tranSMART Community Meeting 5-7 Nov 13 - Session 2: Developing a TR Community around the tranSMART Platform

Code Content Community

The Paris Workshop4-November-2013

Building a Robust Translational Research Community around the Open-Source tranSMART Platform



Translational ResearchTranslational Research Is the process of applying ideas, insights, and discoveries generated through basic scientific inquiry to the treatment and prevention of human disease – the critical bridge between basic and clinical research.

The steps in translational research are designed to ensure that the discoveries that advance into human trials have the highest possible chance of success in terms of both safety and efficacy. Catalyzing Translational Innovation

CHRISTOPHER P. AUSTIN, M.D. DIRECTOR, NCATS


The Translational Challenge

Basic Science Clinical DevelopmentTranslational Science

Target Validation

Discovery

Lead Optimization

Non Clinical Safety

First in Human

Phase II

FDA Approval

Phase III

MarketLaunch

** Sources: Michael J. Fox Foundation for Parkinson’s Research; Faster Cures 2013

NIH$29 Billion/Yr **

Biotech and Pharma$64 Billion/Yr **

The Translational Gap


Research Data is IncreasingGEO Sample Counts Over Time

Framing the Challenge


Athey and Omenn, 2009

Translational Science is Becoming an Information Science Data Integration & Analysis

Populations


Addressing the Innovation Challenge


tranSMART – A platform and a Community• Open-source and open-

data translational biomedical research community

• Scientists, Developers, Service Providers, Clinicians

tranSMART: More than just a Platforman approach to enable translational science

A Community…


tranSMART Foundation Ethos: From the Linux Foundation Playbook

Open communication• With an open community and publicly visible and accessible

communication channels, anyone can join the community and meet hundreds of other community members just like them.

Licensing of work• Every contribution to the community is licensed in such a way that it

benefits the entire community. The fair licensing of all contributions adds a strong sense of confidence to the security of the community.

Open tools• Anyone with an Internet connection and a computer can contribute.

All of the development tools and documentation are entirely free and open to access. This provides a low barrier to entry, and lets new users play with the technology.


Clinical Group• Trial design• Patient stratification• Response prediction

Preclinical Group• Animal models• Drug sensitivity• Toxicity

Discovery Group• Target validation• Biomarker discovery

tranSMART Creates Value: Collaboration Between Groups and Functions


THE TRANSMART FOUNDATION

TreasurerAshley George, PhD, GlaxoSmithKline, Pistoia

Chief Science OfficerKeith Elliston, PhDSeneca Creek Research

Chief Technology OfficerYike Guo, PhD Imperial College London

Executive DirectorKevin Smith, MSISUniversity of Michigan

Co-Chief Executive OfficerMichael Braxenthaler, PhDRoche, Pistoia Alliance

Co-Chief Executive OfficerBrian Athey, PhDUniversity of Michigan

Ops

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www.transmartfoundation.orgA Not for Profit Corporation



The tranSMART FoundationVision

Realizing the promise of translational biomedical research by provision and continuous improvement of a open source code base for data sharing and analytics.

MissionThe tranSMART Foundation enables effective sharing, integration, standardization, and analysis of heterogeneous data from collaborative translational research by mobilizing the tranSMART open-source and open-data community.

Code Content CommunityCode Content Community

THE ROLE OF THE TRANSMART FOUNDATION

Community

Code

Content

What if... Scientists working at every university, non-profit research organization, pharmaceutical and biotechnology company in the world could share their pre-competitive clinical and molecular biology data – working together to turn scientific discoveries into medical breakthroughs?

Foster a global community of Users, Developers, and Commercial Service Providers

Serve as a gateway to high value tranSMART contentV1.1 (Sep-13) V1.2 (Q2-14) V2.0 (TBD)

Serve as a gateway to high value tranSMART contentCatalogs coming in late 2013

Continuity>$50M in public/private investment in tranSMART-related projects so far


The tranSMART Foundation Goals

1. Establish and sustain tranSMART as the preferred data sharing and analytics platform for translational biomedical research.

2. Link academic, non-profit and corporate research communities for collaborative research facilitated by tranSMART.

3. Align and grow a vibrant developer network around the scientific goals of the tranSMART community.

4. Reduce barriers to entry through use of advanced technologies and an active marketplace.


• Community– Community Coordination

Developer and User infrastructure

Workshops, Hackathons, Scientific Meetings

– tF Certified Program• Ensure the quality of content

and services

– Business / Marketplace Development• Bring new products and services

to the tranSMART Community

Foundation Key Initiatives

• Code– Version 1.x Roadmap

Version 1.1 released 9/15/13• Version 1.2 planned

– Version 2.x Roadmap• Initial architecture design planned

6/30/14• Initial release planned 6/30/15

• Content– Public release of high quality

curated datasets

• Continuity– Membership program

Ensure the sustainability of the platform and community


• International Research Initiatives– IMI – eTRIKS, EMIF– CTMM – TraIT

• Pharma & Biotech– Sanofi, Millennium, Pfizer, JNJ, Roche

• Government aligned Institutions– FDA

• Non-Profits– 1Mind4Research, Orion Bionetworks

• Hospitals / Academics– U Michigan, John’s Hopkins, St. Jude

• Service Providers– Thomson Reuters,

Recombinant(Deloitte), theHyve, Rancho Biosciences, BTGS

Start Organization Type Stage2008 Johnson & Johnson Pharma Production 2008 Recombinant by Deloitte Services Multiple2010 Sage Bionetworks Non profit Production 2010 Thomson Reuters Services Support2010 U-BIOPRED Consortium Production 2011 SAFE-T Consortium Pilot 2011 University of Michigan,

Comprehensive Cancer Center (UMCCC)

Academic Production

2012 BT Cure Consortium Pilot 2012 CTMM/TraIT Consortium Development2012 FDA Government Development2012 IMI/eTRIKS Consortium Development2012 Merck Pharma Pilot2012 Millennium Pharmaceuticals Pharma Production 2012 One Mind for Research (1M4R) Non profit Production 2012 Pfizer Pharma Production 2012 Roche Pharma Evaluation2012 Sanofi-Aventis Pharma Development2012 St. Jude Non profit medical center Development2012 University of Michigan,

Department of Computational Medicine & Bioinformatics (DCM&B)

Academic Development, Pilot

2013 Agios Biotechnology Evaluation2013 APHP-HEGP Paris France Academic Production 2013 Boehringer Ingelheim Pharma Pilot2013 Bristol Myers Squibb Pharma Evaluation2013 BT Global Services Services Pilot2013 Accelerated Cure Project for MS Non profit Development

The tranSMART Platform is Being Adopted:over 35 organizations have implemented tranSMART


TM 1.1

The tranSMART FoundationCoordinates Development to Ensure a Clear Direction

All new development will be based upon the new tranSMART V1.1 core


TM 1.1eTRIKS

TraIT


Teams develop within the context of their projects


TM 1.1eTRIKS

TraIT


Foundation Led Team Gathers and Helps Decide What to Include in tranSMART v1.2


eTRIKS

TraIT


Code Integration Phase Driven by Requirements


TM 1.2eTRIKS

TraIT


The Foundation will convene a Release Team to Manage the Process


The tranSMART Codebase


The tranSMART Project


The tranSMART ProjectImpact of the Foundation

Amsterdam Workshop

Initial OSS Release Ann Arbor Workshop

Version 1.1 Release


Top Committers to the Codebase



Phase 1 4/15/13 - 12/31/13 Deliver tranSMART v1.1 Establish Operations team Initiate membership program

• Phase 2 – 1/1/14 – 12/31/14– Formalize and Stabilise all Operations– Deliver tranSMART v1.2– Initiate development of v2.0– Initiate Content Repository– Convene new member-driven BOD

• Phase 3 – 1/1/15 – beyond– Growth to sustainability, governed by

members– Implementation of v2.x platform

• 3 year plan – growth to sustainability for the

Foundation, Community and Platform– Organize and enhance the tranSMART

Community

• Focus on geographical centers of excellence– North America, Europe and Asia

• Ensure the quality and usability of the content and services– tF Certified Program

• Define the Intellectual Property Landscape– Open source licenses for Code and

Content

The Foundation’s Plan and Timeline

Code Content CommunityCode Content Community

GOVERNANCE STRUCTUREBoard of Directors

(15 Members)

Ops Team(Officers)

Community workgroup/s• User community• Developer community• Marketplace• Documentation & Training

Code workgroup/s• Architecture group• Release life cycle mgm’t

Content workgroup/s• Scientific AB• Public content• Functionality requirements

Community Committee Code Committee Content Committee

Management

establish and oversee

Governance/Oversight


• Community– Community Activities

• Workshops, hack-a-thons, conferences

– Business Development• New service providers, technology

partners, etc.

• Code– Organization of new releases– Communicating user requirements– Deploying and managing developer

infrastructure– Developing quality standards

Providing a Nucleus to Build and Grow the tranSMART Community

• Content– Encouraging content contributions

to the community– Community directed content

curation• Continuity

– Ensuring that investments in tranSMART projects benefit the whole community

– Securing new investments in the platform and community

Foundation Value-Adds


• Become a member– Support the Foundation– Participate in Governance and Direction

• Advocate for the platform– Building the community is critical for long term success and

sustainability• Participate in the Community– Software Development– Software Testing– Documentation Development– Scientific Input

What the Foundation needs from you…

Health & Medicine

tranSMART Community Meeting 5-7 Nov 13 - Session 2: Developing a TR Community around the tranSMART Platform