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.
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 firstname.lastname@example.org.
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: https://www.kbase.us/research. If you used KBase for your research, and we are missing your publication, please let us know at email@example.com!
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!!!
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 https://www.kbase.us/learn/, 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!