Scale-up

Pathways elimination

GEM preparation

Given a collection of SBML files with the heterologous pathways, calculate the FBA and the Gibbs free energy of the pathways.

Flux balance analysis is a mathematical approach for analyzing the flow of metabolites through a metabolic network. It is performed for heterologous pathways generated by RetroPath2.0. The tool performs the following steps:
-Merges a user-defined GEM SBML model with each given heterologous pathway individually.
-Performs FBA using the CobraPy package. Three different analysis methods are proposed; two of which are native CobraPy methods - standard FBA and Parsimonious FBA, the other one proposed
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