Ishwar Chandramouliswaran, Cancer Research, fged_seattle_2013

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Empowering Cancer Research through Open Development,

Empowering Cancer Research through Open Development,

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  • 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
  • 14. Realizing open innovation and accelerated research Democratize access Foster communities Open development NCIP HUB ODI Cancer  Cloud
  • 15. 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
  • 16. 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
  • 17. 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
  • 18. Q&A