KBase users had another great year in 2022!
Jan 13, 2023

Quarterly User Update (October – December 2022) and review of 2022

Welcome to the final Quarterly KBase User update of 2022, where we celebrate accomplishments for the year from the team, users, and collaborators. 

Community Highlight

In 2022, the KBase team and collaborators continued to add new features to the platform to support researchers and the community of users. 

KBase gave a shout out to the team behind the new functionality behind importing multiple data objects into the Narrative in the latest Team Spotlight. Read about the team and new features: https://www.kbase.us/spotlight-bulkdata/.

Our team worked with collaborators to create the “Ten simple rules for getting and giving credit for data” in an effort to discuss how researchers and infrastructure can support data contributions and follow FAIR data principles. The publication is openly available:  https://doi.org/10.1371/journal.pcbi.1010476

The team joined Protein Data Bank (PDB) and Rutgers University for a workshop on how to use KBase to access PDB structure and comp structure models. Principal Investigator Chris Henry (Argonne National Lab) demonstrated using KBase to access PDB Structures and computed structure models built from artificial intelligence and machine learning. The recorded workshop is available here: https://youtu.be/7eMmU3pZUfU

To see all KBase highlights, visit our News page. If you are interested in a KBase Highlight about your work or project, email us at engage@kbase.us.

Publications using KBase

The platform and team behind KBase continued to support users work with their data and follow the FAIR (findable, accessible, interoperable, reusable) data principles, which culminated in a very productive 2022. In fact, KBase User surpassed last year’s record number of publications citing KBase for data analyses and sharing! Studies spanned from characterizing metabolism of microbes in basic environments (Trutschel et al. 2022) to a college class isolating high-quality draft genomes (McLoon et al. 2022). Notable projects that used KBase also included the ‘macro-microbe’ that identified a centimeter-long bacterium (Volland et al. 2023) and changes in soil microbiome after wildfires (Dove et al. 2022).

We issued 9 Static Narrative DOIs for user publications this past year, and we are tracking dataset metrics to understand how the community uses published KBase data. If you are curious about how we are working to measure the impact of your data analysis efforts, beyond just the publications, please contact us!

Graph showing an increase in publications and mentions for KBase from 2014 to 2022.

KBase Publications and Mentions per Year.

All publications using KBase are available at: https://www.kbase.us/research. If you used KBase for your research, and we are missing your publication, please let us know at engage@kbase.us

New Webinars

Rounding out the year, Dylan Chivian hosted a webinar to accompany the Nature Protocols article “Metagenome-assembled genome extraction and analysis from microbiomes using KBase” which presented an in depth workflow on processing metagenomic data. The paper is openly available here: https://rdcu.be/cZCh7, and is accompanied by two static Narratives: https://kbase.us/n/33233/628/ and ​​https://kbase.us/n/62384/334/. The recording is viewable at: https://youtu.be/unFFU3iu92s.

All webinars are available on the KBase YouTube Channel: https://www.youtube.com/doekbase

Over the course of the full year, KBase hosted 14 virtual workshops and 8 webinars during 2022, reaching over 1700 KBase users attending live!


And finally, to close out our update, here is a summary of our amazing 2022 user numbers. 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 December 15 2022. Help Board Tickets had 275 total, including 9 Feature Requests, 116 Closed Questions, 40 Open Questions, 43 Open Bugs and 67 Closed Bugs that fill out a pie chart. Twitter had 113,00 Impressions, 84,000 Profile Visits, 162 new followers and 1981 total followers. YouTube had 11 new videos posted with 15,400 views, 280 new subscribers for a total of 811 subscribers; the kbase.us site had 28,400 new visitors, 33,00 total visitors and 90,000 visits to the site. There were 6188 new user accounts added to the platform for a total of 27319 accounts. The total number of Narratives is 62,600 with 16,600 new Narratives. User data grew by 161 terabytes for a total of 518 terabytes. Publicly available data that was last updated in July 2022 has a total of 16.7 terabytes. Thirty five new publications cited using KBase for a total of 414 publications since 2014. Top App categories were assembly, metagenomics, and annotation.

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.