A VIVO VIEW OF CANCER RESEARCH: Dream, Vision and Reality


Published on

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).

  • Be the first to comment

  • Be the first to like this

No Downloads
Total views
On SlideShare
From Embeds
Number of Embeds
Embeds 0
No embeds

No notes for slide
  • The projects help to define how best to select and implement tools & infrastructure @ OHSL
  • Gasson’s ethnographic study investigates how a project group deals with the contradiction between distributed knowledge in boundary-spanning collaborative processes and the expectation that he software system will provide unified, codified knowledge. The study explores how knowledge and expertise were translated across organizational boundaries, and identifies four stages in the development of group understanding of how to manage sensemaking and expertise across knowledge boundaries: focus on defining shared goals; acknowledging and sharing tacit knowledge about organizational practice; identifying external influences; and explicit knowledge generation. Most common misconception is that there is a hierarchy of data.Proper knowledge management occurs on multiple interconnected platforms and needs to be within its context of application and transferable to another context in the case of OHSL.Knowledge can be in the process in learning directionality and across sectors and sciences.Domain experts also don't have to house all the expertise if there is a collective method of storing, assessing, and transferring the knowledge (beyond emails).This does require all members to be a community of practice – open and sharing and jointly engaged.Benefits of a Broker-facilitatorPooling Existing knowledgeCollective learningProvide workflow frequentlyAlign common taxonomyGroup knowledge eliciting and sharingExternal (distributed) knowledge elicitation, sharing and dissemination 
  • Adapted version Pennington “Knowledge Synthesis Model”You will find this process to be very heavy in the beginning – why is that? Because the collaborators we engage see the value and invest their time and effort and share processes throughout the project cycle to enhance their and their partner capacities. This could be in simply learning about funding opportunities or solutions for lab work. They can be trusted to be facilitated and not walked through each project management step – it also allows us to maintain ownership by the collaborators.You will find that the project design occurs half-way through the project – this is how we allow for true collective thinking and make room for other ideas born of this collaboration.Preceding that an immense amount of network and information is captured and stored when not applied.We are not heavy in evaluation
  • Anil & I both were involved in the caBIG program & met at one of the joint NCI-NCRI meetings where we discussed the challenges of supporting collaborative, international cancer research.
  • A VIVO VIEW OF CANCER RESEARCH: Dream, Vision and Reality

    1. 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. 2. Agenda • Background • Dream • OHSL Vision • Reality
    3. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 15. Reality – ICTBIOMED Achievements
    16. 16. Example of mutual interdependence: OCGN & OHSL
    17. 17. OHSL Current • Communications, Collaboration & Knowledge Management: – GoToMeeting for meetings, teleconferences – Confluence Wiki • Core RNS support: – SugarCRM, VIVO
    18. 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. 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!