leveraging the web to make science more collaborative

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

brian.bot@sagebase.org @BrianMBot

Synapse engineering team

Michael Kellen, Director Christopher Bare Marcel Blonk John Hill Jay Hodgson Bruce Hoff Xavier Schildwachter