Read about KBase users accomplishments over the last quarter!
Oct 6, 2021

Quarterly User Update (July – September 2021)

Welcome to the 2nd Quarterly KBase User update. We are excited to keep sharing your awesome accomplishments over the last 3 months. Also, be sure to look out for the end of the year summary in Dec, when we will likely celebrate our 20,000th KBase User and our 50,000th KBase Narrative! 

Community Highlight

This quarter, we highlighted Dr. Eneas Aguirre von Wobeser, a researcher with Centro de Investigación y Desarrollo en Agrobiotecnología Alimentaria (CONACYT) in Mexico City, Mexico (translation – Center for Research and Development in Food Agrobiotechnology). Dr. von Wobeser created one of the DOI Static Narratives in KBase for a research publication, “Barks from avocado trees of different geographic locations have consistent microbial communities“. His taxonomic analysis of these samples can be found here.  

Eneas took a few moments out of his summer vacation to share his research on avocado bark microbiomes, give some good advice for young researchers, and advocate for advancing open research with KBase. Please watch his interview on KBase YouTube here.

If you are interested in publishing your research with KBase, please email us at engage@kbase.us, and we would be happy to review your Narratives and get them ready for show time!

Publications using KBase

KBase was profiled in a variety of publications this quarter, ranging from studies on (endo)symbionts (Reis et al. 2020, Kiefer et al. 2021) to modeling syncoms (Wang et al. 2021), to relationships between peat type and microbial ecology (St. James et al. 2021). You can explore all the publications using KBase 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 ! In addition, 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

Another community developer webinar was held in early July, featuring the Ecosystems and Networks Integrated with Genes and Molecular Assemblies (ENIGMA) Science Focus Area (SFA). Details on their contributions to the platform are available on the ENIGMA Collaboration page. The ENIGMA webinar entitled Functional and Taxonomic Profiling of MAGs (available here) was presented by John-Marc Chandonia (Lawrence Berkeley National Laboratory), Alexey Kazakov (Lawrence Berkeley National Laboratory), and Anni Zhang (Massachusetts Institute of Technology). The tools featured include: 

  • Fama – examines the genetic potential of a microbial community and the taxonomy of functional genes by direct mapping of individual sequence reads to a curated reference set of proteins. 
  • StrainFinder – assigns strain genotypes and assesses strain frequencies for subpopulations of microbial communities with maximum likelihood estimates based on allele frequencies. 

Links to all our webinars can be found at https://www.kbase.us/learn/, or the KBase YouTube channel.

KBase also participated in the 2021 Environmental Molecular Sciences Laboratory (EMSL) and Pacific Northwest National Laboratory (PNNL) summer school on Multi-Omics Modeling of Biochemical Pathways. Links to all the course material and resources can be found on the course webpage, which is under KBase Learn page – Tutorial Narratives.

Summary

And finally, to close out our update, here is a summary of our user numbers to date. Keep doing great science in KBase. The KBase team is here to support you!

Quarterly Report of User Numbers displayed in a visual format.

Elisha Wood-Charlson
Elisha Wood-Charlson | Engagement Lead
Lawrence Berkelely National Laboratory

Elisha M Wood-Charlson is KBase’s User Engagement Lead. She has a PhD and 10+ years of experience as a microbial ecologist focused on host-microbe-virus interactions in the marine environment. Since leaving the research bench, she has moved into the realm of scientific community engagement, with the goal of making microbiome data science more efficient through effective collaboration, building trust in online communities, and developing shared ownership throughout the scientific process.

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

On Wednesday, October 27, we will be performing system maintenance from 11am-1pm PDT (1-3pm CDT).  narrative.kbase.us and appdev.kbase.us may be unavailable or unstable, and compute jobs may fail, during this time.