A collaborative, open environment for systems biology

of plants, microbes and their communities

KBase: The U.S. Department of Energy Systems Biology Knowledgebase

In KBase, you can create shareable, reproducible workflows called Narratives that include data, analysis steps, results, visualizations and commentary.

Research Highlights

KBase annotation and metabolic modeling pipelines were used to analyze a 13-species electrosynthetic community that captures electrons from a cathode and fixes carbon dioxide. Metabolic models of the predominant community members revealed that Acetobacterium is the primary carbon fixer for the community, excreting large amounts of acetate which serves as the main carbon source for the rest of the community.

In a Journal of Cellular Physiology cover article, KBase scientist Christopher Henry and collaborators demonstrate strategies for constructing genome-scale metabolic networks that simulate two species in a microbial consortium exchanging metabolites to sustain life.

Integrated Data and Tools

Analyze a wide range of public bioinformatics data together with your own data.


Explore KBase’s analysis tools (Apps) in the App Catalog.


Transfer high-throughput sequencing data from   the JGI Genome Portal to KBase for analysis.


KBase is an open platform — find out how to add your own analysis tools!


Latest News

KBase User Meeting in San Francisco, March 13-14, 2018

The 2018 KBase User Meeting will take place March 13-14 as part of the DOE Joint Genome Institute’s Genomics of Energy and Environment Meeting in San Francisco. A poster and four workshops will show attendees how to use KBase to build, execute and share systems biology analysis workflows including genome analysis, functional analysis, exploration of […]

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