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 Licence
Attribution-ShareAlike 2.0
www.ukoln.ac.uk
A centre of expertise in digital information management
http://www.ukoln.ac.uk/ukoln/staff/e.j.lyon/publications.html#november-2009
•Open Science at Web-Scale
1.
2.
3.
4.
5.
6.
Scale, Complexity, Predictive Potential
Continuum of Openness
Citizen Science
Credentials, Incentives, Rewards
Institutional Readiness & Response
Data Informatics Capacity & Capability
•Keynote Presentations:
•eResearch Australasia Nov 2009
•CNI, Baltimore April 2010
•Consultation:
•Write-To-Reply
•http://www.ukoln.ac.uk/ukoln/staff/e.j.lyon/presentations.html
$1000 genome in <15 minutes ....by 2013?
...Next next generation technology race to market
...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unpublished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
therapies
Genome scale network biology
Genomic data as a commodity
They
have
shared
their
data….
Share
my
data?
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
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?