enabling communities of researchers working together across institutional boundaries

brian m. bot | sage bionetworks | @BrianMBot

mayo clinic - 2015 jan 28

enabling communities of researchers working together across institutional boundaries

sage bionetworks~40 FTEs

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

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

open

sage bionetworks

open 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

sage bionetworks

open access

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

sage bionetworks

open 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

a non-profit organization which pilots a variety of components that are necessary to build a scientific research commons

tool for collaborative

science

re-imagined informed consent

patients as

partners

sage bionetworks

a non-profit organization which pilots a variety of components that are necessary to build a scientific research commons

enables sharing of all resources (data, code, results) and their relationships to one another

provides mechanism to communicate in real time instead of only at time of publication

supports open scientific collaborations for clear, reproducible science

sage bionetworks

a non-profit organization which pilots a variety of components that are necessary to build a scientific research commons

enables sharing of all resources (data, code, results) and their relationships to one another

sage bionetworks

a non-profit organization which pilots a variety of components that are necessary to build a scientific research commons

sage bionetworks

open RESTful APIs

www.synapse.org

programmatic clients

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 bionetworks

User registration/certification User agreement to

Terms and Conditions of Use Data Use Procedure Data privacy Policy

User certification

Removal of direct identifiers Tier access Login requirement, encryption in and out, firewalls IT policy Training- Auditing- Monitoring Consequences for violation (intentional or not)

Synapse Governancea complete process

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

“biomedical research needs to empower patients with the voice and the tools they need to manage their health, understand their disease and partner in research”

a non-profit organization which pilots a variety of components that are necessary to build a scientific research commons

sage bionetworks

patients as partners

a non-profit organization which pilots a variety of components that are necessary to build a scientific research commons

sage bionetworks

“participants will be provided real-time graphical representations of their data, access to their own data at

will (to provide to healthcare professionals, donate to other studies, etc.), and also research notifications when new

insights are available”

sharing two ways

a non-profit organization which pilots a variety of components that are necessary to build a scientific research commons

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

a non-profit organization which pilots a variety of components that are necessary to build a scientific research commons

written by a doctor reviewed by a lawyer edited by a committee

sage bionetworks

a non-profit organization which pilots a variety of components that are necessary to build a scientific research commons

interaction design prioritizes the user and the experience

patient-centered consent (pcc) toolkit

sage bionetworks

a non-profit organization which pilots a variety of components that are necessary to build a scientific research commons

deploy consent as a process via mobile, web

patient-centered consent (pcc) toolkit

sage bionetworks

a non-profit organization which pilots a variety of components that are necessary to build a scientific research commons

assist informedness for complex documents

patient-centered consent (pcc) toolkit

sage bionetworks

icons representing concepts

a non-profit organization which pilots a variety of components that are necessary to build a scientific research commons

patient-centered consent (pcc) toolkit

sage bionetworks

sage bionetworks

metadata&

survey&

sensor&tasks&

wearables&

Consent&Toolkit&

Bridge&Server&

Synapse&

Stores&study&data&Assigns&study&code&De<iden=fies&&Syndicates&

Consent&Data&capture&No=fica=ons&

Study<specific&folder&Auto<deposit&aAer&embargo&period&Authorized&users&

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

end game is not collaboration

supports communities of researchers working collaboratively across disciplines

do good research

supports communities of researchers working collaboratively across disciplines

impact on health

collaboration around common data

collaboration around common question

“systematic exploration of the entire spectrum of genomic changes involved in

more than 20 types of human cancer”

TCGA Pan-Cancer Consortium

analysis of: 12 tumor types 6 molecular profiling platforms

18NPG papers

68core projects248

researchers

28institutions

1070datasets1723

results

TCGA Pan-Cancer Consortium

TCGA Pan-Cancer Consortium

TCGA Pan-Cancer Consortium

doi:10.7303/syn1710680.4

TCGA Pan-Cancer Consortium

CommonMind Consortium

large public / private partnership

phase I: prefrontal cortex

~300 SCZ, 300 control, 60 BD

processing pipelines developed in collaboration between sage and mssm

public release: February 2015

CommonMind Consortium

public release: February 2015

CommonMind Consortium

public release: February 2015

CommonMind Consortium

public release: February 2015

collaboration around common data

collaboration around common question

CRC Subtyping Consortium

A

B

C

D

E

F

1

2

3

4

5

6

CRC Subtyping Consortiumexpert team data subtype

A

B

C

D

E

F

1

2

3

4

5

6

...

CRC Subtyping Consortiumexpert team data subtype

CRC Subtyping Consortium

collaborative analyses

cloud-based file storage

CRC Subtyping Consortium

code associated with results

CRC Subtyping Consortium

CRC Subtyping Consortium

collaboration around common data and question

public / private partnership between NIH, 10 biopharmaceutical companies

and several non-profit organizations

Accelerating Medicines Partnership

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

mt sinai mayo / ufl / isb

broad / rush emory

integrated network analysis target discovery

300 case-control rnaseq, genotype, clinical

1000 case-control rnaseq, methylation, genotype, clinical

300 ad, tauopathy, control rnaseq, clinical

200 AD, MCI, control Proteomic, clinical data

Accelerating Medicines Partnership

iPS neurons and astrocytes Mouse hippocamal slices Drosophila model

Genetic analysis aB and Tau mouse models rAAV delivered models

Proteomics Cultured neurons & astrocytes iPS compound screens

Proteomics Cell Culture, Mouse Models Drosophila model

mt sinai mayo / ufl / isb

broad / rush emory

target validation

2

3

5

12

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

AMP-AD Collaborative

Workspace

Quarterly Depositions

Broad/RUSH

Mt. Sinai

U Fl/ISB/Mayo

Emory

Sage

Other Partners

Individual Partner Workspaces AMP-AD Data Portal

Consortium Space

Public space

AMP-AD Synapse Project Structure

increasingly decentralized research ecosystem

democratization of research

cloud infrastructure

gov’t agencies and public pushing for > sharing

increasingly decentralized research ecosystem

mayo clinic - 2015 jan 28

brian m. bot ——————

brian.bot@sagebase.org @BrianMBot

sage bionetworks

enabling communities of researchers working together across institutional boundaries