MATLAB Code for the PKMF Model

This model is a mathematical model that predicts flux for monolignol biosynthesis, in wildtype Populus trichocarpa"The Plant Cell 26: 894-914". If you use this information the National Science Foundation and the Journal must be referenced and acknowledged.

The package linked below contains the MATLAB code for the proteomic based Predictive Kinetic Metabolic-Flux (PKMF) model of the monolignol biosynthetic pathway in Populus trichocarpa.
Contained Files:
(1) Pathway_ODE.m
(2) Calculate_Flux_Pathway.m
(3) Parameter_Setting.m
(4) Execute_lignin_Pathway.m
(1) - Contains the flux definitions for all the reactions in the pathway, which are solved as Ordinary
        Differential Equations (ODE).
(2) - Calculates the steady-state metabolic-flux using the ODE in file (1).
(3) - Contains the wildtype absolute protein abundance in P. trichocarpa stem differentiating xylem (SDX)
        and all the reaction and inhibition kinetic parameters of the 21 P. trichocarpa monolignol pathway
(4) - Contains the ODE solver to obtain the steady-state flux. The file uses the initial conditions, the time
        interval and options for the ODE15s function to solve the ODE function (1). Executing this file would
        predict the steady-state steady-state fluxes for the monolignol biosynthetic pathway in P. trichocarpa