biomedical research in an increasingly digital world

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brian m. bot | sage bionetworks | @BrianMBot department of defense breast cancer research program vision setting meeting 2015 biomedical research in an increasingly digital world

Transcript of biomedical research in an increasingly digital world

brian m. bot | sage bionetworks | @BrianMBot

department of defense breast cancer research program vision setting meeting 2015

biomedical research in an increasingly digital world

biomedical research in an increasingly digital world

biomedical research in an increasingly digital world

6%

21%

8%

11%

54%cannot reproduce

can reproduce in principle

can reproduce w/discrepancies

can reproduce from processed data w/discrepancies

can reproduce partially

the status quo tolerates poor communication of findings

Ioannidis A. et al. Nature Genetics 2009

“Scientists often study the past as obsessively as historians because few

other professions depend so acutely on it. Every experiment is a conversation with

a prior experiment, every new theory a refutation of the old”

-Siddhartha Mukherjee, The Emperor of All Maladies

scientific method1. define a question

2. gather information and resources (background research)

3. form a hypothesis

8. retest (frequently done by other scientists)

4. test hypothesis experimentally

5. analyze experimental data

7. publish results

6. draw conclusions based on data

7. publish results

finitein

∞...

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

sage bionetworks

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

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

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

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

nouns and verbs

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

sentences via animation

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

accelerate research

supports communities of researchers working collaboratively across disciplines

end disease

supports communities of researchers working collaboratively across disciplines

end breast cancer

end breast cancer

incentives of the individual don’t align with

greater goals of the field

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

doi:10.7303/syn1710680.4

TCGA Pan-Cancer Consortium

collaboration around common data

collaboration around common question

CRC Subtyping Consortium

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CRC Subtyping Consortium

A

B

C

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E

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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

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

harmonize

incentives of the individual

with the greater goals of the field

department of defense breast cancer research program vision setting meeting 2015

brian m. bot ——————

[email protected] @BrianMBot

sage bionetworks

biomedical research in an increasingly digital world