The HUBzero Collaborative
Infrastructure and Biomedical Research
™
William K. Barnett, Indiana University
Indiana CTSI
barnettw@iu.edu
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Agenda
• The Changing Nature of Scholarly Research
• Overview of the HUBzero Platform
• Institutional HUB: The Indiana CTSI
• Project HUB: Cancer Care Engineering
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The Changing Nature of Scholarly
Research
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The Changing Nature of Scholarly Research
• Research intellectual capital is distributed.
• Collaborative research is increasingly becoming the
norm.
• Translational research depends on interdisciplinary or
transdisciplinary (the resulting focus is something new)
teams.
• The resources necessary for competitive research are
no longer found in any one research lab.
• Distributed facilities and data are changing the
research resource landscape.
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Team Science and Virtual Organizations
• Team Science is a higher risk, higher reward approach to
research.
• Types of Collaborations include:
• Social Networking
• Knowledge Networking
• Resource Networking
• With the current suite of Web 2.0 tools, it inevitably involves
virtual collaboration and the creation of virtual organizations.
• Includes ‘traditional’ collaboration tools of telephones and
conference calls, email, and teleconferencing.
(Noshir Contractor, presentation at the 2010 VIVO Conference, Queens, NY)
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Issues in Team Science and Virtual Organizations
Persistence beyond face to face relationships requires:
• Motivations and Rewards
• Trust
• Dealing with cultural differences
• Governance and Management
• Shared Infrastructures and resource management
• Metrics and Assessment
• Sustainability – financial, intellectual, infrastructure
“Building Effective Virtual Organizations” (NSF) and “Collaboration & Team Science: A Field Guide” (NIH)
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Different Styles of Virtual Organizations
• Highly distributed communities of independent scholars who
share educational content and tools (NanoHUB).
• Institutional collaborations that accelerate research workflows
(Open Science Grid, Indiana CTSI HUB).
• HUBs that accelerate distributed research projects (cceHUB).
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Overview of the HUBzero Platform
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History of HUBzero
2002
2007
• Feb 2007: 1 hub
• Feb 2008: 5 hubs
• Feb 2009: 8 hubs
• Today: 30 hubs
Each hub has its own
funding stream
Outside institutions:
EPA, NYSTAR, Rice
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What is a Hub?
Basic Features:
nanoHUB.org
Different than a Web Portal:
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It supports computational tools
Ties seamlessly to HPC backends
It supports multimedia content
Publishable references
User Profiles and Private groups
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Interactive Simulation Tools
Online Presentations
Mechanism for Uploading New Resources
Tool Development Area
Ratings and Citations
Content Tagging
Wikis and Blogs
User Groups for Private Collaboration
User Support Area
Usage Metrics
News and Events
Feedback mechanisms
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Scalability and Usage Metrics
nanoHUB.org users
161,142 users worldwide
As much traffic as www.purdue.edu
Users at all Top 50 US Engr Schools
19% of all .edu domains
116 classes at 97 institutions in 2009
8,800 users ran 348,000 simulations
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Other Hubs
32,107 users worldwide
9,433 users worldwide
3,609 users worldwide
2,433 users worldwide
1,431 users worldwide
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Demonstrate Your Own Impact
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Educational Use Is Growing
116 classes
at 97 institutions
in 2009
nanoHUB.org Educational Usage
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Uploading Resources
Tools
Tags
Supporting Resources
Reviews
Research
Education
Reviews
Demo >>
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Rappture: Rapid Application Infrastructure
Rappture
=
Simulation
Code
• Works with your favorite
programming language
• Open Source
• Online at http://rappture.org
• Used by 200 projects and
300 developers
Scientist
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Hundreds of tools online!
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Cyberinfrastructure for Running Tools
Linux/Apache/MySQL/PHP
Physical Machine
Content
Database
Maxwell’s
Daemon
Middleware
Virtual Machine
0101
1011
1001
nanowire job
tool session cluster
Rendering Farm
nanoVIS
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Start Your Own Hub!
Open Source Release: LGPL v3 license
Debian GNU/Linux 5.0 - 64bit
HUB-in-a-box: VMware images
At HUBzero.org:
• Downloads
• Documentation
• Make Wishes
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HUBzero Consortium
hubzero.org
• Four founding members provide financial and
governance sustainability
• Ongoing development of HUBzero core
• Yearly conference: HUBbub
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New Features for 2011
• Moodle Integration
• Multifaceted Identity Management (via Shibboleth, ADS, Google)
• User groups with fine grained authorization and document management
• Integration with Fedora repositories
• Scientific workflows via Pegasus Workflow Management System
• Wiki template pages and new wiki macros
• Blogs for personal profiles and groups
• Support for MATLAB Parallel Toolbox job submission
• Direct Condor job submission
• Access control layer for support tickets
• Completely new and improved search engine with plug-ins
• Auto-completer for tags, members, groups
• Twitter feed module
Contributed by Projects and Community and Consortia members
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Institutional HUB:
the Indiana CTSI
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Projects: The Indiana CTSI HUB
Statewide multi-institutional
initiative
‘Translation’ of research from
basic to pre-clinical to clinical
research, ultimately to improve
health care.
Focus on research process
improvement (funding,
collaboration, research
administration)
http://www.indianactsi.org
Includes community
organization and industry
partnership tools
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Indiana CTSI HUB Tools
Federated Identity Support for ease of use and improved trust for
sensitive data
Ontology-based tagging of HUB content with the National Center for
Biomedical Ontology
Grant Management (based on Open Journal System)
Alfresco Share – file sharing among distributed teams (Open Source)
500 Users and 5 GB of documents
REDCap – web based data collection and management (Vanderbilt)
175 Users and 110 Projects.
i2iconnect.org – Technology transfer matchmaking
914 Listings
CTSA2Community.org - a repository of best practices for community
engaged research
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Future Directions
VIVO and many CTSAs are creating a national faculty
profiling architecture and applications for research
networking, competitive intelligence, etc. See
demonstration at direct2experts.org
CTSAs are working with Eagle-I, RDS, biositemaps, BRO,
NIF, etc to create a national resource networking
architecture to manage facilities, repositories, etc. and
applications like ‘core marketplaces’ that can leverage
them.
The Booz Allen Hamilton RFA10-001 to 1) create Linked
Open Data repositories and 2) develop applications that
leverage LOD for translational research.
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Some Other Translational Research Platforms
Harvard Catalyst (Harvard) and Profiles (UCSF and
Minnesota)
VIVO (Cornell and Florida)
Loki (Iowa)
Community Academic Profiles (Stanford)
Digital Vitae (Pittsburgh)
CTSA Sharecenter (Oregon and UCSF)
SciVal (Elsevier at a number of institutions)
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Project HUB:
Cancer Care Engineering
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Projects: The Cancer Care Engineering HUB
Sample
Collection
Predictive
Modeling
Single portal integrates
clinical and analytical data
collection and analysis
across 6 geographically
distributed teams
Includes tools for:
• sample tracking,
Clinical
Patient
Data
Visual
Analytics
Laboratory
Analysis
• data browsing,
• instrument data
collection,
• modeling,
• visual analytics
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Thank You
Questions?
barnettw@iu.edu
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