News from 2016

Release 3.0: What’s New?

The latest release of KBase has a lot of changes “under the hood” (involving the Jupyter Notebook code that underlies our user interface) that make the software more reliable and easier to update. The changes that will be visible to users are relatively minor and won’t change the basic mode of interacting with KBase. New […]

New KBase Help Board

KBase is committed to helping all our users to utilize our tools and datasets for their computational biology research. To make our support process more effective, we are rolling out a new, more interactive way for users (and prospective users) to report bugs, ask questions, or suggest new features, using an issue tracking system called […]

System update on Tuesday, December 6 will cause downtime

The latest release of KBase will be rolled out on Tuesday, December 6. This will make KBase functionality unavailable starting at 8:00am PST until possibly as late as 5pm PST. The new release has a lot of changes “under the hood” that make it more reliable and easier to update. The changes that will be […]

KBase App Replacement Coming Soon

KBase recently introduced a Software Development Kit (SDK) that simplifies the process of integrating analysis tools as KBase apps and also unifies the release and update process, making it easier for developers to support and upgrade KBase functionality. This will result in the KBase platform evolving more rapidly to better serve the requirements of our […]

KBase demo at ACM-BCB

Robert Cottingham, Co-PI of KBase at Oak Ridge National Laboratory, will chair the Demo Presentations at this year’s ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB). He will present a KBase demo titled “Developing collaborative analyses of biological function using Narratives and the App Catalog” showcasing capabilities of interest to this audience, including […]

The PlantSEED Resource in KBase

PlantSEED was developed to streamline the process of annotating plant genome sequences, constructing metabolic models based on genome annotations, and using models to predict gene functions. The PlantSEED resource is available within KBase and can be used to build metabolic models of plant primary metabolism. The Narrative tutorial available at https://narrative.kbase.us/narrative/ws.15250.obj.1 demonstrates how to start with […]

Journal of Cellular Physiology cover features research done in KBase

Life as we know it depends on the existence of microbial communities (microbiomes), in which multiple species of microbes function collaboratively with each other to extract nutrients and energy from their environment. A novel way to model and predict these cross-species metabolic interactions using KBase tools and datasets is described in the cover article of the November 2016 issue of the Journal of Cellular Physiology. [..]

Research Highlight: Using KBase to model central metabolism and energy biosynthesis across microbial life

Predicting biosynthetic energy yields is a challenging problem, even with the increasingly sophisticated metabolic modeling tools that are available. In particular, some of the key pathways involved in energy biosynthesis and the electron transport chain tend to be poorly represented in metabolic models, especially when these pathways interlink. Another challenge in improving the accuracy of […]

User Testimonials

On the new Testimonials page (http://kbase.us/testimonials/), several scientists describe what they like about KBase and how they’re using it to accelerate their research. If you’re interested in being featured on the Testimonials page, please contact us. We’d also be happy to consider your research Narratives for our Narrative Library, which showcases some of the computational experiments done in […]

Publications that mention KBase

A growing number of scientists are using KBase’s tools and data to facilitate their research. Our new Publications page lists and links to published papers that mention work done using KBase. Some of these have Narratives associated with them that let you see and reproduce the workflows described in the papers. (Additional research Narratives, not […]

PlantSEED Metabolic Modeling Workshop

The 2016 PlantSEED Metabolic Modeling Workshop, co-organized by KBase scientists Chris Henry and Sam Seaver, was held at Northwestern University in Evanston, IL from August 4-5, 2016. The workshop included talks and hands-on training on using PlantSEED and KBase to do plant genome annotation, metabolic modeling (including gap filling and flux balance analysis) and transcriptome […]

Poster at Pan–American Congress on Plants and BioEnergy

At the 5th Pan–American Congress on Plants and BioEnergy last week in Santa Fe, New Mexico, KBase scientist Vivek Kumar presented a poster titled, “The DOE Systems Biology Knowledgebase: A cyberinfrastructure for sharing and integrating data and analytical tools to accelerate bioenergy feedstock research.” The poster described KBase’s growing array of tools for analyzing plant […]

KBase at ASPB Plant Biology 2016

KBase attended the 2016 ASPB Plant Biology conference in Austin, TX, from July 9-13. Staff hosted an exhibit booth shared with the DOE Joint Genome Institute, and participated in a shared workshop session on Plant Bioinformatics Resources. Nearly 100 people came by the booth to learn more about KBase and let staff know their needs […]

KBase Workshop and Booth at 2016 ASM Microbe

KBase staff attended the American Society for Microbiology (ASM) Microbe 2016 Conference in Boston, Massachusetts, from June 16-20. The KBase workshop held June 16, “Genome-scale Metabolic Modeling of Environmental Isolates and Communities using the DOE Systems Biology Knowledgebase (KBase),” was a success, as was the KBase exhibit booth, together drawing more than 170 people interested […]

Matt DeJongh KBase keynote at Metabolomics 2016

KBase scientist Matt DeJongh will deliver a keynote address describing his research in creating metabolic modeling software at the 2016 Metabolomics Conference in Dublin, Ireland. Matt’s talk, titled “Building the Killer App for Modeling Metabolism: from ModelSEED to KBase” will describe the development of the RAST genome annotation service, the ModelSEED project for automated reconstruction […]

Great Lakes Bioenergy Research Center Workshop

On May 17, 2016, about 30 scientists attended a KBase workshop at the Great Lakes Bioenergy Research Center 2016 Annual Science Meeting held in Lake Geneva, Wisconsin. The workshop, entitled “Annotation, Modeling, and Comparison of Plant and Microbial Genomes in KBase,” was moderated by KBase scientist Chris Henry, with presentations by Janaka Edirisinghe and Sam […]

Workshop at the University of Nebraska

A two-day KBase workshop at the University of Nebraska, Lincoln, kicked off today with an overflowing group of 65 attendees. Led by KBase staff members Ben Allen, José Faria, Priya Ranjan and Roman Sutormin, the workshop started with an introduction to using KBase’s Narrative Interface to analyze data for single organisms, and then moved on […]

JGI Push to KBase Fixed

The DOE Joint Genome Institute’s (JGI) Genome Portal has a “Push to KBase” feature that lets users transfer some types of microbial reads and genome assembly data from JGI to KBase’s Narrative Interface for analysis using our apps. Recent changes to the JGI Genome Portal temporarily disabled the Push to KBase functionality. We are pleased to report that […]

KBase Workshop at ASM Microbe Conference – Register Now!

KBase will be hosting a full-day workshop at the American Society of Microbiology (ASM) Microbe Conference in Boston. Title: Genome-scale Metabolic Modeling of Environmental Isolates and Communities using the DOE Systems Biology Knowledgebase (KBase) The workshop date will be Thursday, June 16, from 8:15am-4:15pm in BCEC Meeting Room 157B. Read more about our workshop at: […]

Second Annual KBase User Meeting

44 researchers attended the Second Annual KBase User Meeting in Walnut Creek, California on March 22, 2016. After a brief overview of KBase, attendees were led through the use of the assembly, annotation and comparative genomics tools in the system and given an opportunity to try them on their own data. The next session focused […]

Modeling Microbial Communities in KBase

KBase has a suite of tools and data that support the reconstruction, prediction, and design of metabolic networks in individual microbes and microbial communities. A recent review article in Hydrocarbon and Lipid Microbiology Protocols by KBase scientist José P. Faria and colleagues discusses and compares approaches to modeling the growth and behavior of communities of […]

Major release 2.0

We have now released KBase version 2.0. Major changes in this release include: Significant changes to the user interface code “under the hood.” The Narrative Interface, which previously used the IPython Notebook, is now backed by the latest version of Jupyter. You will notice some changes to the look and feel of the user interface, […]

New Narrative Library

You don’t need a library card to check out the Narratives in our new Narrative library – just a free KBase account! The Narrative library showcases a few of the many types of Narratives that can be created in KBase. The initial focus is on Narratives that represent computational experiments or reproducible publications, as well […]

Second Annual KBase User Meeting: Tuesday, March 22, 2016

The second annual KBase User Meeting will include talks, discussions about KBase, and opportunities for hands-on experience. The meeting will be held Tuesday, March 22, from 9:00 am–3:00 pm, in conjunction with the DOE Joint Genome Institute’s Genomics of Energy and Environment Meeting (March 21-24, 2016) in Walnut Creek, CA. The all-day KBase session will include […]

KBase minor release

A minor update to KBase is now complete. This includes a minor release of the Narrative Interface (version 1.1.0). This release fixes some issues in the user interface (see release notes for more details), as well as in some of the tools, including annotation and data upload. The next time you open a Narrative, you may see a green […]

KBase Scientific Advisory Committee (SAC)

A new KBase Scientific Advisory Committee (SAC) was formed in January 2016. Members are eminent scientific leaders who will help us ensure that, moving forward, KBase serves the current and future needs of the broad biological research community. They will be active participants in feature prioritization and community engagement to help guide the development of […]

KBase at the 2016 DOE Genomic Science Annual Contractors Meeting

KBase will host two events for attendees at the invitation-only 2016 DOE Genomic Science Annual Contractors Meeting scheduled for March 6–9: a Developers’ Workshop and the KBase Experience Hands-On Session. The Developers’ Workshop, set for Monday, March 7 from 1 to 5:30 p.m., will demonstrate how researchers can integrate their command-line tools into the KBase […]

PAG 2016

KBase will be at the 2016 Plant and Animal Genome Conference (PAG) in San Diego from Jan. 9-13 (www.intlpag.org), providing several opportunities to learn more about our data and analysis tools. On Tuesday, Jan. 12, from 4:00-6:10 pm in the San Diego Room, join us for a workshop on “Plant Science at the JGI and KBase.” This workshop […]