Jonathan Izant Sage Bionetworks www.sagebase.org "Why we do it" Open Source Drug Discovery #oss2010
Mike Chelen,
Patricia F. Anderson,
joergkurtwegner,
Paul Bacchus,
Martin Fenner,
Open Science Info,
Deepak Singh,
Mr. Gunn,
Walter Jessen,
and
Jenny
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We don't yet know how to use genomics for drug development.
- Ruchira S. Datta
The pharma drug development pipeline is broken.
- Ruchira S. Datta
Standards of care are inadequate: people are getting treatments that aren't appropriate for them, with concomitant side effects.
- Ruchira S. Datta
We need to look in the mirror for blame: many of the blocks are in academia.
- Ruchira S. Datta
Oswald Avery found that DNA is the substance of genes, Watson & Crick solved the structure.
- Ruchira S. Datta
We used to focus on single genes. Gene regulation circa 1990: everyone looked at single gene pathways.
- Ruchira S. Datta
1996: See interconnecting pathways in Wnt gene regulatory network.
- Ruchira S. Datta
2002: See very complex system with many different genes. But now very confusing: for therapeutics, which is the correct target?
- Ruchira S. Datta
How is genomic data used to understand biology? GWAS identifies causative DNA variation but provides NO mechanism. Profiling approaches (microarrays) at genome scale provide correlates of disease, but what is cause and effect?
- Ruchira S. Datta
Biological systems are very flexible. They work around single perturbations.
- Ruchira S. Datta
Looking at integrating genetics approaches and clinical data.
- Ruchira S. Datta
Steven Friend started Rosetta Informatics, which was acquired by Merck. Integrate multiple Bayesian models to make predictive models of where to perturb for effective therapeutics.
- Ruchira S. Datta
Computationally intensive: keep updating Bayesian networks.
- Ruchira S. Datta
>60 publications over 5 years substantiating probabilistic causal bionetwork models. Use these to make detailed priority lists of what is important.
- Ruchira S. Datta
Cancer and metabolic diseases are very diverse among patients. Opportunity for individual medicine.
- Ruchira S. Datta
Mission of Sage Bionetworks is to create a Commons where integrative bionetworks are evolved by contributor scientists.
- Ruchira S. Datta
New non-profit, over a year. Lease offices at Fred Hutchinson Cancer Research Center. Now an NIH research center.
- Ruchira S. Datta
Small, plan to stay small. Rather, work with partners including commercial groups.
- Ruchira S. Datta
Many of the commercial groups are actually some of the best partners for open access sharing. E.g., Merck, Lilly have found very early stage research should be open--very difficult to value very early stage research.
- Ruchira S. Datta
See The Sage Commons website. Get highly annotated, globally coherent data with multiple layers of data.
- Ruchira S. Datta
Have datasets stratified in different stages.
- Ruchira S. Datta
Challenges from Sage Commons Congress (scientists, funders, policy experts, publishers): workgroups on Standards (data, annotation), Tools (combining, analyzing), Citation (recognition), Internationalization, Public Engagement
- Ruchira S. Datta
especially, how to engage patient advocacy groups
- Ruchira S. Datta
Many barriers to openness, trying to work through with partners
- Ruchira S. Datta
Problem: 'Accessible' data often isn't.
- Ruchira S. Datta
Checked the scientific social network of attendees at the Congress. Many hubs.
- Ruchira S. Datta
IT experts tended to collaborate w/ everyone; media, policy, funders weren't as interested in talking with them!
- Ruchira S. Datta
Biomedical research developed as a Cottage Industry.
- Ruchira S. Datta
Resulted in current complex ecosystem w/ FACULTY and TENURE.
- Ruchira S. Datta
Have rapid information transfer within labs, very slow between labs. This is costing lives.
- Ruchira S. Datta
Incentive issues. The Federation Experiment: fuse four research labs.
- Ruchira S. Datta
What about Stanford & The Mission Bay Campus? "New non-profit, over a year. Lease offices at Fred Hutchinson Cancer Research Center. Now an NIH research center"
- Attila Csordas
Attila, are they there too? Got no indication from the talk or their website.
- Ruchira S. Datta
Surprised that among all the meanings of SAGE from which Sage Bionetworks distinguishes themselves, no one mentioned the OSS math system http://www.sagemath.org Slogan similar in spirit: "instead of reinventing the wheel, let's build the car". Founder William Stein also now Seattle-based (fellow Berkeley math PhD).
- Ruchira S. Datta
Well, it's logical to assume that the sage guys want to expand to the Bay Area too :)
- Attila Csordas