The National Cancer Informatics Program

(NCIP) Initiatives

accelerating research through open science

Ishwar Chandramouliswaran, Program Manager, NCIP

July 29 2014

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

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.

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

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

Building scientific communities via the NCIP Hub

Community Driven:

•Research

•Collaborate

•Teach & learn

•Share & publish

HUBzero ®

http://hubzero.org/

Make research useful for others

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

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

9

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?

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)

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

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

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

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

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

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

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

http://hubzero.org/

Ishwar Chandramouliswaran Program Manager

National Cancer Informatics Program

Ishwar.chandramouliswaran@nih.gov

More information

Realizing open innovation and accelerated research

Democratize access

Foster communities

Open development

NCIP Hub

ODI

Cancer Cloud