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DOE Genomic Science Microbial Systems Biology Knowledgebase Workshop (Feb. 9, 2010)

Workshop Report now available - click here to download report 

The DOE Genomic Science Contractor-Grantee and Knowledgebase Workshop will be held February 8-11, 2010 in Washington, D.C. Research projects supported by the DOE Genomic Science program are working towards achieving a predictive, systems-level understanding of plants, microbes, and biological communities, via integration of fundamental science and technology development, to enable biological solutions to DOE mission challenges, including energy, environment, and climate. The Genomic Science program objectives are:
  1. Determine the genomic properties, molecular and regulatory mechanisms, and resulting functional potential of microbes, plants, and biological communities central to DOE missions.
  2. Develop the experimental capabilities and enabling technologies needed to achieve a genome-based, dynamic systems-level understanding of organism and community functions.
  3. Develop the knowledgebase, computational infrastructure, and modeling capabilities to advance the understanding, prediction, and manipulation of complex biological systems.
 

The DOE Genomic Science Microbial Systems Biology Knowledgebase Workshop (Breakout Session D)

Tuesday, February 9, 2:00-5:00pm
 
This workshop will bring together researchers from the Genomic Sciences community in microbial systems biology, computational biology and bioinformatics. This workshop is open to all participants attending the DOE Genomic Science Contractor-Grantee Workshop, however, we ask that you pre-register at the meeting website: http://www.orau.gov/gtl2010/.
 
The goal of this workshop is to outline the near, mid and long term trajectory of microbial sciences for energy and the environment. A second scientific objective is to map the associated workflows and data integration methods that can inform the specifications and requirements for the future development of the DOE Systems Biology Knowledgebase. A fully functional Systems Biology Knowledgebase is envisioned to be a cyber-infrastructure for systems biology information and data that not only includes data storage, retrieval and management, but also enables new knowledge acquisition and management, through free and open access to data, analysis tools, and information for the scientific research community.
 

Important Topics Relevant To This Workshop

  • Near, mid and long term scientific goals of a Systems Biology Knowledgebase
  • Development of workflows for systems biology
  • Bridging data and integration

Workshop Organizers

Susan Gregurick, Department of Energy
Bob Cottingham, Oak Ridge National Laboratory
 

Co-Chairs

Adam Arkin, University of California
Bob Kelly, North Carolina State University
 

Charge Questions and Responses

We are soliciting responses to the charge questions listed below (not more than 2 pages).  Please email your response to kbasewiki@ornl.gov by January 24th, 2010. Please use PDF, ASCII or DOC formats.  Responses will be posted here.
  1. For systems biology of interest to Genomic Sciences, what are scientific objectives that a knowledgebase could address in the 5 year timeframe and in the longer timeframe?  
  2. What are the key workflows that could be developed to accomplish these goals? Provide comprehensive usage examples that lead to scientific objectives.
  3. What types of data are required to accomplish the objective?
  4. What are bottlenecks to data integration and data usability that need to be addressed to accomplish these goals?
  5. What are the bottlenecks in bioinformatic and computational algorithms that need to be addressed to accomplish these goals?
  6. What would success look like? What would the benefit be?

List of Charge Question Responses

(Click here to read responses to the Charge Questions)
  
   1. Response to Charge Questions, Louis Sherman
   2. Response to Charge Questions, Kerstin Kleese Van Dam, et al.
   3. Response to Charge Questions, Costas Maranas
   4. Response to Charge Questions, Christopher Chang
   5. Response to Charge Questions, Brian Davison
   6. Response to Charge Questions, Jake McKinlay
   7. Response to Charge Questions, Frank Collart
   8. Response to Charge Questions, Gordon Anderson, et al.
   9. Response to Charge Questions, James Brainard
  10.Response to Charge Questions, Michael Seibert
  11.Response to Charge Questions, William Cannon
  12.Response to Charge Questions, David Pletcher
  13.Response to Charge Questions, Paul Blum
  14.Response to Charge Questions, Ronan Fleming
  15.Response to Charge Questions, Jeffrey Lewis
  16.Response to Charge Questions, Dylan Chivian
  17.Response to Charge Questions, David Reiss
  18.Response to Charge Questions, Xiao-Jiang Feng
  19.Response to Charge Questions, Tatiana Karpinets
 

 

Agenda (Breakout Session D)

 2:00 - 2:30 p.m.

Bob Cottingham, Microbial Systems Biology Knowledgebase: Scientific Objectives and Current Prospects

  Focus on examples of scientific objectives, benefits and outcomes
 
 
 2:30 - 3:00 p.m. Discussion
 3:00 - 3:30 p.m. Bob Kelly, Near-Term Prospects for Functional Microbial Genomics: Moving Beyond the Monoculture Paradigm
  One organism to two organism, adding complexity
 
 

Subpages (1): Charge Question Responses