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Open Science at Genome Scale

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Presentation given at the Survive or Thrive Workshop, Manchester in June 2010.

Presentation given at the Survive or Thrive Workshop, Manchester in June 2010.

Published in: Technology

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  • 1. UKOLN is supported by: Open Science at Genome Scale Dr Liz Lyon, Director, UKOLN, University of Bath, UK Associate Director, UK Digital Curation Centre Survive or Thrive Workshop, Manchester, June 2010 . This work is licensed under a Creative Commons Licence Attribution-ShareAlike 2.0
  • 2.
    • Scale, Complexity, Predictive Potential
    • Continuum of Openness
    • Citizen Science
    • Credentials, Incentives, Rewards
    • Institutional Readiness & Response
    • Data Informatics Capacity & Capability
    http://www.ukoln.ac.uk/ukoln/staff/e.j.lyon/publications.html#november-2009
    • Open Science at Web-Scale
    • Consultation:
    • Write-To-Reply
    • Keynote Presentations:
    • eResearch Australasia Nov 2009
    • CNI, Baltimore April 2010
    • http://www.ukoln.ac.uk/ukoln/staff/e.j.lyon/presentations.html
  • 3.  
  • 4. ...Next next generation technology race to market $1000 genome in <15 minutes ....by 2013?
  • 5. ...data deluge challenges....
    • Large-scale data storage that is:
      • Cost-effective (rent on-demand)
      • Secure (privacy and IPR)
      • Robust and resilient
      • Low entry barrier / ease-of-use
      • Has data-handling / transfer / analysis capability
    • Move sequencing out of genome centres
    • “ .... analyse an entire human genome in a single day sitting with a laptop at your local Starbucks. ”
    ...cloud services?
  • 6. Clients in the cloud
  • 7. The “new” genome informatics ecosystem The case for cloud computing in genome informatics. Lincoln D Stein, May 2010
  • 8. “ Data sets are becoming the new instruments of science”
  • 9. Post-genome decade Human genomes: >24 published & almost 200 unpublished
  • 10. “ P4 medicine : Predictive, Personalised, Preventive, Participatory.” Leroy Hood – Institute for Systems Biology
    • ...“medicine is going to become an information science”...
    Image from Scientific American
  • 11. P4 medicine
    • Each patient’s genome sequenced
    • Your genome is basis of your medical record
    • New method to anonymise medical records for genomics research at Vanderbilt Univ (April ‘10)
    • New predictive models of health and disease
    • Personalised treatments focus on preventative therapies
    Genome scale network biology Genomic data as a commodity
  • 12. They have shared their data….
  • 13. Share my data?
  • 14.
    • Sage Bionetworks : Integrative genomics
    • Open data in the Sage Commons repository
    • Human and mouse: clinical and genetics data
    • Develop predictive models of disease: liver / breast / colon cancer, diabetes, obesity
    • Crowd-sourced effort : global scope
    Stephen Friend
  • 15. Participatory medicine : Empowering the patient... Sage Congress San Francisco April 2010
  • 16. Calls for action, new metrics
  • 17. How to cite large-scale predictive network models?
    • Incentivise: get credit
    • Attribution granularity
    • Multiple data sources & standards
    • Linked data approach
    • Workflow integration
    • Curate the data......
  • 18. Human Genome printed http://www.flickr.com/photos/johnjobby/2252981353/sizes/l/ Discuss....
    • Scaleable data infrastructure?
    • Personal genomics - share your data?
    • Transform 21stC medicine / bioscience?
    • Credit & attribution for data and models?