News from 2017

New KBase modeling protocol available from Springer

KBase offers a comprehensive suite of tools for generating and refining metabolic models. Modeling researchers have observed that genome-scale metabolic models (GEMs) generated from automated reconstruction pipelines often lack accuracy in energy biosynthesis. It is therefore often useful to construct a simplified version of a GEM: a core metabolic model (CMM) that is comprised of […]

Research Highlight: Modeling an Electrosynthetic Microbiome

Microbial electrosynthesis is a renewable energy and chemical production platform that employs microbial communities to generate industrially important chemical products (such as biofuels or commodity chemicals) by fixing carbon dioxide using an electric current as the electron donor. In a recent study published in Scientific Reports, researchers applied KBase annotation and metabolic modeling pipelines to […]

KBase’s modeling tools to be presented at American Institute of Chemical Engineers (AIChE) 2017 Annual Meeting

KBase is used by scientists in a range of fields, including systems biology, genomics, biochemistry and even chemical engineering. That last group is the focus of the American Institute of Chemical Engineers (AIChE) 2017 Annual Meeting, which will draw about 7000 chemical engineering researchers to Minneapolis the week of October 29 – November 3, 2017. […]

New “Quickstart” Video Tutorial

KBase has changed a lot since we released our first video tutorial in October 2015, as we continually improve the system based on user feedback, so we just released a new “KBase Quickstart” video tutorial ( In just over 5 minutes, you will learn the basics of how to use KBase to upload and analyze […]

New Testimonials about KBase

Mikaela Cashman (University of Nebraska, Lincoln) Juan C. Villada (City University of Hong Kong)     KBase’s mission is to enable computational systems biology research that would be difficult or impossible otherwise. A growing number of scientists are finding KBase useful in their work. A few of these have kindly volunteered to write testimonials about how […]

KBase at ACM-BCB 2017

KBase will have a demo presentation and exhibit booth at this year’s ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB). Robert Cottingham, Co-PI of KBase at Oak Ridge National Laboratory, will present a KBase demo titled “Benefits of deploying your bioinformatics tools using KBase” showing bioinformatics researchers how to integrate their open-source tools […]

Protocol for Genome Assembly and Annotation in KBase

A protocol paper in Current Protocols in Microbiology demonstrates an example workflow for taking a comparative and iterative approach to assembly and annotation of prokaryotic genomes using KBase. This approach can be used by microbiologists seeking to perform isolate analysis in a rapid and reproducible fashion. There is also a tutorial Narrative in KBase ( […]

Workshop at ESA 2017: Using KBase for microbial ecology

The upcoming Ecological Society of America conference (ESA 2017) in Portland, Oregon will include a KBase workshop. Organized by KBase team members José Faria and Chris Henry, along with ANL collaborator Pamela Weisenhorn, the topic of the workshop is “Comparative ‘Omics and Modeling Microbial Community Interactions Using the DOE Systems Biology Knowledgebase (KBase).” The workshop, […]

Edirisinghe to speak at International Conference on Systems Biology 2017

Janaka Edirisinghe, a KBase scientist at ANL, will present a talk entitled “Automated pathway curation and improving metabolic model reconstruction based on phylogenetic analysis of pathway conservation” at the 2017 International Conference on Systems Biology in Blacksburg, Virginia ( on August 10, 2017 at 10:50am. Edirisnghe and colleagues developed a gapfilling algorithm that improved the […]

Metabolic Pathway Analysis 2017

Two KBase research scientists will be giving talks at the Metabolic Pathway Analysis (MPA) 2017 conference in Bozeman, Montana next week. KBase Co-PI Chris Henry of ANL will give an invited talk entitled “Progressing towards a deep integration of chemistry and biology to discover new protein functions, pathways, and ecological principles” on July 28 at 9:00am. José Pedro Lopes Faria will discuss “Improving automated model reconstruction” at 1:40pm on July 28. Both talks will include demonstrations of the KBase resources that were used to accomplish the science.

KBase at ASPB Plant Biology 2017

The ASPB Plant Biology 2017 conference kicked off today in Honolulu, Hawaii and will continue through June 28, 2017. KBase has a shared booth (#303) with the DOE Joint Genome Institute (JGI), a talk, and two posters. The full ASPB schedule can be found at Dr. Vivek Kumar of CSHL is giving a talk […]

New Sign-up/Sign-in System

On June 9, KBase will be switching to a new system for signing up and signing in. (Note that KBase will be unavailable for several hours during this conversion.) Users who already have KBase accounts will have to navigate through a new authentication process the first time they sign on after the changeover to convert […]

Using KBase for Biological Sampling, Inference, Modeling, and Prediction

KBase power user and University of Nebraska-Lincoln graduate student Mikaela Cashman has created a Narrative showcasing a workflow called BioSIMP (Biological Sampling, Inference, Modeling, and Prediction) that models and predicts the behavior of biological organisms. Based on phenotypic response to combinations of environmental factors BioSIMP uses software testing techniques to sample, classify the results to […]

Video Tutorials: Data in KBase

New video tutorials that explain how to find, upload and manage data in KBase are now available on our YouTube channel: The first short video discusses how to search for data that’s already in KBase and add it to your Narrative for analysis, as well as how to upload data from your computer. The second […]

Third Annual KBase User Meeting (March 21, 2017)

The third annual KBase User Meeting will include talks on the objectives of KBase, discussions about the science that can be accomplished using KBase, interactive tutorials, and opportunities for attendees to ask questions and offer feedback and suggestions. The workshop will be held Tuesday, March 21, from 9am-3pm, in conjunction with the DOE Joint Genome […]

KBase at the 2017 DOE Genomic Science Annual Contractors Meeting

KBase will host three events for attendees at the invitation-only 2017 DOE Genomic Science Annual Contractors Meeting scheduled for February 5-8: A Software Development Kit (SDK) Workshop, Tutorial Presentations, and the KBase Experience Hands-On Session. The KBase Software Development Kit (SDK) Workshop is Monday Feb 6 9am-5pm in the Potomac V room.  The session will […]

PAG 2017

KBase staff demonstrated new analysis tools and highlighted research accomplishments at the 2017 Plant and Animal Genome Conference (PAG) in San Diego from Jan. 14-18 ( . The “Plant Science at the JGI and KBase” workshop featured seven presentations showcasing work done by DOE Joint Genome Institute (JGI) and KBase scientists and collaborators to advance plant science for bioenergy and environmental […]

KBase paper preprint available

The first paper about KBase is now available as a preprint on bioRxiv ( The paper describes both the underlying structure and components of KBase and the way it can be used by researchers to perform large-scale systems biology analyses and share their data, results and conclusions. To illustrate how KBase facilitates collaborative research, the […]