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A centre of expertise in digital information management
www.ukoln.ac.uk
UKOLN is supported by:
Open Science at Genome Scale
Dr Liz Lyon, Director, UKOLN, University of Bath, UKAssociate Director, UK Digital Curation Centre
Survive or Thrive Workshop, Manchester, June 2010
.
This work is licensed under a Creative Commons LicenceAttribution-ShareAlike 2.0
1. Scale, Complexity, Predictive Potential 2. Continuum of Openness3. Citizen Science4. Credentials, Incentives, Rewards5. Institutional Readiness & Response6. 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
...Next next generation technology race to market
$1000 genome in <15 minutes ....by 2013?
...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?
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24 published &almost 200 unpublished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
Image from Scientific American
...“medicine is going to become an information science”...
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 therapiesGenome scale network biologyGenomic data as a commodity
They have shared their data….
Share my
data?
• 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
Participatory medicine :
Empowering the patient...
Sage Congress San Francisco April 2010
Calls for action, new metrics
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......
Human Genome printed http://www.flickr.com/photos/johnjobby/2252981353/sizes/l/
Discuss....1. Scaleable data infrastructure?
2. Personal genomics - share your data?
3. Transform 21stC medicine / bioscience?
4. Credit & attribution for data and models?