KBase: The Department of Energy Systems Biology Knowledgebase

KBase is an open platform for comparative functional genomics and systems biology for microbes, plants and their communities, and for sharing results and methods with other scientists.


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 […]

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