enabling communities of researchers working together across institutional boundaries
TRANSCRIPT
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 ——————
[email protected] @BrianMBot
sage bionetworks
enabling communities of researchers working together across institutional boundaries