Fall 2016 Newsletter
The U.S. Department of Energy (DOE) Systems Biology Knowledgebase (KBase) is a software and data platform designed to help researchers predict and understand biological function. 

This newsletter contains information about KBase’s newest features, user documentation, upcoming workshops and events, social media pages, and more.

Research Spotlight: Modeling Metabolism Across Microbial Life
Predicting biosynthetic energy yields is a difficult problem, even with increasingly sophisticated metabolic modeling tools. 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 requirement for improving the accuracy of metabolic modeling is the need for extensive gapfilling to support complex biomass reactions.

To overcome these challenges, KBase scientists led by Chris Henry and Janaka N. Edirisinghe developed new analysis tools and integrated them into KBase. Their work was recently published in BMC Genomics in the research article “ Modeling Central Metabolism and Energy Biosynthesis across Microbial Life.” Please see our new Research Highlights page for more information, and check back periodically for new highlights!

The analysis workflow described in the article can be viewed as a KBase Narrative. You can copy the Narrative to your KBase account and repeat the analysis, or even try running the analyses on your own data.

Image from Edirisinghe, J. N., et al. “Modeling central metabolism and energy biosynthesis across microbial life.” BMC Genomics 17, 568 (2016). DOI: 10.1186/s12864-016-2887-8

KBase App Upgrades 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.

We are in the process of upgrading all of the KBase Apps to be SDK compatible. As a result, we are deprecating older tools and replacing them with upgraded versions.

If you have Narratives that include apps that are about to be retired, you will no longer be able to rerun those app cells. However, any results previously generated will still be saved in your Narrative and will be accessible in your data panel. If you want to repeat the analyses in your Narrative, you will need to replace the obsolete Apps with the corresponding new Apps.

We will ensure that published Narratives and all original results will remain available.

Please see the KBase App Replacement page for more information about the upcoming changes and what they mean to you. 

KBase at Plant Biology Meetings
The KBase team has been on the road promoting our plant biology capabilities and training users how to use KBase!

KBase scientists Chris Henry and Sam Seaver co-organized the 2016 PlantSEED Metabolic Modeling Workshop, held at Northwestern University in Evanston, IL from August 4-5. The workshop included talks and hands-on training for using PlantSEED and KBase to do plant genome annotation, metabolic modeling, and transcriptome analysis. KBase scientist Sunita Kumari gave a talk and live demo on “RNA-seq expression analysis using KBase.”

At the 2016 ASPB Plant Biology conference in Austin, TX, KBase staff participated in a shared workshop session on Plant Bioinformatics Resources and staff hosted an exhibit booth shared with the DOE Joint Genome Institute.

Check out the KBase Events page to see more information about future workshops and lectures!
User Testimonials and Featured Narratives
On the new Testimonials page, several scientists describe how they are using KBase to accelerate their research. If you’re interested in being featured on the Testimonials page, please contact us.

We are also building our Narrative Library, which showcases some of the research done in KBase. Please contact us if you would like to propose any Narratives to feature in the library.
New Public Help Board for KBase
KBase is rolling out a new interactive way for users to report bugs, ask questions, or suggest new features - a JIRA Help Board.

Using the Help Board, you’ll be able to:
  • See the current status of your bug report or question
  • Engage in a two-way dialog with KBase staff as they track down and resolve your issue
  • Search bug reports, questions, and suggestions submitted by other users
  • Increase your productivity in KBase by seeing other users’ suggestions and fixes for reported issues
We would like to have a few external beta testers test the new Help Board before we open access for all users. Please contact us if you’re interested!
Newsletter #3 November 28, 2016
We'd love your to get feedback about KBase! We prioritize future development plans based on user input.