Quarterly User Update (April – June 2022)

Community Highlight

The team was able to meet up with users at several events over the past few months from conferences to workshops, both in person and virtual! 

KBase participated in the Joint Berkeley Initiative for Microbiome Sciences Spring Seminar this past May, bringing together established and early career researchers from University of California – Berkeley and Lawrence Berkeley National Laboratory. 

We held several workshops for users in June. Two workshops took place at the CROPS Conference hosted by HudsonAlpha on Plant Science and the KBase Educators program. KBase also hosted workshops on metagenomics for the University of California – Riverside Microbiome Initiative Metagenomics and metabolic modeling for S2M2 – Summer School in Metabolic Modeling. Then we introduced the National Summer Undergraduate Research Project (NSURP; https://nsurp.org/) to the Narrative platform, how to create a workflow, and everyone joined the NSURP 2022 Organization!

If your group is interested in learning how to advance their science in KBase, please reach out at engage@kbase.us.

Publications Using KBase

KBase was referenced in 20 publications this quarter for analyses across a wide span of studies and locations; from identifying microbial communities rich in thiosulfate and sulfate-reducing microorganisms in the Permian Basin of West Texas to draft isolate genomes of Pseudomonas from the Permafrost of Svalbard, Norway, an island near to the North Pole (Tinker et al. 2022; Sipes et al. 2022).

You can also read about how tools in the Narrative platform were applied to projects researching lignin-degradation for biofuel applications and modeling metabolic interactions of gut microbiome (Chaput et al. 2022; Catlett et al. 2022). A JGI research team imported paired-ends reads into the Narrative to assemble reads from a huge bacterium – called a “‘macro’ microbe” – found in Guadelupe mangroves (Volland et al. 2022). Explore more publications at: https://www.kbase.us/research.

If you used KBase for your research, and we are missing your publication, please let us know at engage@kbase.us!

We want to work with you to better support citation metrics for your work in KBase and are piloting a “Publishing with KBase” project. Please contact us if you are preparing a manuscript for publication!!!

New Webinars

Dr. Adam Arkin, KBase’s lead Principal Investigator, hosted a webinar on multi-omic analysis of environmental sampling data to drive their research using the platform. Adam demonstrated how he and his team used the KBase Samples services to organize multiple collection campaigns from the Ecosystems and Networks Integrated with Genes and Molecular Assemblies (ENIGMA) project and then analyze linked measurements of amplicons, metagenomes, and chemical abundances. 

View the recorded webinar here: https://youtu.be/TXXXgDgZgiw.

Summary

In closing, we celebrate our user numbers this quarter – from data in the system to publications to the online community. We even surpassed 24,000 total user accounts! Keep doing great science in KBase. The team is here to support you, from helping you get started through publishing your research. 

User Numbers from the KBase Quarterly Report from April through June 2022.