Advancing biology research
KBase allows users to run sophisticated systems biology workflows, perform large-scale analyses, and combine multiple lines of evidence to investigate genes, organisms, and their communities. Below we highlight how scientists are using KBase in their research.
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.
This study explores the complexity and prevalence of fermentation with a comprehensive analysis of the phenotype and genotype of fermentative prokaryotes.
Investigation of a Bacillus cereus strain isolated from the Oak Ridge Reservation (ORR) subsurface, contaminated with high levels of nitric acid and multiple heavy metals.
Exploration of metagenome-annotated genomes from Amazonian soils to understand microbial diversity the responses of these microorganisms to land-use change.
Publications using KBase
A pangenomic atlas reveals eco-evolutionary dynamics that shape type VI secretion systems in plant-pathogenic Ralstonia. mBio. 2024;0: e00323-24. doi:10.1128/mbio.00323-24
Determining how oxygen legacy affects trajectories of soil denitrifier community dynamics and N2O emissions. Nat Commun. 2024;15: 7298. doi:10.1038/s41467-024-51688-w
Overexpression of RuBisCO form I and II genes in Rhodopseudomonas palustris TIE-1 augments polyhydroxyalkanoate production heterotrophically and autotrophically. Applied and Environmental Microbiology. 2024;90: e01438-24. doi:10.1128/aem.01438-24
Biogeochemistry of the rare sulfidic glaciovolcanic cave system on Mount Meager, British Columbia, Canada. Front Geochem. 2024;2. doi:10.3389/fgeoc.2024.1410338
A genome-scale metabolic model of a globally disseminated hyperinvasive M1 strain of Streptococcus pyogenes. mSystems. 2024;9: e00736-24. doi:10.1128/msystems.00736-24
Collaborations
Collaborative projects represent formal partnerships that support the KBase mission and KBase user science. Collaborations fall into several themes forming KBase User Working Groups (UWGs). Example UWG members include several Dept. of Energy (DOE) Science Focus Areas (SFAs). SFAs are research projects funded by the DOE to further scientific advancement and support the DOE’s Office of Science mission.
UWG themes include: Microbiome, Metabolism, Functional Metabolism, and Data Science. Additional details are presented on the User Working Group page.
Developing detailed models of biological function within an environmental context enables researchers to explore prediction and design of ecosystem services that address challenges of climate change, land and water use, and other anthropogenic impacts.
Functional genomics collaborations investigate a range of multivariate genotype-phenotype relationships to study how genes or genomic regions are predictive of biological function in a particular environmental context.
Collaborations around metabolic networks explore how cells (free-living, host-associated, or multicellular) communicate with other cells, collaborate or compete for resources, and interact with their environment.
Microbes are diverse and pervasive, existing across space and time. Collaborations focused on understanding microbiome communities explore what microbes are where, and what they are doing there.
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.
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.
