Confluence Retirement

Due to the feedback from stakeholders and our commitment to not adversely impact USGS science activities that Confluence supports, we are extending the migration deadline to January 2023.

In an effort to consolidate USGS hosted Wikis, myUSGS’ Confluence service is targeted for retirement. The official USGS Wiki and collaboration space is now SharePoint. Please migrate existing spaces and content to the SharePoint platform and remove it from Confluence at your earliest convenience. If you need any additional information or have any concerns about this change, please contact Thank you for your prompt attention to this matter.
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Recording and Presentation:

The Webex recording and slides and are available to CDI Members. Log in to view the recording and slides. If you would like to become a member of CDI, email

Topic: Department of Energy Systems Biology Knowledgebase (KBase)

Ben Allen from ORNL presented on KBase.


KBase is a software and data platform designed to meet the grand challenge of systems biology: predicting and designing biological function. Users can perform large-scale analyses and combine multiple lines of evidence to model plant and microbial physiology and community dynamics.


KBase is the first large-scale bioinformatics system that enables bench biologists and bioinformaticists to upload their own data, analyze it alongside collaborator and public data, build increasingly realistic models, and share their workflows and conclusions.


We will cover a variety of analyses for microbes and microbial communities, including a rich collection of bioinformatics tools for quality control and assessment of reads, de novo assembly, prokaryotic genome annotation, and how to analyze structural and functional features of genomes within KBase.

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