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ISBE An infrastructure for European (systems) biology

ISBE An infrastructure for European (systems) biology. Martijn J. Moné. Seqahead meeting “ ICT needs and challenges for Big Data in the Life Sciences ” Pula, Italy | June 6, 2013. Background. Rationale.

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ISBE An infrastructure for European (systems) biology

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  1. ISBEAn infrastructure for European (systems) biology Martijn J. Moné Seqahead meeting “ICT needs and challenges for Big Data in the Life Sciences” Pula, Italy | June 6, 2013

  2. Background Rationale • The amount of detailed data and information on components of living systems continues to increase • But our ability to understand dynamic interactions within systems remains a challenge • It has not been possible to tackle these challenges effectively because of: • Technical limitations • Limited access to a small number of specialist groups

  3. The Opportunity Rationale • This situation is now rapidly changing • So, it is now timely to develop an infrastructure to coordinate the distributed European research effort in Systems Biology

  4. Why now? Rationale • High-speed DNA sequencing • NGS • Powerful computers • Broadband networks • The Internet • The influence of engineering, physical science, computer science, mathematics

  5. ISBE Rationale • Will enable researchers to address how the interaction of biological components leads to the functioning of living organisms in constantly changing environments • Create models of living organisms at various scales representing these interactions • Exploit this information to generate major socio-economic benefits in areas including health, agriculture, environment

  6. ISBE The Facility • Objective 1 • Interconnect hubsoftechnological excellence in systemssiology • throughofferingthebest in European researchexpertise, andexperimentalandmodellingfacilities, necessaryforsystemsbiology • Objective 2 • Establishandmakeavailablerepositoriesofdataandmodels • Objective 3 • Enable (real-time) connectionswithinandbetweencomponents 1 and 2 andwithexternaluserlaboratories • This will bedoneasmuchaspossiblethroughtheprovisionof high performanceconnectionstoexisting high capacitynetworkinfrastructures

  7. ISBE The Facility

  8. Centres (or Nodes / Hubs) The Facility • Hubs will contribute specific skills and expertise to functional clusters focussed on a variety in an operational matrix • Some Hubs may have groups that participate in different and/or multiple clusters

  9. Facilitate Interaction The Facility • The aim will be to facilitate efficient interaction with the substantial technology development efforts (relevant to systems biology) already funded by national and EU programmes • ISBE will enable all European laboratories to model and conduct experiments and undertake essential activities remotely – where they cannot be done locally

  10. Status of the Project Status • The 3-yr Preparatory Phase started in Aug 2012 • The work packages include: • Project management and co-ordination • Model and data management • Overall infrastructure, eligibility and accessibility • Data generation • Community building and synergies • Strategy, vision and advocacy • Modelling infrastructure and expertise • Technology and science watch • Training and education • Funding, governance and legal • Connections • Innovation, impact and exploitation

  11. Challenges • Complexity of the project • Interface between WPs • Interfacing with other research infrastructures • Engagement with stakeholders

  12. Challenges Connecting the nodes • Data generation: • High throughputofimaging/anatomicalinformation • Integration ofotherlevelsofinformationintomolecularmodels • Standards, SOPs • Data analysis/stewardship: • Automation ofdataanalysis • Training for non-bioinformaticians • Data integration/modeling: • Toolbox for non-SBists, modelrepository • Model building, couplingofscales (temporal, spatial) • Support forplanningandgenerationofappropriatedata

  13. Challenges Connecting all the nodes • to define and design all possible connections between ISBE nodes that will promote European systems biology • to design interfaces among all ISBE nodes that enable (computer assisted) connecting •  to design ways in which large systems biology tasks can be partitioned over nodes and the results reintegrated

  14. Single point of entry/exit Modelling-centric e.g. ELIXIR DSCs DGCs DGCs DIC

  15. ISBE nodes and connections Connections – Nodes (or node collectives) Generation Generation Generation Stewardship Integration

  16. ISBE nodes and connections Reinforcement by output OUTPUT

  17. Data integration vision Connecting data, models and expertise • ISBE as the driver of (a) visionary project(s) with great scientific and societal impact. • ISBE + main driver would serve – and transform – life sciences. • Virtual maize, virtual yeast, virtual human • Can draw from the same resources

  18. Thank you!See us at ICSB 2013 – Copenhagen 30/8 - 3/9 • Martijn Moné, Hans Westerhoff • VU University Amsterdam

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