eResearch South Workshop

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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 .
UKOLN is supported by
This work is licensed under a Creative Commons
LicenceAttribution-ShareAlike 2.0
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http//www.ukoln.ac.uk/ukoln/staff/e.j.lyon/public
ations.htmlnovember-2009

• Open Science at Web-Scale

1. Scale, Complexity, Predictive Potential
2. Continuum of Openness
3. Citizen Science
4. Credentials, Incentives, Rewards
5. Institutional Readiness Response
6. Data Informatics Capacity Capability

• Consultation
• Write-To-Reply

• Keynote Presentations
• eResearch Australasia Nov 2009
• CNI, Baltimore April 2010

• http//www.ukoln.ac.uk/ukoln/staff/e.j.lyon/presen
  tations.html

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1000 genome in lt15 minutes ....by 2013?
...Next next generation technology race to market
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...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?
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Clients in the cloud
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The new genome informatics ecosystem The case
for cloud computing in genome informatics.
Lincoln D Stein, May 2010
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Data sets are becoming the new instruments of
science
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Post-genome decade
Human genomes gt24 published almost 200
unpublished
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P4 medicine Predictive, Personalised,
Preventive, Participatory.Leroy Hood
Institute for Systems Biology
Image from Scientific American

• ...medicine is going to become an information
  science...

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P4 medicine

• Each patients 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
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They have shared their data.
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Share my data?
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Stephen Friend

• 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

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Participatory medicine Empowering the
patient...
Sage Congress San Francisco April 2010
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Calls for action, new metrics
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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......

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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?