Spring 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, useful links to documentation, upcoming workshops and events, social media pages, and more.

 
Research Spotlight: Collin Timm's Plant-Microbe Interactions Paper
"Using KBase's metabolic modeling and flux balance anaylsis tools, we have studied differences in metabolic properties of Pseudomonas fluorescens isolates from Populus trees. As a first-time user of metabolic modeling tools, I found it very fast (~15 minutes) and easy (~5 steps) to go from genome sequence to draft models that could be used for biological discovery. Using these tools, we found that bacterial isolates from the endosphere (internal root compartment) have significantly different metabolic properties than rhizosphere isolates (external root compartment), which highlights the complexity in the system and importance of microenvironment within the microbiome of the plant. This work helps us rapidly characterize new bacterial isolates and will help identify processes important for plant-microbe interactions.

KBase is a great environment with many tools that are easy to use, and developers have been very helpful throughout the launch process. The interface allows for easy organization of steps and data for easy documentation of modeling steps, meaning it is easy to show my work to others and document what I did during analyses." - Collin M. Timm, Postdoctoral Research Associate, Biosciences Division, Oak Ridge National Laboratory

Timm, C. M., et al. 2015. "Metabolic functions of Pseudomonas fluorescens strains from Populus deltoides depend on rhizosphere or endosphere isolation compartment," Frontiers in Microbiology, 6. DOI:10.3389/fmicb.2015.01118

 
New Video: Intro to KBase Narrative Interface
KBase’s Narrative Interface lets you design and carry out collaborative computational experiments while creating Narratives: interactive, shareable, and reproducible records of your data, computational steps, and thought processes. The tutorial video demonstrates how to create a Narrative, find data, use Apps and Methods to perform data analysis, and share your Narratives with other KBase users. This video is the first in a series that will show how to leverage KBase’s functionality and data to perform various types of systems biology analyses.

 
KBase User Meeting: March 22, 2016
Join us for the second annual KBase User Meeting on Tuesday, March 22, from 9:00 a.m.–3:00 p.m., in conjunction with the DOE Joint Genome Institute’s (JGI) Genomics of Energy and Environment Meeting (March 21-24, 2016) in Walnut Creek, CA.

The KBase User Meeting will include discussions of KBase objectives, how it differs from other systems, the science that can be accomplished using KBase, and interactive tutorials.

If you are registering for the JGI User Meeting, you can add the KBase User Meeting session to your registration.

 
New Library Showcases Narratives
The Narrative Library features many types of Narratives that can be created in KBase, including those that represent computational experiments or reproducible publications, as well as Narrative tutorials that use some of KBase’s analysis tools and data sets. Copy and build upon these Narratives to fit your own research needs. If you have written a Narrative with interesting results and would like it included in the library,  let us know!

 
Add Tools with the Software Development Kit
The  KBase Software Development Kit (SDK) offers a mechanism to add open-source, open-license tools that run on KBase’s computational architecture and are available through the  App Catalog. Community developers can even write new programs that take advantage of the KBase Structured Data Types and  Public Data Resources.

 
KBase Scientific Advisory Committee
A new KBase Scientific Advisory Committee (SAC) was formed in January 2016. Members are eminent scientific leaders who are ensuring that KBase serves the needs of the broad biological research community. They are active participants guiding and prioritizing the development of new scientific functionality in KBase.

Newsletter #1 March 14, 2016
SOCIAL MEDIA
   
USEFUL LINKS
 
FEEDBACK
We'd love your feedback about KBase! We prioritize future development plans based on user input.

http://kbase.us/feedback 
CONTACT US

http://kbase.us/contact-us/