20140813 FHCRC

1. Synapse
leveraging the web to make science more collaborative
brian m. bot | sage bionetworks | @BrianMBot

2. sage bionetworks
35 FTEs - hiring 5 additional
1/2 research - 1/3 platform - 1/6 leadership & support

3. sage bionetworks
a non-profit organization which pilots a
variety of components that are necessary
to build a scientific research commons
focused on a world where biomedical research
will fundamentally change to be
more open and collaborative
supports communities of researchers
working collaboratively across disciplines

4. sage bionetworks
focused on a world where biomedical research
will fundamentally change to be
more open and collaborative

5. open
sage bionetworks
focused on a world where biomedical research
will fundamentally change to be
more open and collaborative

6. open
sage bionetworks
access
focused on a world where biomedical research
will fundamentally change to be
more open and collaborative

7. sage bionetworks
accessibility
focused on a world where biomedical research
will fundamentally change to be
more open and collaborative

8. open
sage bionetworks
access
focused on a world where biomedical research
will fundamentally change to be
more open and collaborative

9. open
sage bionetworks
focused on a world where biomedical research
will fundamentally change to be
more open and collaborative

10. open
sage bionetworks
data
focused on a world where biomedical research
will fundamentally change to be
more open and collaborative

11. open
sage bionetworks
science
focused on a world where biomedical research
will fundamentally change to be
more open and collaborative

12. sage bionetworks
science
focused on a world where biomedical research
will fundamentally change to be
more open and collaborative

13. sage bionetworks
a non-profit organization which pilots a
variety of components that are necessary
to build a scientific research commons
focused on a world where biomedical research
will fundamentally change to be
more open and collaborative
supports communities of researchers
working collaboratively across disciplines

14. sage bionetworks
tool for
collaborative
science
re-imagined
informed
consent
patients
as
partners
a non-profit organization which pilots a
variety of components that are necessary
to build a scientific research commons

15. sage bionetworks
enables sharing of all resources (data, code, results)
and their relationships to one another
multi-channel communication
instead of uni-directional broadcasting
aides in reproducibility by
enabling communication throughout the research process
not only at time of publication
a non-profit organization which pilots a
variety of components that are necessary
to build a scientific research commons

16. sage bionetworks
distributed & versioned file system
rich annotations (metadata)
customizable schemas for structured data
agnostic to storage solution (cloud, local server, etc.)
wiki authoring
access controls (share whatever with whomever)
a non-profit organization which pilots a
variety of components that are necessary
to build a scientific research commons

17. sage bionetworks
a non-profit organization which pilots a
variety of components that are necessary
to build a scientific research commons
open RESTful APIs
www.synapse.org
programmatic clients

18. sage bionetworks
a non-profit organization which pilots a
variety of components that are necessary
to build a scientific research commons
User
registra*on/cer*fica*on
User
agreement
to
Terms
and
Condi*ons
of
Use
Data
Use
Procedure
Data
privacy
Policy
Removal
of
direct
iden*fiers
Tier
access
Login
requirement,
encryp*on
in
and
out,
firewalls
IT
policy
Training-­‐
Audi*ng-­‐
Monitoring
Consequences
for
viola*on
(inten*onal
or
not)
Synapse Governance
a complete process

19. sage bionetworks
a non-profit organization which pilots a
variety of components that are necessary
to build a scientific research commons
focused on a world where biomedical research
will fundamentally change to be
more open and collaborative
supports communities of researchers
working collaboratively across disciplines

20. sage bionetworks
supports communities of researchers
working collaboratively across disciplines

21. CRC Subtyping Consortium
DREAM Challenges
Progenitor Cell Biology Consortium
TCGA Pan-Cancer Consortium
CommonMind Consortium
PsychENCODE
Accelerating Medicines Partnership
Resilience Project
Influenza Vaccinations
Dengue Fever
Psychosis Spectrum Disorder
Oncology Molecular Classifiers
Next Gen Scientific Publishing
Mozilla Science Labs
sage bionetworks

22. DREAM Challenges

23. DREAM Challenges
Columbia Professor Dimitris Anastassiou
MPEG-2 compression of digital audio and video signals
Modules of co-expressed genes shared across cancers
Belief that these ‘attractors’ represent underlying biological
mechanisms (bioinformatic ‘hallmarks of cancer’1)
1D. Hanahan, R. A. Weinberg. Hallmarks of cancer: The next generation. Cell 144, 646–674 (2011)

24. DREAM Challenges
17 April 2013

25. DREAM Challenges

26. CRC Subtyping Consortium
DREAM Challenges
Progenitor Cell Biology Consortium
TCGA Pan-Cancer Consortium
CommonMind Consortium
PsychENCODE
Accelerating Medicines Partnership
Resilience Project
Influenza Vaccinations
Dengue Fever
Psychosis Spectrum Disorder
Oncology Molecular Classifiers
Next Gen Scientific Publishing
Mozilla Science Labs
sage bionetworks

27. Accelerating Medicines Partnership
public / private partnership between NIH,
10 biopharmaceutical companies
and several non-profit organizations

28. Accelerating Medicines Partnership
biopharma
AbbVie
Biogen Idec
Bristol-Myers Squibb
GlaxoSmithKline
Johnson & Johnson
Lilly
Merck
Pfizer
Sanofi
Takeda
non-profit
Alzheimer’s Association
Alzheimer’s Drug Discovery Foundation
American Diabetes Association
Arthritis Foundation
Foundation for the NIH
Geoffrey Beene Foundation
Juvenile Diabetes Research Foundation
Lupus Foundation of America
Lupus Research Institute/Alliance for Lupus Research
PhRMA
Rheumatology Research Foundation
USAgainstAlzheimer’s

29. Accelerating Medicines Partnership
($ Millions)
Total
Project
Total NIH
Total
Industry
Alzheimer’s
Disease
129.5 67.6 61.9
Type 2
Diabetes
58.4 30.4 28
Rheumatoid
Arthritis
41.6 20.9 20.7
TOTAL 229.5 118.9 110.6

30. Accelerating Medicines Partnership
cross-project data generation
shRNA
compounds
RNAi
human
mouse
drosophila
iPSC
RNA-seq
Whole exome
WGS
methylation
miRNA
proteomics
phenotypic measurements
modificationssystems data generation
X X

31. Accelerating Medicines Partnership
Target
Discovery
Target
Discovery
Target
Discovery
Target
Discovery
Target
Validation
Target
Validation
Target
Validation
Target
Validation
Shared
Information for
Target Identification
coordinate sharing of early-phase
target identification insights

32. Accelerating Medicines Partnership

33. Accelerating Medicines Partnership

34. CRC Subtyping Consortium
DREAM Challenges
Progenitor Cell Biology Consortium
TCGA Pan-Cancer Consortium
CommonMind Consortium
PsychENCODE
Accelerating Medicines Partnership
Resilience Project
Influenza Vaccinations
Dengue Fever
Psychosis Spectrum Disorder
Oncology Molecular Classifiers
Next Gen Scientific Publishing
Mozilla Science Labs
sage bionetworks

35. TCGA Pan-Cancer Consortium
18NPG papers
68core projects
248researchers
28institutions
1070datasets
1723results

36. TCGA Pan-Cancer Consortium

37. TCGA Pan-Cancer Consortium
Cyriac Kandoth

38. TCGA Pan-Cancer Consortium
doi:10.7303/syn1710680.4

39. CRC Subtyping Consortium
DREAM Challenges
Progenitor Cell Biology Consortium
TCGA Pan-Cancer Consortium
CommonMind Consortium
PsychENCODE
Accelerating Medicines Partnership
Resilience Project
Influenza Vaccinations
Dengue Fever
Psychosis Spectrum Disorder
Oncology Molecular Classifiers
Next Gen Scientific Publishing
Mozilla Science Labs
sage bionetworks

40. CRC Subtyping Consortium

41. CRC Subtyping Consortium
A
B
C
D
E
F
1
2
3
4
5
6
groups datasets subtypes

42. CRC Subtyping Consortium
A
B
C
D
E
F
1
2
3
4
5
6
groups datasets subtypes
…

43. collaborative analyses
cloud-based file storage
CRC Subtyping Consortium

44. code associated
with results
CRC Subtyping Consortium

45. CRC Subtyping Consortium

46. Synapse
leveraging the web to make science more collaborative
brian m. bot
m1-a111
brian.bot@sagebase.org
@BrianMBot
Synapse engineering team
Michael Kellen, Director
Christopher Bare
Marcel Blonk
John Hill
Jay Hodgson
Bruce Hoff
Xavier Schildwachter