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 (https://www.kbase.us/gsp-2023/). 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: https://www.kbase.us/data-management/.
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.
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 engage@kbase.us.
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: https://www.kbase.us/research.
If we are missing your research publication that uses KBase, 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 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: https://www.kbase.us/berac-rfi-2023/.
Summary
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!
KBase by the numbers from the Quarterly Report covering April through June 2023.
