KBase: Open-source Platform for Collaborative Biological Data Analysis and Publication
The U.S. Department of Energy's Systems Biology Knowledgebase (KBase; www.kbase.us) is an open, collaborative platform that integrates data, models, and analysis tools to accelerate discovery in microbiology, plant biology, and environmental systems. Recently, KBase expanded as a comprehensive, multi-omics ecosystem. KBase enables representation of scientific samples, long-read sequence analysis, protein structure integration, and scalable modeling of microbial communities across diverse environments. KBase also generates digital notebooks as citable, executable research objects that link data, methods, and interpretation. KBase also supports a global education community focused on training the next generation of scientists to use high-performance computational tools. Together, these advances position KBase as a central hub for open, reproducible systems biology. In turn, this enables us to integrate many of the emerging advances in data federation, semantic interoperability, and agent-assisted analysis, paving the way for KBase to support the next generation of AI-driven discovery tools.
Authors
- Paramvir Dehal (ORCID: https://orcid.org/0000-0001-5810-2497)
- Prachi Gupta (ORCID: https://orcid.org/0009-0001-1692-2304)
- Christopher J. Neely (ORCID: https://orcid.org/0000-0002-2620-8948)
- Andrew P. Freiburger
- Dylan Chivian (ORCID: https://orcid.org/0000-0001-8189-8729)
- Shane Canon (ORCID: https://orcid.org/0000-0002-8440-738X)
- Robert W. Cottingham (ORCID: https://orcid.org/0000-0002-2775-3905)
- Boris Sadkhin (ORCID: https://orcid.org/0000-0003-2759-8850)
- Keith Keller (ORCID: https://orcid.org/0000-0002-1546-7522)
- Dileep Kishore (ORCID: https://orcid.org/0000-0003-4859-8681)
- Priya Ranjan (ORCID: https://orcid.org/0000-0002-0357-1939)
- D.Dakota Blair
- Sam Seaver
- Filipe Liu
- Dan Klos
- Janaka N. Edirisinghe
- Roy Kamimura
- José P. Faria
- Zach Crocket
- Ziming Yang
- Gazi Mahmud
- Pamela Weisenhorn
- AJ Ireland
- David Lyon
- William J. Riehl
- Kathleen Bielsmith
- Gwyneth A. Terry
- Mikaela Cashman
- Ellen Dow
- Ben Allen
- Gavin Price
- Adam P. Arkin
- Sean Jungbluth
- Christopher Henry
- Tianhao Gu
- Yue Wang
- Shinjae Yoo
- Ahmed Khan
- Katherine O’Grady
Institutions
- Argonne National Laboratory (US)
- Oak Ridge National Laboratory (US)
- Lawrence Berkeley National Laboratory (US)
- Brookhaven National Laboratory (US)
Publication Details
- Journal
- Journal of Molecular Biology
- Published
- 2026-02-01
- DOI
- https://doi.org/10.1016/j.jmb.2026.169676
- Primary Topic
- Scientific Computing and Data Management
- Type
- article
- Field-Weighted Citation Impact
- 0.00