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!

 

News
Latest News


New KBase modeling protocol available from Springer

KBase offers a comprehensive suite of tools for generating and refining metabolic models. Modeling researchers have observed that genome-scale metabolic models (GEMs) generated from automated reconstruction pipelines often lack accuracy in energy biosynthesis. It is therefore often useful to construct a simplified version of a GEM: a core metabolic model (CMM) that is comprised of […]

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