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.
Summary
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!
