Ishwar Chandramouliswaran, Cancer Research, fged_seattle_2013
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Transcript of Ishwar Chandramouliswaran, Cancer Research, fged_seattle_2013
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Empowering Cancer Research through Open Development
Ishwar ChandramouliswaranProgram Manager, National Cancer Institute
Center for Biomedical Informatics and Information Technology June 21 2013
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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
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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.
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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/
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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
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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
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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
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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
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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
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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
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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.
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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
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Realizing open innovation and accelerated research
Democratize access
Foster communities
Open development
NCIP HUB
ODI
Cancer Cloud
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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
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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
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More informationhttp://cbiit.nci.nih.gov/ncip
Ishwar ChandramouliswaranProgram ManagerNational Cancer Institute, [email protected]
Empower communities
Access data, tools & standards
Support open development
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Q&A