This repository contains code to produce the results presented in the publication "Proteomics and constraint-based modelling reveal enzyme kinetic properties of Chlamydomonas reinhardtii on a genome scale"
- R (tested on version 4.2.1)
- matlab (tested on version 2020b & 2022b)
- COBRA toolbox (tested on 2022 release)
- [RAVEN] (https://github.com/SysBioChalmers/RAVEN) (tested on version 2.5.0)
- GECKO toolbox (tested on version 2.0.2)
- Gurobi solver (tested on version 9.5.2)
After making sure all dependencies are installed and properly setup (see links above). Switch working directory to this git repository and open an R console and from within run
source("Rsetup.r")
to install nescessary R packages.
Edit the Matlab_startup.m
file to add the paths of the installed dependencies.
Reproducing results (on linux machine - scripts produce verbose output to comman line no reason to worry)
-
Set this repository as working directory
-
Run
Rscript Program/fit_chemostatdat.r
to obtain a model for maximum acetate uptake. (On windows it is sometimes only possible to source the scripts from within the R console usingsource("Program/fit_chemostat.r")
)(~2-3s on Ryzen5 4000 16 GB RAM) -
Run
Rscript Program/QCC_smy_main2.r
to process the raw QCC data into and generate plots of QconCat proteomics overview statistics. (Also here on windows alternatively you can usesource("Program/QCC_smy_main2.r")
)(~90s on Ryzen5 4000 16 GB RAM) -
In Matlab run
Matlab_startup
to set path for depenencies (edit as mentioned above) (1s on Ryzen5 4000 16 GB RAM) -
In Matlab run
GECKO_startup
to generate pcGEMs from autotrophic, mixotrohpic and heterotrophic chlamydomonas models. This will create a log file with GECKO output in the working directory. (~3h on Ryzen5 4000 16 GB RAM) -
In Matlab run
iCreNIDLE
to estimate kapps with NIDLE and generate obtain comparison values for pFBA and BRENDA/SABIORK (~10 min on Ryzen 5 4000 16 GB RAM) -
In Matlab run
comp_ecModel_rescale
to generate metabolic model predictions from the GEM and pcGEMs. (~2m on Ryzen5 4000 16 GB RAM) -
Run
Rscript Program/manuscript_fig.r
to generate figures and statistics presented in the paper. (60s on Ryzen5 4000 16 GB RAM)