What has the KBase community and team been up to over the Summer season?
Oct 6, 2023

Quarterly User Update (July - September 2023)

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

Community Highlights

This summer we hosted two high school interns through the Berkeley Lab K-12 Experiences in Research program that wrapped up in July. Using data shared through our partnership with the Ecosystems and Networks Integrated with Genes and Molecular Assemblies (ENIGMA) Science Focus Area, the interns learned how to assemble and annotate genomes and develop workflows applying American Society for Microbiology – Microbiology Resource Announcement (MRA) standards within the Narrative research environment.

We’d also like to let everyone know that in addition to submitting raw data to SRA, KBase is a trusted ASM database for ‘omics data! If you have a KBase account, you can use the MRA template Narratives for isolate genome and metagenome-assembled genome (MAG) announcements. Access copy and editable versions in the Narrative here: isolates, MAGs.

In August, the KBase Educators Program held our annual Fall Orientation. This webinar-style community event gives an introduction to the KBase Educators Community and teaching resources. Attendees learned how to join the Org, access teaching workflows, and find instructor support. We also introduced new resources, including teaching workflows written in Spanish and the ASM MRA Narrative templates. View the recorded webinar: https://youtu.be/PwV9QXukkE4?si=CHCqyuT5oofPmO5p.

If you are interested in using MRA Narrative Templates in KBase and have questions, please reach out to the team at engage@kbase.us.

Publications Using KBase

Users cited KBase across a variety of research topics in 27 publications this quarter. Published articles included DOE-funded research from distinguishing microbial assembly and function in root systems (King et al. 2023), to applications of KBase tools to build draft genome-scale metabolic models (Greisemer and Navid 2023), to annotating genomes in a fungal endobacteria study (Longly et al. 2023). You can explore all publications using KBase at: https://www.kbase.us/research.

If you have a research publication that uses KBase and it is not in our list, 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!

Your Input Still 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).

Provide your input before October 31 via form: https://bit.ly/BERACUnifiedDataRFI. This form does require a valid email to submit and includes the prompts listed in the request for information (RFI): https://www.govinfo.gov/content/pkg/FR-2023-04-17/pdf/2023-08029.pdf.

If you have any questions about the RFI, please contact Dr. Tristram O. West at Tristram.west@science.doe.gov.


Lastly, to close out our update, here is a summary of the numbers and statistics from our third quarter of 2023. Keep doing great science. The whole KBase team is here to support you!

The graphic provides the following statistics for KBase from July to September 2023. Help Board Tickets had 2 Open Feature Requests, 1 Closed Feature Request, 30 Closed Questions, 21 Open Questions, 23 Open Bugs and 13 Closed Bugs that fill out a pie chart. Twitter had 19,600 Impressions, 5 new followers and 2085 total followers. LinkedIn had 998 impressions, 183 page views, and 93 followers. YouTube had 4300 views, 41 new subscribers for a total of 1022 subscribers; the kbase.us site had 10,000 new visitors, 13,000 total visitors and 49,000 visits to the site. There were 1448 new user accounts added to the platform for a total of 32,794 accounts. User data grew by 51 terabytes for a total of 702 terabytes. Public Data grew by 394 gigabytes to 17.3 terabytes. 24 new publications cited KBase, making a total of 519 publications since 2014. The total number of Narratives is 76,000 with 4271 new Narratives. Top App categories were communities, annotation, and assembly.

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.