Supplementary code for "Thermodynamically-consistent, reduced models of gene regulatory networks"

Scripts

This repository contains the Julia code required to run the bond graph model in the study Thermodynamically-consistent, reduced models of gene regulatory networks. The following files will generate the results figures as indicated below:

Script	Figures
elongation_model_comparison.jl	Fig. 7
translation_model_comparison.jl	Figs. 8, 9, S2
gene_regulation_sims.jl	Figs. 10-11, S3
resource_dependence.jl	Figs. 12-14
heterogeneity.jl	Fig. 15
toggle_phase_plane.jl	Fig. S1

Instructions for running code

The code can be run using a Julia installation, using the steps below. The code has been tested on Julia 1.9.1.

1. Install Julia (https://julialang.org/downloads/) and Git (https://git-scm.com/downloads)
2. Clone this repository locally by running the following in the terminal: git clone https://github.com/mic-pan/bg_gene_expression
3. Start Julia: julia
4. Change into the code directory: cd("bg_gene_expression")
5. Press the ] key to enter the package manager
6. Activate the environment: activate env
7. Install the required packages: instantiate
8. Exit the package manager by pressing the backspace key
9. The scripts can be run by using the command include("script_name.jl")