Source files required to reproduce analysis from the paper "An in silico analysis of the metabolic regulation of the photosynthetic electron transport chain in C3 plant species" including the source code of the model and the R scripts required to reproduce all figures in the paper.
Before making use of the scripts, please run the INSTALL.R script to install all dependencies. This will require an Internet connection. Also, if you are using Windows, make sure to have Rtools installed.
The scripts required to reproduce the simulations are located in the folder Code. The file Figures.R generates all the figures and calls the different scripts that perform the necessary simulations. For example HPR.R implements the code to simulate and plot the effect of the H^+^/ATP ratio on the regulation of the electron transport chain.
The results of the simulations are cached as binary R files in the folder Intermediate, whereas the final figures will be located in the folder Output.
The model was implemented using the ODEDSL library in Julia, and converted into an R package using the SimulationModels R package. This R package is included in the Packages folder under the name ThylakoidMetabolism. Performing simulations with the model only requires this R package (plus all dependences installed by the INSTALL.R file). The actual implementation of the model can be found in the file Packages/ThylakoidMetabolism/src/ThylakoidMetabolism.cpp. This file was automatically generated from a high-level description of the model (see below) so no documentation or comments are provided.
The model was implemented using an ad-hoc domain specific language written in the Julia programming language via the ODEDSL.jl library. Thus, although the model may be extended by modifying the source code inside the ThylakoidMetabolism package provided here, it is more convenient to use ODEDSL and generate a new R package with the new version. For that purpose, the ThylakoidMetabolism.ode file is provided.