KBase: The Systems Biology Knowledgebase

The DOE Systems Biology Knowledgebase (KBase) is a collaborative effort designed to accelerate our understanding of microbes, microbial communities, and plants. It will be a community-driven, extensible and scalable open-development software framework and application system that will leverage major existing scientific capabilities and supercomputing facilities within the DOE national laboratory complex. KBase will offer free and open access to data, models and simulations, enabling scientists and researchers to easily build new knowledge and share their findings. It will also integrate commonly used core tools and their associated data, and construct new capabilities on top of the integrated data. New functionality will allow users to visualize data, create models or design experiments based on KBase-generated suggestions.
A cloud-style project, KBase will make biological data and analysis capabilities available behind a series of well-structured APIs that will be accessible by remote users. These abstractions will permit scaling the computing infrastructure and services that provide these APIs to meet community needs.
Several universities and DOE national laboratories have partnered to create the first implementation of this comprehensive platform. The collaboration includes Argonne, Lawrence Berkeley, Brookhaven and Oak Ridge National Laboratories. Also participating in the multi-institutional program are Cold Spring Harbor Laboratory; University of California, Davis; Hope College in Michigan; the University of Illinois at Urbana-Champaign; and Yale University. The Joint Genome Institute, the DOE InterBRC knowledgebase, and several university knowledgebase projects are also identified as important contributors.


This work is supported by the U.S. Department of Energy, Office of Biological and Environmental Research under Contract DE-AC02-06CH11357.

Chicago Systems Participants

  • Rick Stevens (PI)

  • Folker Meyer (UC, CI, IGSB, and ANL)

    UC Partner Participants (ANL):

  • Ross Overbeek (ANL)
  • Chris Henry (ANL)
  • Bob Olson (ANL)
  • Narayan Desai (ANL)
  • Andreas Wilke (ANL)
  • Elizabeth Marland Glass (ANL)
  • Terry Disz (ANL)
  • Veronika Vonstein (ANL)
  • Scott Devoid (ANL)
  • Sam Seaver (ANL)
  • Bruce Parrello (ANL)
  • Gordon Pusch (ANL)
  • Travis Harrison (ANL)
  • Tobias Paczian (ANL)
  • Jaren Wilkening (ANL)
  • Kevin Keegan (ANL)
  • Peter Larsen (ANL)
  • Jennifer Fessler Salazar (ANL)
  • John-Paul Navarro (ANL)

    For More Information:

    See http://genomicscience.energy.gov/compbio/