A VIVO VIEW OF CANCER RESEARCH: Dream, Vision and Reality2013 VIVO Conference Presentation

Paul K. Courtney, Dana-Farber Cancer InstituteAnil Srivastava, OHSL

August 15, 2013St. Louis, MO

Agenda

• Background• Dream• OHSL Vision• Reality

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.

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

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

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

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

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

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

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)

Collaborator and Knowledge network

Recording and Analysis

Project Z

processExplicit (what)

KnowledgeTacit (how)Knowledge

OHSL Project X

New Discipline/Individual

Idea Generation

Talent Integration

Capital Search

Collective Thinking [Project Y](idea refining and branding)

XDSPKnowledge

XDSPHuman Network

XDSPIndividual Benefit

XDSPShared Vision Innovation

Measurement

Knowledge CaptureCollaboration Capital

Collaborative Needs Assessment

Project Management

Team AssemblyProject InitiationProject Planning

Project ExecutionProject Leadership

Project Monitoring and Controlling

Project Presentation/Granting

Project Conclusion

OHSL Process Map: adapting Pennington’s model

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.

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

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) .

Reality – ICTBIOMED Achievements

Example of mutual interdependence: OCGN & OHSL

OHSL Current

• Communications, Collaboration & Knowledge Management:– GoToMeeting for meetings, teleconferences– Confluence Wiki

• Core RNS support:– SugarCRM, VIVO

Global Cancer Collaboratory Timeline20

11

2012

2013

Poster describing the Vision at 2nd Annual VIVO Meeting

Aug 2011

Project: Collaborate with CDAC & OHSL to implement a shared VIVO instanceTechnical infrastructure: VIVO Server needs and parametersOrganizational: Assess SciTS at OHSLProject 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

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!