A centre of expertise in digital information management UKOLN is supported by: Open Science at...

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

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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24 published &almost 200 unpublished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?