Genome scale metabolic modeling of Solanum tuberosum.
This repository holds the Genome Scale Metabolic Reconstruction of Solanum tuberosum, as first obtained by means of KBase automatic model generation and following manually refinement and testing.
This reconstruction was started using the complete Solanum tuberosum genome sequencing.
Basic Matlab session for the analysis of this reconstruction
Original XLS and SBML (xml) files as obtained from KBase.
Holds the media used for the initial reconstruction: "Plant Heterotrophic Media" as provided by KBase, in this narrative. This file holds the media components as downloaded from KBase. Please note that the media components could differ when inspected online and when downloaded from KBase website.
Also holds detailed information on the components of Biomass objective function, in this models as well a comparative with other models.
Holds the metabolic phenotype of original reconstruction. Used mainly to inspect for infinite fluxes (-1000/1000) that could be indicative of Type III loops.
is the same "*.ori" model but exported from COBRA. This file was created in order to make sure that we will not have issues then importing to COBRA. This file is going to be used as basis for modifications on Biomass objective functions to reflect, first, changes in Biomass composition as obtained from the work of Guevara.