3. What is the real problem?
• Profit margin too low?
• No one willing to pay?
• No one able to pay?
• Internal research costs too high?
• Low hanging fruit picked?
• Genome has not delivered?
• Companies can’t execute on strategy?
• Regulatory hurdles too high?
• Clinical trials too difficult and expensive?
In fact, all are true but none is the real problem
4. the real problem
• We need to rebuild the drug discovery
process so that we better understand
disease biology
• We need to reshape the way researchers,
citizens, companies and funders interact
7. The opportunity
• Stunning technologies are generating heaps of
genomic and clinical data
• Bionetworks using integrative genomic approaches
can highlight the non-redundant components-
can find drivers of the disease and of therapies
• Need to develop ways to host massive amounts of
data, evolving representations of disease as
represented by these probabilistic causal disease
models
8. Network biology collaborations involve multiple
specialized labs, big data, sophisticated methods and
the results are often published in open access journals
Collaboration
- Multiple labs; specialized;
- Biologists, clinicians,
statisticians, engineers, etc
Technology
- Sophisticated technologies
Data
- >5x108 data points
Methods
- Computationally intensive
(5000 node cluster)
Publish
- Open access journal
- 18 figures, 19 tables
- Gigabytes of data
9. Catalytic nonprofit formed in 2009
Vision: to create a “Commons” where
integrative bionetworks are evolved
by contributor scientists with a shared
vision to accelerate the elimination of
human disease
10. Principles
Understanding human biology requires a new community-based vision of open access innovation that
respects and links all stakeholders and supports a new culture of cooperative, data-intensive science.
We pledge to take up this challenge and have drafted the Sage Bionetworks Commons Principles to guide
the development of an open source community where computational biologists can develop and test
competing models built from common resources.
1. The purpose of the Commons is to expedite the pathway to knowledge,
treatment, and prevention of disease.
2. We will promote collaborative discovery through the creation and support of a
broadly accessible digital Commons consisting of curated data and methodological tools in
which analytical results are shared in a transparent, open fashion.
3. The Commons will respect the rights and interests of all contributors
including individuals from whom data are derived, researchers who collect and analyze data,
and scientists and physicians who develop and implement healthcare advances. Those not
respecting these rights will be excluded from the Commons.
4. Contributions to the Commons shall be appropriately acknowledged and
attributed.
5. The Commons will promote data and tool sharing and distribution using standards that
enable efficient reuse, compilation and comparison.
6. The Commons will hold no intellectual property rights in, and will not permit
encumbrances on, data and other elements within the Commons. This will not, however,
preclude individuals from protecting new goods and services developed using data and other
elements from the Commons.
11. What is Sage Bionetworks? - People
• Stephen Friend, MD, PhD
• Jonathan Derry, PhD >20 research scientists with
Rosetta • Adam Margolin, PhD
PhDs/MDs.
• Jonathan Izant, PhD
Inpharmatics, • Solly Sieberts, PhD
• Xia Yang, PhD 537 peer-reviewed scientific
Merck & Co • Eric Huang, MD PhD
publications.
• Christine Suver, PhD
University of Washington
Research
• Thea Norman, PhD
Duke University • Zhi Wang, PhD 385 combined years of
• Chris Gaiteri, PhD biomedical research
Broad Institute of MIT and Harvard • Charles Ferte, MD PhD
• Elias Neto, PhD
experience in academia and
B&M Gates Foundation industry.
• Lara Mangravite, PhD
Jackson Labs • Justin Guinney, PhD
• Qingying Meng, PhD 7 software engineers.
------
University of California Davis • Mette Peters, PhD
University of Michigan • Vitalina Komashko, PhD
• Brig Mecham, PhD 90 years of industry
Ambryx • Andrew Twister, MD PhD experience: Deployment of
Software
University of Pittsburgh • Matt Furia professional software
• Brian Bot applications to over 100
Mayo Clinic • In Sock Jang, PhD
million users.
University of Wisconsin
• Mike Kellen, PhD
Children’s Hospital of Oakland Institute • Nicole Deflaux, PhD 5,000 node in-house
• Bruce Hoff, PhD
Columbia University supercomputer cluster, and
• Dave Burdick
• John Hill tight integration with cloud-
Institute for Systems Biology
• Xa Schildwachter compute vendors.
Teranode • Brian Holt
Amazon
12. What is Sage Bionetworks? - Partners
Funders &
Nonprofits
Pharma
& IT
Research
Partners
13. Synapse
Sage Synapse : Contribute to the Cure http://synapse.sagebase.org/
• Open computational resource offering network
models of disease and the underlying datasets
REGISTER LOGIN
and algorithms used to construct them.
WELCOME TO SYNAPSE
Synapse is an online community built for a new biology... more open, more collaborative, more data-driven, and more reproducible. • Synapse integrates a data and network
repository, the IT infrastructure in which the data
are housed and the tools that allow manipulation
Everything SEARCH
Development Update
Synapse is currently in Alpha development. This prototype has been developed to
demonstrate our vision for the technology and solicit feedback from the community.
The ability to create accounts and download Sage-hosted data is operational now.
Call for ALPHA USERS
Are you interested in working with Sage to start a pilot project on Synapse? Please let
us know at synapseInfo@sagebase.org
and analysis.
Some of the other functionality of the site is still under development. CREATE AN ACCOUNT
Projects in the
Spotlight
FEDERATION AGING SAGEBIOCURATION START YOUR OWN
• Synapse is an innovation space where
researchers can compute and collaborate on
Project spotlight description... PROJECT PROJECT!
The Sage Bio Curation project is an
The Federation Aging project is umbrella for all Sage Bionetworks- Get started using Synapse today by
exploring the large effect of age on curated projects. creating your own Project.
START A PROJECT
human gene expression by
genomic datasets, use tools to build models of
exploring a set of genes whose
expression levels are tightly
associated with age.
Synapse News Top Synapse Contributors
human disease, and modify those built by others.
What's happening on Synapse Synapse users who are actively contributing data
New Normalization Analysis Charles Sawyers et al, MSKCC
• Contributors are active participants that build
12-Apr-2011: A new analysis method for Schadt's New Diabetes Model DNA copy number, mRNA expression profiles, candidate gene resequencing, and
normalizing data was published by Brig 08-Apr-2011: Eric Schadt and colleagues clinical traits from 218 prostate tumors.
Mecham. have published an article on a new model for
diabetes. Amanda Myers, University of Miami
collective content in effect ‘crowdsourcing’ the
Genotypes, mRNA expression profiles, and clinical traits from 176 Alzheimer
disease and 188 non-diseased brain samples.
Beatriz Carvalho & Gerrit Meijer, VUMC
evolution of disease models creating an
DNA copy number, mRNA expression, and tumor traits from 36 colorectal
adenocarcinoma and 33 adenoma tumors.
See all contributors...
WITH SUPPORT FOLLOW CONTACT INFO
accelerated mechanism for the dissemination of
knowledge.
FROM US ON Sage Bionetworks
1100 Fairview Ave N
Seattle, WA 98109
synapseInfo@sagebase.org
Copyright 2011 Sage Bionetworks Home / Privacy Policy / Platform support / Creative Commons License / FAQ / Submit feedback
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14. “WE CONSENT”
Portable Legal Consents
Compliant and standardized
tool for engaging with
and empowering citizens
and patients
16. Clinical Trial Comparator Arm
Partnership (CTCAP)
Description: Collate, Annotate, Curate and Host Clinical
Trial Data with Genomic Information from the Comparator
Arms of Industry and Foundation Sponsored Clinical Trials:
Building a Site for Sharing Data and Models to evolve
better Disease Maps.
Public-Private Partnership of leading pharmaceutical
companies, clinical trial groups and researchers.
Neutral Conveners: Sage Bionetworks and Genetic
Alliance [nonprofits].
Initiative to share existing trial data (molecular and
clinical) from non-proprietary comparator and placebo
arms to create powerful new tool for drug development.
Started Sept 2010
16
17. The Federation Experiment
Stephen Friend
Sage Bionetworks
Andrea Califano
Columbia U.
Gary Nolan Eric Schadt
Stanford Mount Sinai
Trey Ideker
UCSD
20. Lessons
• Building transformative technology
is (relatively) easy
• Transforming people is hard