Quarterly User Update (July – September 2024)
Community Highlights
We shared three News highlights featuring members from the KBase Community that each participated in different workshops featuring KBase!
For July, Dr. Lauren Cole-Osborn shared how she used an RNA-seq workflow in KBase that she learned at a workshop during the American Society of Plant Biologists Plant Biology Meeting in 2021 to analyze biosynthesis gene regulation in medicinal plants: https://www.kbase.us/news/lauren-cole-osborn/.

Lauren watering plants. Photo credit – Ruby Wallau, Northeastern University
In August, Dr. Aimee Kessell told us about her contributions to the Soil Microbiome Science Focus Area collaboration between the Song Lab at the University of Nebraska – Lincoln, Pacific Northwest National Laboratory, and KBase. Aimee visited Argonne National Laboratory as part of her work to update metabolic modeling tools in KBase through the addition of OMEGGA (OMics-Enable Global GApfilling) to ModelSEED2: https://www.kbase.us/news/aimee-kessell/.
Our final highlight of the quarter was Dr. Jennifer Goff, a new professor at SUNY College of Environmental Science and Forestry (ESF) and prior post-doc on the DOE-funded ENIGMA Science Focus Area. Alongside sharing her experiences attending the bioinformatics portion of the Long-read Isolate Sequencing and Assembly Workshop in December 2023, Jennifer shared about how she uses KBase to train and provide opportunities for her students to author data publications: https://www.kbase.us/news/jennifer-goff/.

Jennifer Goff leading a workshop at State University of New York College of Environmental Science and Forestry. Photo courtesy of Jennifer Goff, SUNY ESF.
If you are interested in a KBase Highlight on your work or projects, email us at engage@kbase.us.
Workshops and Training
The KBase team held a few webinars for the community, including the annual Fall Educator Orientation that introduces instructors to teaching resources developed by the community of educators using KBase with their students. Learn about KBase Educators here: https://www.kbase.us/engage/educators/. Ben Allen also hosted an Introduction to KBase in September, which is available on the KBase YouTube Channel: https://www.youtube.com/@DOEKBase.
Part of the User Engagement team traveled to Cape Town, South Africa in August to support a workshop as part of the 19th Meeting for the International Society of Microbial Ecology, alongside the Colorado State Microbiome Center (CoSMiC) and National Microbiome Data Collaborative (NMDC). The From Reads to Function Workshop trained 25 in-person participants from African countries in metagenomic analyses tools and workflows using a dataset from the Congo River. The lecture portion was hybrid, with 200 virtual participants from over 50 countries registered! Learn more about the workshop, and the great group of African delegates that participated here: https://www.kbase.us/isme19-workshop/.

Workshop participants and instructors at Stellenbosch University in Cape Town, South Africa.
Publications using KBase
The platform and team behind KBase supports users from analyzing their data and following FAIR (findable, accessible, interoperable, reusable) data principles through publication. In Q3 (July-September), 46 published studies cited using KBase to analyze microbes collected from environments across the globe! This means our community has already surpassed the total number of publications from 2023! Recent publications range from projects investigating subsurface bacterium (Thorgersen et al. 2024), to methods for refining metabolic models built from metagenomic datasets (Majzoub et al. 2024).
We have community guidelines with best practices on how to publish in KBase. If you are curious about how we are working to measure the impact of your data and analysis efforts, beyond publications, please contact us!
All publications using KBase are available at: https://www.kbase.us/research. If we are missing your publication citing KBase in your methods, please let us know at engage@kbase.us.
Summary
To close out our update, here is a summary documenting July through September 2024 user numbers. Keep doing great science in KBase. The KBase team is here to support you!

KBase by the numbers from the Quarterly Report covering July through September 2024.