Constraint-based modeling of photorespiratory mutants using metabolomics in TMFA

This repository contains all code that has been generated for the constraint-based modeling of photorespiratory mutants in the following publication:

von Bismarck, T., Wendering, P., Perez de Souza, L. et al. Growth in fluctuating light buffers plants against photorespiratory perturbations. Nat Commun 14, 7052 (2023). https://doi.org/10.1038/s41467-023-42648-x

Prerequisites

• MATLAB (tested with releases 2020a and 2020b)
• IBM CPLEX solver (v12.9)
• matTFA toolbox (please use the enh/parallelization branch of my GitHub fork)
• COBRA toolbox (v3.0)
• the code was tested and run under both Ubuntu 20.04.3 LTS and Windows 10

Setup

1. Clone this repository

git clone https://github.com/pwendering/model-prm

2. Clone the enh/parallelization branch of the matTFA fork

git clone -b enh/parallelization https://github.com/pwendering/matTFA

Steps to replicate the results

The script at Code/model_prm.m performs the complete analysis.

To run any of the scripts, please change your working directory to model-prm/Code.

Please note that you may have to adjust the following variables before you run the model_prm.m script:

COBRA_PATH

Path to the top directory of the COBRA toolbox.

CPLEX_PATH

Path to the MATLAB functions that come with the CPLEX solver.

MATTFA_PATH

Path to the top directory of the matTFA toolbox.

N_CPU

Set to one if you do not want to run the code parallelized or set to the desired number of cpus. This affects both variability analysis and sampling.

N_SAMPLES

Set the number of flux samples.