Read about what the KBase community and team has been up to lately!
Jul 11, 2023

Quarterly User Update (April – June 2023)

Welcome to the second quarterly update of 2023. Learn about what the community has been up to over the past 3 months.

Community Highlights

The KBase team continued its journey on the road in April! 

Alongside Science Focus Area (SFA) collaborators, KBase attended the U.S. Department of Energy Office of Science Genomic Science Program Principal Investigator meeting in April ( It was exciting to see how the SFAs utilizing and developing new tools for KBase build upon one another to model systems biology more effectively across talks and posters! Ben Allen led a workshop for 25 DOE-funded researchers at the meeting. To support DOE and collaborative efforts, KBase released resources for Data Management Plans (DMPs) and Promoting Inclusive and Equitable Research (PIER) Plans available, which can be found here:

We held our third hybrid working at University of Massachusetts – Amherst in April, providing a hands-on experience for 30 participants to dig into more complex analyses. 

As the summer National Science Foundation Research Experiences for Undergraduates (REU) programs started in June, KBase was called in to introduce students to the platform. We presented to the University of Tennessee – Knoxville Microbiology REU to about 20 participants in person and to the virtual National Summer Undergraduate Research Project REU for 43 participants online. 

KBase Team Member Zach Crockett presents to a room full of student interns seated in rows in bright blue chairs with their laptops.

Zach Crockett leading a workshop on KBase for UTK Microbiology REU interns.

We are also participating in the Berkeley Lab K-12 Experiences in Research program. This summer, two high school interns are learning how to assemble and annotate genomes and develop workflows applying American Society for Microbiology – Microbiology Resource Announcement (MRA) standards within the Narrative research environment. Anyone can use MRA template Narratives for their isolate genome and metagenome-assembled genome (MAG) announcements. Access copy and editable versions in the Narrative here: isolates, MAGs

If you are interested in having KBase run a workshop at your institution or for your program, please reach out to the team at

Publications Using KBase

KBase was cited across a variety of research topics in 52 publications this quarter. Published articles included DOE-funded research, including analysis of woodchip bioreactor microbiomes and functional capabilities (McGuire, et al. 2023) to establishing best practices through new minimum standards for describing methanogenic archaea taxa (Prakash, et al. 2023) to hydrocarbon-degrading marine microcosm metagenome-assembled genomes (MAGs) resource announcements (Barnes, et al. 2023). You can explore all publications using KBase at:

If we are missing your research publication that uses KBase, let us know at!

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!!!

Your Input Requested!

The Biological and Environmental Research Advisory Committee is looking for feedback! The US Department of Energy’s Office of Science is seeking input on the need and the structure of a unified data framework that links or integrates existing data activities within the Biological and Environmental Research Program (BER).

Learn more about the Request for Information and provide your input before October 31 here:


Lastly, to close out our update, here is a summary of the numbers and statistics from April through June. Keep doing great science. The KBase team is here to support you!

The graphic provides the following statistics for KBase from April to June 2023. Help Board Tickets had 3 Feature Requests, 42 Closed Questions, 18 Open Questions, 13 Open Bugs and 21 Closed Bugs that fill out a pie chart. Twitter had 17,700 Impressions, 3,600 Profile Visits, 16 new followers and 2080 total followers. YouTube had 4,700 views, 81 new subscribers for a total of 981 subscribers; the site had 8,660 new visitors, 11,000 total visitors and 29,000 visits to the site. There were 1685 new user accounts added to the platform for a total of 31,346 accounts. The total number of Narratives is 72,000 with 3,701 new Narratives. User data grew by 63 terabytes for a total of 647 terabytes. Public Data grew by 36 gigabytes to 16.9 terabytes. Fifty two new publications citing KBase made a total of 494 publications since 2014. Top App categories were communities, assembly, and annotation.

KBase by the numbers from the Quarterly Report covering April through June 2023.

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.