Empowering Cancer Research through Open Development,

1. Empowering Cancer Research through
Open Development
Ishwar Chandramouliswaran
Program Manager, National Cancer Institute
Center for Biomedical Informatics and Information Technology
June 21 2013

2. 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

3. The program encourages open innovation to
accelerate research
• Promote mechanisms to democratize access to data,
tools, and standards within NCI and across the cancer
research community.
• Foster a community of experts to support open innovation
of tools, data and standards supporting cancer research.
• Enable the scientific goals of the NCI through community
driven open development and support of informatics
programs.

4. Democratizing access to data, tools & standards
through 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/

5. 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

6. Enabling community driven development via the
open 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

7. Request for input on open development ecosystem
Summer 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

8. 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

9. 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

10. Establishing the NCIP GitHub Channel http://github.com/ncip
10

11. Project Activities & Phases
• License adoption
• Establishing process & migrating code
• Developing SOPs, checklists & resources
• Outreach

12. 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.

13. 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

15. Realizing open innovation and accelerated research
Democratize access
Foster communities
Open development
NCIP HUB
ODI
Cancer
Cloud

16. 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

17. 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

18. More information
http://cbiit.nci.nih.gov/ncip
Ishwar Chandramouliswaran
Program Manager
National Cancer Institute, CBIIT
Ishwar.chandramouliswaran@nih.gov
 Empower communities
 Access data, tools & standards
 Support open development

19. Q&A