Presentation made by Paul Courtney (Dana-Farber Cancer Institute, Boston, MA and OHSL, MD) and Anil Srivastava (OHSL) at the 2013 VIVO conference in St. Louis, MO. Material contributed by Rubayi Srivastava (OHSL), Swati Mehta (Centre for Development of Advanced Computing, India), Juliusz Pukacki (Poznan Supercomputing and Network Center, Poland) and Devdatt Dubhashi (Chalmers Institute of Technology, Sweden).

1. A VIVO VIEW OF
CANCER RESEARCH:
Dream, Vision and
Reality
2013 VIVO Conference Presentation
Paul K. Courtney, Dana-Farber Cancer Institute
Anil Srivastava, OHSL
August 15, 2013
St. Louis, MO

2. Agenda
• Background
• Dream
• OHSL Vision
• Reality

3. Some historical background
• 2004: NCI/CBIIT initiates caBIG program with goal to mobilize digital
capabilities for researchers in order to accelerate scientific
discoveries; fosters creation of cancer informatics community.
• October 2009: NCRR grant to develop VIVO as “Facebook for
Scientists”
• April 2010: First SciTS meeting
• June 2010: NCI-NCRI joint meeting to discuss role of informatics in
supporting/enabling cancer research & researchers
• August 2012: First VIVO meeting
• March 2012: NCI retires caBIG; the National Cancer Informatics
Program (NCIP) will leverage the investments made in, and lessons
learned from, caBIG.

4. Dream: Inspired by mutually
supportive roles of SciTS and VIVO
Science of
Team Science
VIVO
Issues of people and organization,
process reengineering, training,
reframing the research questions,
reframing the goals of program or
staff evaluation.
Issues of technology & infrastructure,
ontologies, dissemination of tool use
(network effects), VIVO
implementation, development &
extension.
Needs informatics tools
Needs real-world use cases

5. Vision: Mutually supportive roles
of OHSL and collaborators
Potential
Collaborators
OHSL Infrastructure:
tools to support
communication,
collaboration,
document
management,
project & program
management
Issues of people and organization,
process reengineering, training,
reframing the research questions,
reframing the goals of program or
staff evaluation.
Issues of technology & infrastructure,
ontologies, dissemination of tool use
(network effects), VIVO
implementation.
Needs informatics tools
Needs real-world use cases

6. Challenge: how to connect and
collaborate?
• With multiple communication technologies
– Skype, Google Chat, VOIP, “Magic Jack”
– GoToMeeting, WebEx, Überconference, Google
Hangout
• And abundant choices for collaboration
– Wikidot, Wikispaces, Confluence, MediaWiki
– VIVO as core software
• Need to stay focused on how to foster & incubate
“team-ness” between face-to-face meetings

7. Connect & Collaborate: Team
Science and RNS
Research Network Systems, Schleyer (2012)
“We propose Research Networking Systems (RNS) as a new
type of system designed to help scientists identify and choose
collaborators, and suggest a corresponding research
agenda.”
Schleyer, T., Butler, B. S., Song, M., and Spallek, H. 2012. Conceptualizing and advancing research networking systems. ACM
Trans. Comput.-Hum. Interact. 19, 1, Article 2 (March 2012), 26 pages. DOI = 10.1145/2147783.2147785
http://doi.acm.org/10.1145/2147783.2147785

8. Challenge: how to adapt?
• With changing technologies
– Workstations, Cray supercomputers, massively
parallel computing, Hadoop distributed computing
• And changing science
– Single gene to genome to epigenome to …
metabolome
– …And now the Microbiome?
• Need to stay focused on how to support the
sharing, integration, synthesis of Knowledge

9. Gasson, S. (2005). The dynamics of sensemaking, knowledge, and expertise in collaborative, boundary-spanning design.
Journal of Computer-Mediated Communication, 10(4), article 14. http://jcmc.indiana.edu/vol10/issue4/gasson.html
Boundary-spanning
collaborative processes

10. A Model of Knowledge Synthesis Across Disciplines, Dr. Deana D. Pennington,
University of Texas at El Paso, Cyber-ShARE Center of Excellence, SciTS Meeting April 18, 2012 SciTS 2012
Pennington’s Knowledge Synthesis
Model (2012)

11. Collaborator and
Knowledge network
Recording and Analysis
Project Z 
process
Explicit (what)
Knowledge
Tacit (how)
Knowledge
OHSL Project X
New Discipline/Individual
Idea
Generation
Talent
Integration
Capital
Search
Collective Thinking [Project Y]
(idea refining and branding)
XDSP
Knowledge
XDSP
Human Network
XDSP
Individual Benefit
XDSP
Shared Vision  Innovation
Measurement
Knowledge Capture
Collaboration Capital
Collaborative Needs
Assessment
Project
Management
Team Assembly
Project Initiation
Project Planning
Project Execution
Project Leadership
Project Monitoring and
Controlling
Project
Presentation/Granting
Project Conclusion
OHSL Process Map: adapting
Pennington’s model

12. Triple-Loop Learning
Downloaded from http://www.thorsten.org/wiki/index.php?title=Triple_Loop_Learning 8/15/2013
• Single-loop learning leads to making minor fixes or adjustments, like using a
thermostat to regulate temperature.
• Double-loop learning works with major fixes or changes, like redesigning an
organizational function or structure.
• Triple-loop learning includes enhancing ways to comprehend and change our
purpose, developing better understanding of how to respond to our environment,
and deepening our comprehension of why we chose to do things we do.

13. Reality - Challenges
• Communication – poor audio (Magic Jack),
differential bandwith availability, spanning
multiple time zones (India at GMT+5:30;
Sweden@ GMT+2; Maryland @ GMT-5;
California @GMT-8)
• Collaboration & Knowledge Sharing – still a
work in progress to keep wiki’s up to date

14. Reality: ICTBIOMED – use case to
exercise the OHSL model
Project Concepts
• Encouraging pre-competitive collaboration among scientists; mapping research resources worldwide;
connecting collaborators leveraging the semantic web and increasing capability of social media and open
source tools.
• Initiating a pre-competitive research consortium for in silico drug design and development from botanical and
herbal molecules
• Mapping sources of funding and support of medical research worldwide and working with funding agencies
and foundations to address the needs of global medical research.
• Building and managing international consortia that will address provocative questions of medical science with
a view to reduce the global burden of disease.
• Promoting open source, interoperable, standards based software and providing inventory, integration,
training, and support.
• Creating a globally shared cyberinfrastructure for medical research including high performance computing
(HPC) for life sciences with advanced network connection, in partnership with University Corporation for
Advancement and Internet Development (UCAID/Internet2), and Mid-Atlantic Crossing (MAX).
• Supporting innovation in biomedical research including biospecimen, biomarkers and clinical trials, especially
emerging models for Comprehensive Dynamic Trials, Adaptive Trials, and Virtual Trials.
• Promoting information proficiency and meaningful use of human-centered, outcomes-oriented appropriate
technology, where the ability to adopt and adapt resides with the user community.
• Creating a global knowledge cloud for medical research and treatment to support global health with a team
science approach and using biomedical informatics, information technology and International Research
Network Cooperation (IRNC) .

15. Reality – ICTBIOMED Achievements

16. Example of mutual
interdependence: OCGN & OHSL

17. OHSL Current
• Communications, Collaboration & Knowledge
Management:
– GoToMeeting for meetings, teleconferences
– Confluence Wiki
• Core RNS support:
– SugarCRM, VIVO

18. Global Cancer Collaboratory Timeline
2011
2012
2013
Poster describing the
Vision at 2nd Annual VIVO
Meeting
Aug 2011
Project: Collaborate with CDAC &
OHSL to implement a shared VIVO
instance
Technical infrastructure: VIVO
Server needs and parameters
Organizational: Assess SciTS at
OHSL
Project goal: align project with
framework development
Goal: VIVO 2012 Panel
Feb 2012
VIVO Team Project
Progress and Needs
Meeting – VIVO
Workshop
Aug 2012
Weekly meetings –
• Comparative Analysis of
harvesting data from
Indian and US sites
• Tool Enhancements and
Troubleshooting Content
• Testing ingesting data from
sites in Poland and other
EU nations.
General Discussion about
the VIVO Collaborative
Research Projects and
RFAs.
Nov 2010
Poster presented at
SciTS 2013 on the
OHSL infrastructure:
Open and Adaptive
Knowledge Cancer
Cloud (OAKCan)
ICTBIOMED initiated, begins to
use & test out Schleyer’s RNS
model for infrastructure along
with Pennington’s Knowledge
Synthesis process model
Jun 2013

19. OHSL
OPEN source
of knowledge
Pertaining to
HEALTH
Information
SYSTEMS as
a tool
LABORATORY
for people to
drive in their
innovations
and ideas
Thank You!