Empowering Cancer Research through Open Development

Ishwar ChandramouliswaranProgram Manager, National Cancer Institute

Center for Biomedical Informatics and Information Technology June 21 2013

NCIP is a cross-NCI program to support biomedical informatics in cancer research

• Announced by NCI Director in Spring 2012• Assess and meet informatics needs of NCI programs• Share the resources generated

The program encourages open innovation to accelerate research

• Promote mechanisms to democratize access to data,tools, and standards within NCI and across the cancerresearch community.

• Foster a community of experts to support open innovationof tools, data and standards supporting cancer research.

• Enable the scientific goals of the NCI through communitydriven open development and support of informaticsprograms.

Democratizing access to data, tools & standardsthrough the cancer genomics knowledge cloud initiative

• Current Informatics challenges• Experience in high-performance computing• Metrics to measure success

http://ncip.nci.nih.gov/nci‐cloud‐initiative

http://ncip.nci.nih.gov/blog/2013/05/31/input‐on‐cancer‐knowledge‐clouds‐key‐themes‐from‐the‐community/

Building scientific communities via the NCIP HUB Pilot

Community Driven:• Research• Collaborate• Teach & learn• Share & publish

HUBzero ® http://hubzero.org/

Make research useful for others

Enabling community driven development via theopen development initiative (ODI)

Establishment of an NCIP ODI is driven by our desire to:

• Support the rapid informatics innovation• Enable better tools by crowdsourcing innovation• Empower the community to drive priorities

Request for input on open development ecosystemSummer 2012

1. Lower the barriers to entry• Migrate to OSI-approved license• Move source code to social coding environment

2. Involve the community• Convene relevant communities• NCI as a participant

3. Take action• Iterative, agile approach to building communities

Selection & Adoption of Open Source License

Criteria:

• Allow free use, modification, & sharing• Popular, widely used & strong communities• Comply with the Open Source Definition• Open Source Initiative (OSI), approved

BSD3-Clause license adoption

Choice of Source Code Repository

Criteria:

• Distributed version control system (DVCS)

• de facto DVCS for distributed open source development

• Terms & conditions pre-negotiated with the federal government http://github.com

Establishing the NCIP GitHub Channel http://github.com/ncip

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Project Activities & Phases

• License adoption• Establishing process & migrating code• Developing SOPs, checklists & resources• Outreach

Poster # 4

Empowering Cancer Research through Open Development

Mervi Heiskanen1, Ishwar Chandramouliswaran1, Juli D. Klemm1, Robert Shirley1, Lawrence Brem2, Luis Ibanez3, Brad King3, Anthony R. Kerlavage1, George A. Komatsoulis1

Author affiliations: 1: National Cancer Institute, Center for Biomedical Informatics and Information Technology; 2: SAIC-Frederick, Inc.; 3: Kitware, Inc.

Communication & community building is the key to success

• Communication and outreach• FGED, June 20-22• Open Source Summit, June 25-26• BOSC/ISMB, July 19-23

• Community building around existing projects• Project teams discuss community building and

governance.• ISA-TAB-Nano codefest, May 6-7• XIP/AVT Hackfest, May, 2013• caTissue Code Jamboree, June 19-21

Realizing open innovation and accelerated research

Democratize access

Foster communities

Open development

NCIP HUB

ODI

Cancer Cloud

Anticipated Impact of these Projects

• Greater visibility to NCI bioinformatics• Reduce redundancies• Bridge gap between bench-scientists & bioinformaticians• Serve as intellectual capital to plan new studies/projects

Acknowledging the team

NCI

• Juli D. Klemm• Mervi Heiskanen• Robert Shirley• Anthony R. Kerlavage• George A. Komatsoulis

SAIC-Frederick, Inc.

• Larry Brem• Sreenath Nampally

Kitware Inc.

• Brad King• Luis Ibanez

More informationhttp://cbiit.nci.nih.gov/ncip

Ishwar ChandramouliswaranProgram ManagerNational Cancer Institute, CBIITIshwar.chandramouliswaran@nih.gov

Empower communities

Access data, tools & standards

Support open development

Q&A