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

Higher N2O production in sequencing batch reactors compared to continuous stirred tank reactors: effect of feast-famine cycles. Front Environ Sci Eng. 2022;17: 50. doi:10.1007/s11783-023-1650-z

Six novel Micromonospora species associated with the phyllosphere and roots of leguminous plants: Micromonospora alfalfae sp. nov., Micromonospora cabrerizensis sp. nov., Micromonospora foliorum sp. nov., Micromonospora hortensis sp. nov., Micromonospora salmantinae sp. nov., and Micromonospora trifolii sp. nov. International Journal of Systematic and Evolutionary Microbiology. 72: 005680. doi:10.1099/ijsem.0.005680

Metagenome-assembled genome extraction and analysis from microbiomes using KBase. Nat Protoc. 2022; 1–31. doi:10.1038/s41596-022-00747-x

Functional and Safety Characterization of Weissella paramesenteroides Strains Isolated from Dairy Products through Whole-Genome Sequencing and Comparative Genomics. Dairy. 2022;3: 799–813. doi:10.3390/dairy3040055

Benchmarking second and third-generation sequencing platforms for microbial metagenomics. Sci Data. 2022;9: 694. doi:10.1038/s41597-022-01762-z

KBase collaborations

KBase 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.

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.

System Maintenance March 31 2023

We will be performing system maintenance on Friday, March 31, 2023, from approximately 10-11am PDT (12-1pm CDT).  There may be 30-60 second interruptions in service during this time.