JBEI + KBase

Quantitative Metabolic Modeling

Researchers in the Quantitative Metabolic Modeling Division (QMM) have developed a method to measure intracellular metabolic fluxes using 13C-labeling experiments and comprehensive genome-scale metabolic models: Two-Scale 13C Metabolic Flux Analysis (2S-13C MFA). This method has been specifically designed to avoid uncontrolled approximations, providing an unbiased and self-consistent way to measure fluxes. It allows researchers to test and rank previously available flux prediction methods. The best of these methods are then used to choose which genetic manipulations (e.g., gene knockouts) to perform in order to improve biofuel production. QMM software developers have integrated this method into the KBase so 2S-13C MFA can be run faster and more efficiently using the computational power of KBase. Initial tests have been performed in order to check that the same results are obtained on the local JBEI server and KBase. A present goal is to make this program available through KBase, however, licensing is the main obstacle. Currently, JBEI is working with KBase to develop password-restricted access to the method to satisfy license constraints.

qmm-kbase2 qmm-kbase1

Labeling pattern fit obtained as output from 2S-13C MFA (left). Red bars are experimental results; blue bars show computational fits. The internal metabolic fluxes corresponding to these labeling patterns are shown in the right panel.