Halfway through 2024! Updates and highlights from the past three months.
Jul 10, 2024

Quarterly User Update (April – June 2024)

Updates from the Team at KBase

In early April, the KBase team attended the Genomic Science Program (GSP) Annual Principal Investigator Meeting. GSP is part of the Department of Energy Biological and Environmental Research (BER) Program in the Office of Science, which funds KBase. KBase hosted four hybrid workshops (find them on the DOEKBase YouTube Channel) for about 90 attendees as a way for several Science Focus Areas (SFAs) to train the community on new data and functionality they have been working with the KBase team to release on our platform. BER SFAs represent large, collaborative research projects that span various National Labs. New SFA-led functionality includes: 

  • Microbial Annotation – Pacific Northwest National Lab (PNNL) and Lawrence Livermore National Lab (LLNL)
  • Microbial Community Modeling – Oak Ridge National Lab (ORNL) and LLNL
  • Long-read isolate sequencing and analysis – Ecosystems and Networks Integrated with Genes and Molecular Assemblies (ENIGMA), Lawrence Berkeley National Lab), and 
  • qSIP analysis – (LLNL SFA and the Joint Genome Institute). 

An overview of all KBase collaborations and more details on the new functionality released by the SFAs can be found on our User Working Groups page: https://www.kbase.us/research/user-working-groups/. And look for upcoming newsletters announcing KBase community webinars on these new tools as well!

KBase also held a conference session on Data Integration to Support (or Refute) Predictions. The goal was to feature examples of research questions and tools that integrate data in KBase, with the goal of building trust in our assertion of the world around us. Presentations were given by KBase team members and collaborators, including Dale Pelletier (ORNL), Shinjae Yoo (Brookhaven National Laboratory), Paramvir Dehal and Elisha Wood-Charlson (LBNL), and Chris Henry (Argonne National Laboratory). 

Community Highlights

In this past quarter, we posted three News highlights featuring members of the KBase Community! For our first highlight of 2024, we shared new developments within the KBase Educators Program, we hosted a workshop in January for educators participating in a pilot project funded by a Research Coordination Network for Undergraduate Biology Education Incubator (NSF #2316244). Read about what the group has been working on here: https://www.kbase.us/news/educator-workshop-jan2024/

Two featured community members were postdoctoral researchers based at DOE National Laboratories. In May, Cliff Bueno de Mesquita (Joint Genome Institute) gave us insights into understanding how sea level rise may affect microbial communities in coastal wetlands: https://www.kbase.us/news/clifton-bueno-demesquita/. Wrapping up the quarter in June, Jia Wang (Oak Ridge National Laboratory) provided us with background on building metabolic models to understand the mechanisms of microbial communities as part of the Plant Microbe Interfaces (PMI) Science Focus Area: https://www.kbase.us/news/jia-wang/. One of Jia’s publications using KBase to reconstruct metabolic models from microbes associated with Poplar trees (Wang et al. 2024) in our Q1 Community Update!

Interested in a Highlight featuring your work in KBase? Email us at engage@kbase.us.

New Features

In June, we introduced Collections for exploring data in KBase. Collections are curated datasets that can be searched using sequence similarity, taxonomy, and function characteristics applying the Genome Taxonomy Database and microTrait. Browse the current collections from GTDB, ENIGMA, PMI, and Genome Resolved Open Watershed (GROW). Read the full announcement here: https://www.kbase.us/news/introducing-collections-for-data-exploration/

Publications using KBase

The platform and team behind KBase supports users from analyzing their data and following FAIR (findable, accessible, interoperable, reusable) data principles through publication. In Q2 (April-June), 52 published studies cited using KBase to analyze microbes collected from environments across the globe! These included projects that identified microbial processes in Arctic soils to characterization of microbial communities of Amazonian leaf litter to the diversity and phage-host interactions associated with algal blooms in Lake Okeechobee, Florida (Li et al. 2024, Freitas et al. 2024, Krausfeldt et al. 2024). 

We have community guidelines with best practices on how to publish in KBase. If you are curious about how we are working to measure the impact of your data and 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.

Summary

To close out our update, here is a summary documenting April through June 2024 user numbers. Keep doing great science in KBase. The KBase team is here to support you!

Statistics for KBase from April to June 2024. There were 1383 new user accounts added to the platform for a total of 38243 accounts. The total number of Narratives is 92800 with 4257 new Narratives. User data grew by 79 terabytes for a total of 954 terabytes. Publicly available data grew by 650 GB to 24.4 TB. New publications cited using KBase came in at 52 for a total of 647 publications since 2014. Top App categories were annotation, communities, and assembly. The kbase.us site had 14,000 new visitors, 12700 active users and 56,000 visits to the site. Help Board Tickets had 103 total, including 47 Closed Questions, 25 Open Questions, 16 Open Bugs and 14 Closed Bugs. X had 8 mentions, 18 new followers and 2108 total followers. LinkedIn had 2394 Impressions, 80 Page Views, and 284 Followers. YouTube had 4,100 views, 57 new subscribers for a total of 1188 subscribers.

KBase by the numbers from the Quarterly Report covering April through June 2024.

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.