leveraging the web to make science more collaborative
TRANSCRIPT
Synapseleveraging the web to make science more collaborative
brian m. bot | sage bionetworks | @BrianMBot
sage bionetworks35 FTEs - hiring 5 additional
1/2 research - 1/3 platform - 1/6 leadership & support
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
sage bionetworksfocused on a world where biomedical research
will fundamentally change to be more open and collaborative
open
sage bionetworksfocused on a world where biomedical research
will fundamentally change to be more open and collaborative
open
sage bionetworks
access
focused on a world where biomedical research will fundamentally change to be more open and collaborative
sage bionetworks
accessibility
focused on a world where biomedical research will fundamentally change to be more open and collaborative
open
sage bionetworks
access
focused on a world where biomedical research will fundamentally change to be more open and collaborative
open
sage bionetworksfocused on a world where biomedical research
will fundamentally change to be more open and collaborative
open
sage bionetworks
data
focused on a world where biomedical research will fundamentally change to be more open and collaborative
open
sage bionetworks
science
focused on a world where biomedical research will fundamentally change to be more open and collaborative
sage bionetworks
science
focused on a world where biomedical research will fundamentally change to be more open and collaborative
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
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
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
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
sage bionetworksa 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
sage bionetworksa 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 Governancea complete process
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
sage bionetworks
supports communities of researchers working collaboratively across disciplines
CRC Subtyping Consortium
DREAM ChallengesProgenitor Cell Biology Consortium
TCGA Pan-Cancer Consortium
CommonMind Consortium
PsychENCODE
Accelerating Medicines Partnership
Resilience Project
Influenza Vaccinations
Dengue FeverPsychosis Spectrum Disorder
Oncology Molecular ClassifiersNext Gen Scientific Publishing
Mozilla Science Labs
sage bionetworks
DREAM Challenges
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)
DREAM Challenges
17 April 2013
DREAM Challenges
CRC Subtyping Consortium
DREAM ChallengesProgenitor Cell Biology Consortium
TCGA Pan-Cancer Consortium
CommonMind Consortium
PsychENCODE
Accelerating Medicines Partnership
Resilience Project
Influenza Vaccinations
Dengue FeverPsychosis Spectrum Disorder
Oncology Molecular ClassifiersNext Gen Scientific Publishing
Mozilla Science Labs
sage bionetworks
Accelerating Medicines Partnership
public / private partnership between NIH, 10 biopharmaceutical companies
and several non-profit organizations
Accelerating Medicines Partnership
biopharmaAbbVie
Biogen Idec Bristol-Myers Squibb
GlaxoSmithKline Johnson & Johnson
Lilly Merck Pfizer Sanofi Takeda
non-profitAlzheimer’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
Accelerating Medicines Partnership
($ Millions) Total Project Total NIH Total
IndustryAlzheimer’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
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
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
Accelerating Medicines Partnership
Accelerating Medicines Partnership
CRC Subtyping Consortium
DREAM ChallengesProgenitor Cell Biology Consortium
TCGA Pan-Cancer Consortium
CommonMind Consortium
PsychENCODE
Accelerating Medicines Partnership
Resilience Project
Influenza Vaccinations
Dengue FeverPsychosis Spectrum Disorder
Oncology Molecular ClassifiersNext Gen Scientific Publishing
Mozilla Science Labs
sage bionetworks
TCGA Pan-Cancer Consortium
18NPG papers
68core projects248
researchers
28institutions
1070datasets1723
results
TCGA Pan-Cancer Consortium
TCGA Pan-Cancer Consortium
Cyriac Kandoth
TCGA Pan-Cancer Consortium
doi:10.7303/syn1710680.4
CRC Subtyping Consortium
DREAM ChallengesProgenitor Cell Biology Consortium
TCGA Pan-Cancer Consortium
CommonMind Consortium
PsychENCODE
Accelerating Medicines Partnership
Resilience Project
Influenza Vaccinations
Dengue FeverPsychosis Spectrum Disorder
Oncology Molecular ClassifiersNext Gen Scientific Publishing
Mozilla Science Labs
sage bionetworks
CRC Subtyping Consortium
CRC Subtyping Consortium
A
B
C
D
E
F
1
2
3
4
5
6
groups datasets subtypes
CRC Subtyping Consortium
A
B
C
D
E
F
1
2
3
4
5
6
groups datasets subtypes
…
collaborative analyses
cloud-based file storage
CRC Subtyping Consortium
code associatedwith results
CRC Subtyping Consortium
CRC Subtyping Consortium
Synapseleveraging the web to make science more collaborative
brian m. botm1-a111
[email protected] @BrianMBot
Synapse engineering team
Michael Kellen, Director Christopher Bare Marcel Blonk John Hill Jay Hodgson Bruce Hoff Xavier Schildwachter