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Summer 2018 Newsletter
The U.S. Department of Energy (DOE) Systems Biology Knowledgebase (KBase) is a knowledge creation and discovery environment designed for both biologists and bioinformaticians.
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| KBase Project Paper in
Nature Biotechnology
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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 to learn more about what KBase can do for your research. Special thanks to all of our users, to the team members who helped build KBase, and to the US Department of Energy for its support of the project. Sign up for a free account today and discover how the cutting edge KBase platform can advance your biology and bioinformatics research!
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Narrative Upgraded to Version 3.8
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The latest version of the Narrative Interface is now online and features several improvements to the main working environment for KBase. You can read the full release notes here on Github. Here are some highlights:
- Major improvements to accessing and adding Public Data from the Data Panel
- Improvements to look and feel of Narratives
- Support for viewing new version of Genome data type
- Adds "show report" button in Data Panel for data associated with reports
- Fixes incorrect name issue when loading Public Data
- Fixes to viewers for various expression data types
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| Recent Publications Using KBase |
Several new publications have been released that showcase the diversity of applications for KBase in genomics research. Check out how scientists are using KBase to explore data, run analyses, and discover new findings.
- Faria JP, Rocha M, Rocha I, Henry CS. Methods for automated genome-scale metabolic model reconstruction. Biochemical Society Transactions. 2018
- Wilhelm RC, Hanson BT, Chandra S, Madsen E. Community dynamics and functional characteristics of naphthalene-degrading populations in contaminated surface sediments and hypoxic/anoxic groundwater: “Dynamics of groundwater naphthalene biodegradation.” Environmental Microbiology. 2018
- Liu R, Liang L, Choudhury A, Garst AD, Eckert CA, Oh EJ, et al. Multiplex Navigation of Global Regulatory Networks (MINR) in yeast for Improved Ethanol Tolerance and Production. Metabolic Engineering. 2018
- Metz ZP, Ding T, Baumler DJ. Using genome-scale metabolic models to compare serovars of the foodborne pathogen Listeria monocytogenes. PLOS ONE. 2018
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| Newsletter #8 |
August 2, 2018 |
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