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Systems Biology for Energy and the Environment

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Genomic Science Program

DOE Systems Biology Knowledgebase
for a New Era in Biology
A Genomics:GTL Report from the May 2008 Workshop

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To promote development of a data and information management system, or knowledgebase, DOE's Office of Biological and Environmental Research (BER) hosted a workshop May 28-30, 2008, in Washington, D.C. Experts from scientific disciplines relevant to DOE missions and from the enabling technologies (e.g., bioinformatics, computer science, database development, and systems architecture) met to determine the opportunities and requirements for developing and managing this knowledgebase for BER's Genomic Science program (formerly Genomics:GTL).

Publication date: March 2009

Suggested citation: U.S. DOE. 2009. U.S. Department of Energy Office of Science Systems Biology Knowledgebase for a New Era in Biology: A Genomics:GTL Report from the May 2008 Workshop, DOE/SC-113, U.S. Department of Energy Office of Science (

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  • Cover and Table of Contents (PDF, 208 kb)
  • Executive Summary (PDF, 276 kb)
  • Introduction (PDF, 1256 kb)
  • Data, Metadata, and Information (PDF, 393 kb)
  • Data Integration (PDF, 472 kb)
  • Database Architecture and Infrastructure (PDF, 367 kb)
  • GTL Knowledgebase Community and User Issues (PDF, 143 kb)
  • Appendices
    1. Information and Data Sharing Policy (PDF, 112 kb)
    2. Use Case Scenarios of Systems Biology Investigations Utilizing the GTL Knowledgebase (PDF, 811 kb)
    3. Systems Biology for Bioenergy Solutions (PDF, 217 kb)
    4. Opportunities and Requirements for Research in Carbon Cycling and Environmental Remediation (PDF, 127 kb)
    5. Summary List of Findings from Introduction (PDF, 89 kb)
    6. Bibliography (PDF, 100 kb)
    7. Descriptions of a Selected Sampling of Databases Having Relevance to the GTL Knowledgebase (PDF, 146 kb)
    8. Genomics:GTL Systems Biology Knowledgebase Workshop: Agenda, Participant List, and Biosketches (PDF, 177 kb)
    9. Glossary (PDF, 127 kb)
    10. List of Web Addresses (PDF, 88 kb)
    11. Acronyms and Abbreviations (PDF, 137 kb)

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