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 video: Adding apps to KBase with the SDK

The KBase Software Development Kit (SDK) allows third-party developers to wrap open source tools into KBase as Apps. KBase users can then run these Apps on their own data in their Narratives and cite the use of these tools in their publications. Our new video explains how to get started with the KBase SDK. For […]

Host a KBase Workshop!

Interested in a workshop to help you get started using KBase for systems biology research? In just the first few months of 2018, KBase has run several hands-on workshops at universities and conferences, with a total of over 200 participants:​ Annual JGI User Meeting Annual DOE GSP Contractor-Grantee Meeting (invitation-only) University of Minho, Portugal (Centre […]

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