the national cancer informatics program (ncip) initiatives accelerating research ... · 2014. 10....
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The National Cancer Informatics Program
(NCIP) Initiatives
accelerating research through open science
Ishwar Chandramouliswaran, Program Manager, NCIP
July 29 2014
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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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Objectives of the NCIP
• Foster a sustainable community of expert members to support open innovation of tools, data and standards supporting cancer research.
• Promote mechanisms to democratize access to data, tools, and standards within NCI and across the cancer research community.
• Enable the scientific goals of the NCI through open &
collaborative development and support of informatics programs.
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NCIP Projects
• Empowering Cancer Research through Open
Development - NCIP GitHub Channel
http://github.com/ncip
• Democratizing access to data, tools & standards
through the Cancer Genomics Cloud BAA
http://ncip.nci.nih.gov/nci-cloud-initiative
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The National Cancer Informatics Program
(NCIP) Hub
A platform for collaboration and sharing of data, tools, and standards
amongst the cancer research community
www.nciphub.org
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Building scientific communities via the NCIP Hub
Community Driven:
•Research
•Collaborate
•Teach & learn
•Share & publish
HUBzero ®
http://hubzero.org/
Make research useful for others
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NCIP Hub: A 360o Approach to Developing and
Sustaining NCI Informatics Resources
• Serve as front-end for Informatics Resources
• Access cancer related datasets
• Support open development projects
• Marketplace for relevant analysis tools
• Evolution of self-sustaining communities via crowd-sourcing
• Model for sharing and as an educational resource
• Increases transparency & incentivizes collaboration to
accelerate research
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NCIP Hub
Biologist – end user Bionformatician – HTP user Computational Scientist - Developer
Marketplace
• Access and explore databases • Upload lab/clinical data generated • Access computational tools • Analyze data and share results • Rate tools and provide feedback
Resources
AppStore
• Develop & upload computational tools • Download other tools • Access to data to test tools • Crowd-sourced development • Gather real-time requirements
Collaboratory
• NCIP News & related blog posts • Create or join groups for collaboration • Explore and analyze data and tools • Contribute other learning resources • Publications, citations
Cloud
Services
Run
Analysis
Access data
Share data
Serve NCI
Serve larger community
Usage Ranking
Feedback Collaboration
Share Source Code
Community Development
Run
Analysis
Access NCI and Other Capabilities
Community Forums
crowd-sourced research contributions & learning
VISION: NCIP Hub
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NCIP Seminar Series
HUBzero: A Web-based Platform
for Research, Education, and
Scientific Collaboration
Michael McLennan, PhD
Director, HUBzero® Platform for Scientific Collaboration
Purdue University
November 28, 2012
Seminar Recording @ NCIP YouTube Channel
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What is HUBzero?
A toolbox for building scientific web sites
Lesser General Public License, LGPL-3.0
Linux/Apache/MySQL/PHP
Download: http://hubzero.org/download
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1 An “app store” for scientists
What is HUBzero?
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Apps created/uploaded by your community
Tool Developer
End User
Registered
Created
Uploaded
Installed
Approved
Published
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Accessible from any machine
Source code bundles Binaries
Hello,
I am grad student from Kazakhstan.
Your tool not compile for me. I get
errors. That’s a not very nice.
Hey, can you help me? It doesn’t work on my machine!
32-bit 64-bit
. . .
Live tools accessible
from any web browser
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Powered by the Cloud
Locally
Installed
Program
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Supports Scientific Workflows
Computational workflows: • Manage thousands of runs
• Simplified access to Condor
• “submit” Pegasus workflows
• Integrate into simulation tools
Ewa Deelman USC Information Sciences Institute
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Tools Kits to build Intuitive Interfaces
Rappture
inputs
outputs
• Rapid Application Infrastructure
• Open Source (rappture.org)
• Interface for real research codes
• Integrated visualization
• Works with your favorite
programming language
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2 A repository for
data and publications
What is HUBzero?
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Simulation &
Modeling Tools
Powered by Your Community
Seminars
Tutorials
Tech Reports
Teaching Materials
Data from
Experiments
More than just apps
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Example: nanoHUB.org
1,890 seminars
535 teaching materials 64 courses
235 simulation tools
Network for
Computational
Nanotechnology
Established in 2002
230,000 users
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Example: NEES.org
974 other
201 projects 9 databases
56 simulation tools
George E. Brown, Jr.
Network for
Earthquake Engineering
Simulation
32,000 users
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Example: pharmaHUB.org
100 other NIPTE-FDA
Excipients
Knowledge Base
22 simulation tools
Collaboration for
Pharmaceutical
Engineering and Science
23,000 users
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Example: cceHUB.org
17 simulation tools
Cancer Care
Engineering
Hub
3,300 users
Collect blood samples Proteomics Statistical analysis
Databases
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3 A collaboratory for
team science
What is HUBzero?
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Community Collaboration
Questions
& Answers
Brainstorming
& Wish Lists
Calendars
& Events
Groups
& Projects
Incentives
& Feedback
Web Analytics
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Tool Development and User Support
http://nanohub.org/tools/cntbands-ext
Collaborative
Development
Questions
& Answers
Brainstorming
& Wish Lists
Bug
Reports
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Collaboration: Source Code
Collaborative
Development
View of source code differences in project repository
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4 An outreach solution
What is HUBzero?
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An Outreach Solution
• Marketplace/repository – Repository for resources with DOIs
– Publications, seminars, reports, tools, data
• AppStore for scientists – Tools uploaded as Apps by the community
– Accessible from any machine
– Cloud powered for intensive computation
– Support workflows/pipelines
– Toolkits to build interfaces
• Collaboratory for team science – Groups, Calendars, wikis, blogs, collections
– Linux Workspace - shared
– Collaborative tool development (ToolsForge) and user support
– Data management (data store)
• Learning Management System (MOOCs)
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Why HUBzero?
Broad set of features for scientific community
Worked for diverse scientific domains
Serves both individual and power users
Provides transparent analytics
Open source; NSF funded, sustainable research project
Aligns with program & cancer community needs
– Establish catalog of (informatics) resources
– Reduce redundancies & enhance transparency
– Content driven by the community
– Support training needs
– Opportunities to innovate
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Anticipated Impact of the NCIP Hub
• Greater visibility to NCI bioinformatics at lower costs
• Serve as intellectual capital to plan new studies/projects
• Bridge gap between bench-scientists & bioinformaticians
• Transformative platform for cross-disciplinary interactions
• Model for collaboration
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Where are we today?
- Community site setup www.nciphub.org
- Hosted at Purdue University
- Understanding use at other federal agencies
- User groups and activities (test drives) underway
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What are the Critical Success Factors?
• Content to drive a vibrant community
• Commitment to dissemination – incentivized
• Support content dissemination for broader audiences
• Need to openly measure impact/success via metrics
• Each user needs to be hands-on and champions
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What can you do on www.nciphub.org ?
1. Join NCIP Hub
2. Join the NCIP Hub user group
3. Familiarize and customize your dashboard
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Identify content to publish & share
User
Compose
Attach
Access
Authors
Tags
Publish
1. Seminars
2. Tutorials
3. Events
4. Workshops
5. Publications
6. Blogs
1. Ask/Discuss questions
2. Vote on ideas
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Where can you get help?
1. Online support via tickets
2. NCIP Hub Knowledgebase
3. NCIP Hub Community support via Q&A
4. NCIP Hub webinars & workshops
5. Organize targeted workshops
1. HUBzero community, documentation, user conference
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http://hubzero.org/
Ishwar Chandramouliswaran Program Manager
National Cancer Informatics Program
More information
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Realizing open innovation and accelerated research
Democratize access
Foster communities
Open development
NCIP Hub
ODI
Cancer Cloud