ishwar chandramouliswaran, cancer research, fged_seattle_2013
DESCRIPTION
Empowering Cancer Research through Open Development,TRANSCRIPT
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, [email protected]
Empower communities
Access data, tools & standards
Support open development
Q&A