Jan 8, 2024

Quarterly User Update (October - December 2023) and review of 2023

Another great year working with the KBase Community!

Welcome to our first update in 2024 – covering announcements and highlights from the last quarter of 2023, and celebrating team, users, and collaborators accomplishments throughout the year.

Community Highlights

KBase returned to in-person (now hybrid) workshops in 2023! In October, Ellen Dow led an Introduction to Metabolic Modeling in KBase at the JGI Microbial Genomics and Metagenomics Workshop (MGM-31). Then in November, Elisha Wood-Charlson represented KBase at the virtual ESS-DIVE Open Data Workshop. 

We wrapped up the year providing support on the tools and functionality of KBase at a Long-read Isolate Sequencing and Assembly (LISA) Workshop. Lauren Lui (ENIGMA) organized this workshop for early career researchers from DOE-funded labs and Science Focus Area affiliated universities. Ben Allen, Elisha Wood-Charlson, Sean Jungbluth, and John-Marc Chandonia provided support on isolate analysis in KBase. More on long-read assembly tools in KBase coming soon!

KBase Educators Community member Carlos Goller (North Carolina State University) joined the team to present on how he uses KBase with undergraduate students, including his application of new long-read tools, at the American Society for Microbiology Conference for Undergraduate Educators and the LISA Workshop. Thank you Carlos! 

Over the course of the full year, KBase hosted and supported 12 in-person/hybrid workshops and 2 webinars during 2023, with over 612 KBase users in attendance! Follow KBase on LinkedIn to hear about upcoming workshops and events! 

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 continues to support users to analyze their data and follow the FAIR (findable, accessible, interoperable, reusable) data principles through to publication. Studies spanned from undergraduate students isolating high-quality draft genomes (McLoon et al. 2023; https://kbase.us/n/152701/14/) to characterizing microbial growth traits to long-term soil warming (Eng et al. 2023) and utilizing metagenome-assembled genomes to map the changing diversity of glacier-associated microbiota (Hay et al. 2023). 

We issued 10 Static Narrative DOIs for user publications this past year, and are able to track dataset metrics to understand how the community uses published KBase data. Read more about Publishing in KBase, and if you are curious about how we are working to measure the impact of your data 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.

New Tools!

KBase released ModelSEED2 this fall! ModelSEED2 brings two new Apps to the platform, including MS2: Build Prokaryotic Metabolic Models and MS2: Improved Gapfill Metabolic Models. This model reconstruction pipeline dramatically increases quality and decreases the amount of curation required to produce a predictive genome-scale metabolic model. New features include more accurate energy metabolism reconstructions for ATP yield, improved Archaea models, and improved pathway annotations and biochemical representations. 

The preprint for ModelSEED2, demonstrating these improvements with 5000 diverse microbial genomes is available on bioRxiv (Faria, et al. 2023).


And finally, to close out our update, here is a summary of our amazing 2023 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 2023. Help Board Tickets had 346 total, including 13 Feature Requests, 132 Closed Questions, 66 Open Questions, 74 Open Bugs and 61 Closed Bugs that fill out a pie chart. X (formerly Twitter) had 83,100 Impressions, 105 new followers and 2093 total followers. LinkedIn had 2690 Impressions, 308 Page Views, and 187 Followers. YouTube had 2 new videos posted with 18,700 views, 244 new subscribers for a total of 1073 subscribers; the kbase.us site had 53,000 new visitors, 46,000 total visitors and 168,000 visits to the site. There were 6591 new user accounts added to the platform for a total of 34861 accounts. User data grew by 221 terabytes for a total of 768 terabytes. Publicly available data grew by 4.9 terabytes to 21.6 TB. The total number of Narratives is 83,200 with 17,500 new Narratives. New publications cited using KBase came in at 116 for a total of 559 publications since 2014. Top App categories were annotation, communities, and assembly.