The first update for 2026 is live! Hear from the KBase Community and team on what we have been working on since the start of the year. https://lnkd.in/gSi-_td4
DOE Systems Biology Knowledgebase (KBase)
Research Services
KBase is a bioinformatics platform designed to investigate microbes, microbial communities, and plants.
About us
The Department of Energy Systems Biology Knowledgebase (KBase) is a software and data science platform designed to run sophisticated systems biology workflows that model plant and microbial physiology and community dynamics. KBase integrates data and tools in a single platform, enabling scientists to upload their own research data to analyze with collaborator and public data in reproducible workflows that can be shared and published. Established in 2011, KBase is run by an interdisciplinary and collaborative team at Lawrence Berkeley National Laboratory, alongside Argonne National Laboratory, Brookhaven National Laboratory, and Oak Ridge National Laboratory. Funded by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research through the Genomic Sciences Program under Award Numbers DE-AC02-05CH11231, DE-AC02-06CH11357, DE-AC05-00OR22725, and DE-AC02-98CH10886.
- Website
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https://www.kbase.us/
External link for DOE Systems Biology Knowledgebase (KBase)
- Industry
- Research Services
- Company size
- 11-50 employees
- Headquarters
- Berkeley
- Type
- Government Agency
- Specialties
- Systems Biology, Genomics, Metagenomics, Data, Plant, Microbe, Data Science, and Bioinformatics
Locations
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Primary
Get directions
Berkeley, US
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Lemont, US
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Upton, US
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Oak Ridge, US
Employees at DOE Systems Biology Knowledgebase (KBase)
Updates
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Our March community highlight features Rian Pierneef, a Senior Lecturer at the University of Pretoria in South Africa. Rian shares the impact of using KBase in train early career researchers during bioinformatics analysis workshops. https://lnkd.in/gqTsGeay
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Elizabeth McDaniel is our featured Community Highlight for February! Elizabeth shares part of her work at Microcosm Foods to develop a fermented foods microbiome database readily accessible to anyone via KBase. https://lnkd.in/dUkSZ7Cx
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DOE Systems Biology Knowledgebase (KBase) reposted this
Learn computational biology skills to carry out identification and analysis of microbial isolate genomes using KBase. Appropriate for all career stages of students, researchers and educators. Save your seat for the first webinar on March 11! Learn more and register today: https://brnw.ch/21wZHhp
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The teams at the DOE Joint Genome Institute (JGI) and the DOE Systems Biology Knowledgebase (KBase) are proud to announce the launch of the first version of a new data transfer service (DTS) between their platforms. The initial version of DTS enables users to push data from their IMG Genome Cart into their KBase Staging Area. Users can search and find genomes of interest to move to KBase using the normal IMG/MER interface. After selecting the genomes to push, add them to your cart. With the genomes selected, go to the "Upload & Export & Save" tab, provide a name and description for the transfer job, then click "Push to KBase" to begin the transfer. File transfers are available for .fna (FASTA sequence only) and .fna + .gff (sequence and annotation). Currently, the JGI-KBase DTS only supports transferring isolate genomes sequenced by JGI. However, MAGs and other data types will be integrated soon. We encourage JGI and KBase users to try out the DTS and report any issues by creating a ticket on the KBase Help Board. Watch this YouTube video tutorial to learn more: https://lnkd.in/eqjSH9_B
Data Transfer Service Tutorial
https://www.youtube.com/
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Maureen Morrow, a professor at SUNY New Paltz, is our first Community Highlight of 2026. Maureen shares how she uses KBase for training students and research-including a Fulbright that brought her to Chile! Read the full highlight: https://lnkd.in/gBzMrib3
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Our latest update shares wins from our community members and wraps up 2025 events! Read our news post here: https://lnkd.in/gu-f999t.
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Interns across the network of national labs contribute to adding new tools and features in KBase every year. Check out our December community highlight for Bridget Allen, a recent graduate from St. John's University who interned this summer at Brookhaven National Laboratory to help build new tools in KBase. https://lnkd.in/gUABY3iG
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Thinking about KBase as a platform for teaching undergraduates? Aaron Schirmer, a professor at Northeastern Illinois University, has been utilizing KBase with his students for several years. Read his perspective in our November Community Highlight: https://lnkd.in/gWHeds5W