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UKOLN is supported  by: Open Science at Genome Scale Dr Liz Lyon,  Director, UKOLN, University of Bath, UK Associate Direc...
<ul><li>Scale, Complexity, Predictive Potential  </li></ul><ul><li>Continuum of Openness </li></ul><ul><li>Citizen Science...
 
...Next next generation technology race to market $1000 genome in <15 minutes ....by 2013?
...data deluge challenges.... <ul><li>Large-scale data storage that is: </li></ul><ul><ul><li>Cost-effective (rent on-dema...
Clients in the cloud
The “new” genome informatics ecosystem  The case for cloud computing in genome informatics.  Lincoln D Stein, May 2010
“ Data sets are becoming the  new instruments of science”
Post-genome decade Human genomes: >24  published & almost 200 unpublished
“ P4 medicine : Predictive, Personalised, Preventive, Participatory.” Leroy Hood –  Institute for Systems Biology <ul><li>...
P4 medicine <ul><li>Each patient’s genome sequenced </li></ul><ul><li>Your genome is basis of your medical record </li></u...
They have shared their data….
Share  my  data?
<ul><li>Sage Bionetworks : Integrative genomics </li></ul><ul><li>Open data in the Sage Commons repository </li></ul><ul><...
Participatory medicine : Empowering the patient... Sage Congress  San Francisco April 2010
Calls for action, new metrics
How to cite large-scale predictive network models? <ul><li>Incentivise: get credit  </li></ul><ul><li>Attribution granular...
Human Genome printed   http://www.flickr.com/photos/johnjobby/2252981353/sizes/l/ Discuss.... <ul><li>Scaleable data infra...
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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.

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Transcript of "Open Science at Genome Scale"

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