastelli (Univ.
  Modena)
• Licensing issues adressed
• One license per grid site deploying Amber
• Use of Amber restricted to grid users coming from
  institutes owning a license
• Access granted to all the nodes where Amber is
  installed
• Deployment of MD calculations on EGEE
• Reranking of the 2500 best hits coming out of the
  first WISDOM data challenge on malaria in
  February
• Selection of 100 best hits
• In vitro tests to start next month at Chonnam
  National University

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Conclusion

• Life science community is really involving two
  communities molecular biologists and
  bioinformaticians
• Both communities have different needs
• BIologists need high level e-science environments
• Bioinformaticians need also growing resources to
  maintain, updata and curate their data bases
• Several grid projects in Europe are targeting
  both communities
• Embrace
• BioinfoGRID
• Significant progresses are witnessed
• Still, need to develop web service interface to
  grid infrastructures to foster adoption

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Les objectifs de lexposé

• Expliquer larticulation entre les projets en
  Europe
• EGEE linfrastructure
• Les liens avec la communauté de bioinformatique
• BioinfoGRID utiliser la grille EGEE telle
  quelle est aujourdhui. Cela signifie demander à
  des biologistes et des bioinformaticiens de
  sadapter
• Embrace mon role est de construire le pont entre
  la culture actuelle de la communauté et les
  grilles actuelles.
• Notion de grid ecosystem
• Need for different services for the biology and
  bioinformatics community
• From MyGrid to EGEE
• Presentation dEMbrace
• Presentation de BioinfoGRID