Web Form Automation for Bonterra Impact Management (fka Social Solutions Apri...
Ishwar Chandramouliswaran, Cancer Research, fged_seattle_2013
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
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.
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