Interested in what your fellow 24,000 KBase users have been up to this spring? Learn what the KBase User community has accomplished from April through June of 2022.
Jul 7, 2022

Quarterly User Update (April – June 2022)

Community Highlight

The team was able to meet up with users at several events over the past few months from conferences to workshops, both in person and virtual! 

KBase participated in the Joint Berkeley Initiative for Microbiome Sciences Spring Seminar this past May, bringing together established and early career researchers from University of California – Berkeley and Lawrence Berkeley National Laboratory. 

We held several workshops for users in June. Two workshops took place at the CROPS Conference hosted by HudsonAlpha on Plant Science and the KBase Educators program. KBase also hosted workshops on metagenomics for the University of California – Riverside Microbiome Initiative Metagenomics and metabolic modeling for S2M2 – Summer School in Metabolic Modeling. Then we introduced the National Summer Undergraduate Research Project (NSURP; https://nsurp.org/) to the Narrative platform, how to create a workflow, and everyone joined the NSURP 2022 Organization!

If your group is interested in learning how to advance their science in KBase, please reach out at engage@kbase.us.

Publications Using KBase

KBase was referenced in 20 publications this quarter for analyses across a wide span of studies and locations; from identifying microbial communities rich in thiosulfate and sulfate-reducing microorganisms in the Permian Basin of West Texas to draft isolate genomes of Pseudomonas from the Permafrost of Svalbard, Norway, an island near to the North Pole (Tinker et al. 2022; Sipes et al. 2022).

You can also read about how tools in the Narrative platform were applied to projects researching lignin-degradation for biofuel applications and modeling metabolic interactions of gut microbiome (Chaput et al. 2022; Catlett et al. 2022). A JGI research team imported paired-ends reads into the Narrative to assemble reads from a huge bacterium – called a “‘macro’ microbe” – found in Guadelupe mangroves (Volland et al. 2022). Explore more publications 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!

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!!!

New Webinars

Dr. Adam Arkin, KBase’s lead Principal Investigator, hosted a webinar on multi-omic analysis of environmental sampling data to drive their research using the platform. Adam demonstrated how he and his team used the KBase Samples services to organize multiple collection campaigns from the Ecosystems and Networks Integrated with Genes and Molecular Assemblies (ENIGMA) project and then analyze linked measurements of amplicons, metagenomes, and chemical abundances. 

View the recorded webinar here: https://youtu.be/TXXXgDgZgiw.

Summary

In closing, we celebrate our user numbers this quarter – from data in the system to publications to the online community. We even surpassed 24,000 total user accounts! Keep doing great science in KBase. The team is here to support you, from helping you get started through publishing your research. 

The graphic provides the following statistics for KBase from April to June 2022. Help Board Tickets for Q2 1 Feature Request, 29 Closed Questions, 10 Open Questions, 6 Open Bugs and 16 Closed Bugs that fill out a pie chart. For Twitter there were 25,000 Impressions, 24,000 Profile Visits, 30 new followers and 1881 total followers. For YouTube 2 new videos were posted, there were 3,700 views, 52 new subscribers for a total of 641 subscribers; for the kbase.us site there were 6746 New visitors, 8840 total visitors and 24,200 visits to the site. There were 1672 new user accounts added to the platform for a total of 24,402 accounts. The total number of Narratives is 54,000 with 3372 new Narratives. User data grew by 46 terabytes for a total of 433 terabytes. Publicly available data that was last updated in July 2021 has a total of 16.2 terabytes. There were 45 new publications cited using KBase for a total of 352 publications since 2014. The top App categories are assembly, community-based tools, and annotation. User Numbers from the KBase Quarterly Report from April through June 2022.

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.

System maintenance Aug 16

We will be performing system maintenance on Tuesday, August 16, 2022, from 11am-3pm CDT (9am-1pm PDT).  narrative.kbase.us, compute jobs, and appdev.kbase.us will be unavailable or unstable for parts of this time.

We do not anticipate any interruption to www.kbase.us.