Computational Infrastructures for Data and Knowledge Management in Systems Biology

  • Fotis Georgatos
  • Stéphane Ballereau
  • Johann Pellet
  • Moustafa Ghanem
  • Nathan Price
  • Leroy Hood
  • Yi-Ke Guo
  • Dominique Boutigny
  • Charles Auffray
  • Rudi Balling
  • Reinhard Schneider


The volume, complexity and heterogeneity of data originating from high throughput functional genomics technologies have created challenges and opportunities for Information technology (IT) departments. These increased demands have also led to increasing costs for IT infrastructure such as necessary computing power and storage devices, as well as further costs for manpower effort, required for maintenance. This chapter describes some of the challenges for computational analysis infrastructure, including bottlenecks and most pressing needs that have to be addressed to effectively support the development of systems biology and its application in medicine.


Bioinformatics Infrastructures Information technology Knowledge management Systems biology Translational research Data centers Storage Computational science Computational infrastructures Computing Scientific computing e-science Data management High performance computing Cluster Grid Desktop grid Cloud 



Three dimensional


Four dimensional typically 3D plus time dimension


Berkeley Open Infrastructure for Network Computing


European Council for Nuclear Research


Central Processing Unit


European Bioinformatics Institute


Enabling Grids for E-sciencE


European Grid infrastructure


European Life Sciences Infrastructure for Biological Information


European Molecular Biology Laboratory


FLoating-point Operations Per Second


Graphical Processing Unit


High Performance Computing


High Throughput Computing


Infrastructure as a Service


Information Technology


Input/Output—typically used in the context of software processing of data


Large Hadron Collider


Message Passing Interface


A collective term to refer to -omics keywords like metabolomics, genomics, proteomics etc.


Platform as a Service


Partnership for Advanced Computing in Europe


Return On Investment


Software as a Service


Systems Biology Markup Language


Worldwide LHC Computing Grid


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Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • Fotis Georgatos
    • 1
  • Stéphane Ballereau
    • 2
  • Johann Pellet
    • 2
  • Moustafa Ghanem
    • 3
  • Nathan Price
    • 4
  • Leroy Hood
    • 4
  • Yi-Ke Guo
    • 3
  • Dominique Boutigny
    • 5
  • Charles Auffray
    • 2
  • Rudi Balling
    • 1
  • Reinhard Schneider
    • 1
  1. 1.Luxembourg Centre for Systems BiomedicineUniversity of LuxembourgEsch-sur-AlzetteLuxembourg
  2. 2.European Institute for Systems Biology and Medicine—CNRS-UCBL-ENSUniversité de LyonLyonFrance
  3. 3.Department of ComputingImperial College LondonLondonUK
  4. 4.Institute for Systems BiologySeattleUSA
  5. 5.Centre de Calcul de l’IN2P3USR6402 CNRS/IN2P3Villeurbanne CedexFrance

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