Acknowledgements

Funding: This work is supported as part of the BER Genomic Science Program. The DOE Systems Biology Knowledgebase (KBase) is funded by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research under Award Numbers DE-AC02-05CH11231, DE-AC02-06CH11357, DE-AC05-00OR22725, and DE-AC02-98CH10886.

 

How to cite KBase:

Project Paper

Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, et al. KBase: The United States Department of Energy Systems Biology Knowledgebase. Nature Biotechnology. 2018;36: 566. doi: 10.1038/nbt.4163

Protocols

Chivian D, Jungbluth SP, Dehal PS, Wood-Charlson EM, Canon RS, Allen BH, et al. Metagenome-assembled genome extraction and analysis from microbiomes using KBase. Nature Protocols. 2022. doi:10.1038/s41596-022-00747-x

Allen BH, Gupta N, Edirisinghe JN, Faria JP, Henry CS. Application of the Metabolic Modeling Pipeline in KBase to Categorize Reactions, Predict Essential Genes, and Predict Pathways in an Isolate Genome. Navid A, editor. Microbial Systems Biology: Methods and Protocols. 2022; 291–320. doi:10.1007/978-1-0716-1585-0_13

Kumari S, Kumar V, Beilsmith K, Seaver SMD, Canon S, Dehal P, et al. A KBase case study on genome-wide transcriptomics and plant primary metabolism in response to drought stress in Sorghum. Current Plant Biology. 2021;28: 100229. doi:10.1016/j.cpb.2021.100229

Allen B, Drake M, Harris N, Sullivan T. Using KBase to Assemble and Annotate Prokaryotic Genomes. Current Protocols in Microbiology. 2017;46: 1E.13.1-1E.13.18. doi:10.1002/cpmc.37