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!

 

News
Latest News

KBase Paper Published in Nature Biotechnology

We are pleased to announce that our team has published a comprehensive overview of KBase and an assessment of its scientific impact in Nature Biotechnology. The paper describes the unique features and infrastructure of the KBase platform, in addition to highlighting scientific use cases that demonstrate its significance for biology research. We encourage you to review the main text and the supplementary information […]

Profile of KBase Engineer Arfath Pasha

KBase staff member Arfath Pasha, an advanced applications engineer at Brookhaven National Lab (BNL), is part of the team working to improve the infrastructure and search capabilities of the knowledgebase. Arfath brings his engineering expertise to the project and highlights how KBase facilitates collaboration between those who use the system and help develop it. He […]

Looking for More?

WE’RE HERE TO HELP

Contact Us