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

Over the past two decades, the scale and complexity of genomics technologies and data have advanced from sequencing genomes of a few organisms to generating metagenomes, genome variation, gene expression, metabolites, and phenotype data for thousands of organisms and their communities. Here we present the DOE Systems Biology Knowledgebase, an open-source software and data platform that enables data sharing, integration, and analysis of microbes, plants, and their communities.

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.

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 at PAG 2019

Want to learn about latest and greatest KBase capabilities for plant science? Be sure to check out the following KBase events at PAG 2019! Ask questions, learn from team members, and participate in hands-on workshops and demos. KBase & JGI Booth: Exhibit Hall Booth 509 Poster: Integrating Transcriptomic & Metabolic Model Analysis using KBase January […]

November 2018 KBase Webinars

Learn about using KBase for your systems biology and bioinformatics research with one of our free webinars! Each webinar will demonstrate workflows, tools, and best practices for analyzing data in KBase. Be sure to create a free KBase account to follow along and begin using KBase! Sign up for the webinars using this link: https://goo.gl/forms/0u4iWjRxJkwH8Zkm1 […]

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