Interested in what your fellow KBase users have been up to?
Jul 13, 2021

Quarterly User Update (April – June 2021)

Welcome to the (new) Quarterly KBase User update! We wanted to start letting our KBase user community know just how awesome you all are by sharing a few updates on what everyone has been accomplishing over the last 3 months.

Community Highlight

This quarter, we highlighted Dr. Lauren Lui, a researcher studying subsurface microbiology at Berkeley Lab. Dr. Lui and her collaborators, including KBase’s Dr. Sean Jungbluth and Dr. John-Marc Chandonia, integrated novel functionality for improving genome circularization form microbial metagenomes. Read more on our Community Highlight of Dr. Lui here. We also reported on a recent collaboration between KBase and several Department of Energy Science Focus Areas that enabled other community developers to integrate a variety of tools into KBase, both for their own research, as well as making those same tools and analyses available to everyone in the KBase user community. A summary of that collaborative effort can be found here

If you are interested in becoming a KBase Community Developer, or think your work in KBase could become a Community Highlight, please reach out at

Publications using KBase

KBase also supported several high profile publications over the last few months. For example, a new tool for dynamic modeling, called NWChem, was developed by researchers at Pacific Northwest National Lab, led by data scientist Dr. Neeraj Kumar. NWChem is a quantum-chemistry-based software that predicts the thermodynamics of a given biochemical reaction in the recently updated ModelSEED database. A summary of the project and publication is available here. A list of all the publications using KBase can be found at: If you used KBase for your research, and we are missing your publication, please let us know at

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

Two new community developer webinars were hosted by KBase in April 2021. Dr. Patrick D’haeseleer, from Lawrence Livermore National Laboratory, demonstrated new functional annotation tools that can be used to improve models (recording available at DOEKBase YouTube here). Dr. Mark Flynn, from Los Alamos National Laboratory, highlighted several new taxonomy tools, including their GOTTCHA2 read-based App (available here). Links to all our webinars can be found at, or the KBase YouTube channel.


And finally, to close out our update, here is a summary of our user numbers to date. We look forward to sharing more accomplishments in Oct 2021. Keep doing great science in KBase. The KBase team is here to support you!

Visual graphic of KBase Quarterly Report by the numbers for April through June 2021.

User Numbers from the KBase Quarterly Report from April through June 2021.

Elisha Wood-Charlson
Elisha Wood-Charlson | Engagement Lead
Lawrence Berkeley 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.