Welcome to the Quarterly KBase User update. We are excited to continue sharing your awesome accomplishments from the past 3 months.
Oct 12, 2022

Quarterly User Update (July – September 2022)

Community Highlight

Learn about the latest releases and updates from collaborations this quarter!

From the KBase Educator Community, Tim Paustian offered his perspective as a Teaching Professor on how introducing students to bioinformatics tools and concepts is more accessible using KBase at the University of Madison – Wisconsin. Read the Highlight here: https://www.kbase.us/tim-paustian/.

Interested in using KBase with your students? Read about the community and how to join here: https://www.kbase.us/engage/educators/, where you can access teaching resources! Including a transcriptomics analysis workflow that applies RNA sequencing data contributed by Kevin Myers Great Lakes Bioenergy Research Center.

KBase attended the Joint Genome Insitute’s 2022 Annual User Meeting in August! We hosted our first hybrid workshop for meeting attendees! Nicholas Dove, AgBiome, presented on mapping out how soil microbiomes respond to wildfires for the KBase short talk. You can check out the research in this Narrative: https://kbase.us/n/118958/38/.

“Ten simple rules for getting and giving credit for data” compiled by KBase members Elisha Wood-Charlson, Zach Crockett, and Adam Arkin, alongside Chris Erdmann, American Geophysical Union, and Carly Robinson, Office of Scientific and Technical Information came out at the end of September. Read the publication here: https://doi.org/10.1371/journal.pcbi.1010476.

If you are interested in publishing your research with KBase or being featured as a highlight, please email us at engage@kbase.us, and we would be happy to review your Narratives and get them ready for show time!

Publications using KBase

Super neat research utilizing the KBase platform came out over the past few months! These stories include a discovery of a ‘giant’ centimeter long bacterium (Volland et al. 2022) by a collaboration that included the Joint Genome Institute (read more about the research from the JGI here), what shapes bacterial community niches on leaves (Murillo-Roos et al. 2022), and metagenome-assembled genomes (also known as MAGs) of three ammonia-oxidizing bacteria strains from agricultural soils (Yerlan et al. 2022).

If you used KBase for your research, and we are missing your publication, please let us know at engage@kbase.us! In addition, we want to work with you to better support citation metrics for your work in KBase and are piloting a “Publishing with KBase” project. Contact us if you are preparing a manuscript for publication!!!

New Webinars & Workshops

In the past three months, the KBase team put together four webinars to share with the community, which are all available on the DOE KBase YouTube Channel. The first two installments in a series on Microbial Genomics Analysis in KBase (available here: https://bit.ly/microbial-genomics-webinars) were hosted by Ben Allen and went through in depth workflows of Drafting and Improving Isolate Genomes in Part 1 and Comparative and Gene Feature Analysis in Part 2. Stay tuned for Part 3 in the coming few weeks!

Zach Crockett presented an updated tutorial on linking environmental sampling metadata to your experimental data in KBase. The suite of Samples features was released just about a year ago in 2021. And Ellen Dow held a Fall Orientation to the Educators Community along with updates on new resources from our working groups.


And finally, to close out our update, here is a summary of our user numbers to date. Keep doing great science in KBase! The KBase team is here to collaborate and support you ⏤ our community.

The graphic provides the following statistics for KBase from July to September 2022. Help Board Tickets for Q3 were 3 Feature Requests, 21 Closed Questions, 16 Open Questions, 20 Open Bugs and 12 Closed Bugs that fill out a pie chart. Twitter had 33,000 Impressions, 19,000 Profile Visits, 79 new followers and 1960 total followers. YouTube had 4 new videos posted with 3,700 views, 86 new subscribers for a total of 735 subscribers; the kbase.us site had 5715 New visitors, 7499 total visitors and 18000 visits to the site. There were 1308 new user accounts added to the platform for a total of 25710 accounts. The total number of Narratives is 57600 with 3355 new Narratives. User data grew by 38 terabytes for a total of 471 terabytes. Publicly available data that was last updated in July 2022 has a total of 16.7 terabytes. Thirty five new publications cited using KBase for a total of 385 publications since 2014. Top App categories were assembly, communities, and annotation.

KBase by the numbers from the Quarterly Report covering July through September 2022.


Ellen Dow
Ellen Dow
Lawrence Berkeley National Laboratory

Ellen G. Dow, Ph.D. is a member of the outreach, communications, and user development team. Inspired by involvement in science outreach throughout graduate school, she left the bench to gain experience in informal education and cultivate community engagement from the general public to science sectors. A molecular biologist by training, Ellen applies her research experience to support scientists and develop resources for the KBase community.