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Read about how the KBase community started off the year!
Apr 11, 2023

Quarterly User Update (January - March 2023)

Welcome to the first Quarterly KBase User update of 2023. Learn about what the community has been up to over the first 3 months.

Community Highlights

In February, KBase team members traveled to Berkeley Lab and enjoyed the Berkeley Botanical Gardens for a team retreat to discuss goals for an upcoming renewal in early 2024. 

Members of the DOE Energy Systems Biology Knowledgebase (KBase) hold their annual All-Hands meeting where the group discusses past successes, issues that need to be resolved, and plan for future projects that they will undertake, at the UC Berkeley Botanical Gardens, Berkeley, California, 02/22/2023. Photo credit: Thor Swift

KBase is finally back to hosting in-person (now hybrid) workshops at DOE-funded institutions! KBase held two workshops in March, at the University of Wisconsin – Madison and North Carolina State University. Participants included 25 in-person and 16 virtual at UW – Madison, and 25 in-person and 30 virtual at NC State. About 75% of the participants at each institution were new to using KBase. 

KBase also hosted a Plant Science workshop at the Plant & Animal Genome Conference reaching about 100 participants. 

If you are interested in having KBase run a workshop at your institution, please reach out at engage@kbase.us.

Publications Using KBase

KBase was used in a variety of research topics across 26 publications this quarter, from studies based on metagenome-assembled genomes (MAGs) from the bacterial metagenomes of octocorals (Keller-Costa et al. 2023) to the microbiomes of peatlands (AminiTabrizi et al. 2023). The metagenome-assembled genome (MAG) extraction and analysis in KBase protocol published at the end of last year in Nature (Chivian et al. 2022) was featured as a 2023 Science Highlight by the Biological and Environmental Research Program in January (https://science.osti.gov/ber/Highlights/2023/BER-2023-01-d)! You can explore all the publications using KBase at: https://www.kbase.us/research.

If you used KBase for your research, and we are missing your publication, 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

While the team has been focused on returning to in-person workshops, the Introduction to KBase webinar was offered on 15 March 2023, with over 250 registered attendees 

All webinars are available on the KBase YouTube Channel: https://www.youtube.com/doekbase or from https://www.kbase.us/learn/.

Summary

And finally, to close out our update, here is a summary of the numbers and statistics from January through March. Keep doing great science in KBase. The KBase team is here to support you!

The graphic provides the following statistics for KBase from January to March 2023. Help Board Tickets had 4 Feature Requests, 37 Closed Questions, 10 Open Questions, 18 Open Bugs and 13 Closed Bugs that fill out a pie chart. Twitter had 29,000 Impressions, 4,400 Profile Visits, 71 new followers and 2063 total followers. YouTube had 1 new video posted with 4,900 views, 71 new subscribers for a total of 800 subscribers; the kbase.us site had 7,877 new visitors, 11,000 total visitors and 25,800 visits to the site. There were 1391 new user accounts added to the platform for a total of 29078 accounts. The total number of Narratives is 66,300 with 2,713 new Narratives. User data grew by 40 terabytes for a total of 567 terabytes. One hundred sixty five different Narratives have been made publicly available, with 9 new Narratives. Twenty six new publications cited using KBase for a total of 463 publications since 2014. Top App categories were annotation, metagenomics, and assembly.

KBase by the numbers from the Quarterly Report covering January through March 2023.

About the Authors

Ellen Dow
Ellen Dow
Lawrence Berkeley National Laboratory
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.

@DOEKBase
DOEKBase
DOE Systems Biology Knowledgebase
engage@kbase.us
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