Advancing biology research

Advancing biology research

Narratives are interactive, dynamic, and persistent documents designed to make systems biology research transparent, collaborative, and reproducible. You can read, copy, and build on these Narratives, and then share your results with the research community. Below we highlight how scientists are using KBase in their research.

For a list of all tools in KBase, check out our App Catalog.

Research Narratives

Research Narratives

These Narratives represent computational experiments or reproducible publications. They capture data and analysis, along with commentary on why each steps was performed and what the results show. You can copy any Narrative to create your own version where you can rerun analyses with your own data, or even change the analyses.

For some Narratives, you may need to sign into KBase to view them. If you do not have a KBase account, you can create a free account to access Narratives and more.

Made by Priya Ranjan

Members of the Ethylene-Response Factor (ERF) gene family encode transcription factors that are involved in various important developmental and physiological processes in plants. In this Narrative, KBase tools are used to discover and characterize ERF

Made by Janaka Edirisinghe

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

Publications using KBase

Publications using KBase

Metagenome-Assembled Genome (MAG) of Oceancaulis alexandrii NP7 isolated from Mediterranean Sea polluted marine sediments and its bioremediation potential. G3 Genes|Genomes|Genetics. 2021 [cited 6 Jul 2021]. doi:10.1093/g3journal/jkab210

Unexpected discovery of hypermutator phenotype sounds the alarm for quality control strains. Genome Biology and Evolution. 2021. doi:10.1093/gbe/evab148

Hymenobacter caeli sp. nov., an airborne bacterium isolated from King George Island, Antarctica. International Journal of Systematic and Evolutionary Microbiology. 71: 004838. doi:10.1099/ijsem.0.004838

A standardized archaeal taxonomy for the Genome Taxonomy Database. Nat Microbiol. 2021;6: 946–959. doi:10.1038/s41564-021-00918-8

Biogeochemistry of the Antrim Shale Natural Gas Reservoir. ACS Earth Space Chem. 2021. doi:10.1021/acsearthspacechem.1c00087

KBase collaborations

KBase collaborations

The following collaborative projects are supported by the Department of Energy’s Science Focus Areas (SFAs). The combined research efforts of these collaborations span more than 90 people across 7 national laboratories, 17 universities, and 2 DOE User Facilities.

Studying lignocellulosic biomass and how it can be used to generate renewable biofuels is the focus of this SFA, located at Oak Ridge National Laboratory (ORNL).

Bacterial-fungal interactions within the soil are the focus of this SFA, located at Los Alamos National Laboratory (LANL).

The ENIGMA SFA is located at Lawrence Berkeley National Laboratory (LBNL) and strives to understand the relationship between molecules, microbes, communities, and the ecosystems they inhabit.

The first of two SFAs located at Lawrence Livermore National Laboratory (LLNL), the Biofuels SFA is focused on the community systems biology of microbial consortia that are closely associated with bioenergy-relevant plants and algae.

Also located at LLNL, the Soil Microbiome SFA studies soil metagenomes to uncover the mechanisms of the critical role that microbes play in the carbon cycle within the soil.

The KBase project paper

The KBase project paper

The KBase project paper details the unique features and infrastructure of the KBase platform, and illustrates how two scientists might use KBase to perform collaborative systems biology analysis, resulting in a reproducible, interactive Narrative for publication.

*How to cite: Arkin AP, Cottingham RW, Henry CS, et al. KBase: The United States Department of Energy Systems Biology Knowledgebase. Nature Biotechnology. 2018;36: 566. doi: 10.1038/nbt.4163

Looking for information on tools and resources?

Check out KBase Documentation for our Getting Started guide and information on tools in the App Catalog. KBase is a fully open source software project available on GitHub.