Implementation of Horvath et al. 2020 cell-free metabolic model, originally developed by the Varner Lab at Cornell. Original code here and original paper here. Tested on Julia 1.4 and 1.5.
The Julia script runs the model and outputs a plot of the kinetic production of chloramphenicol acetyltransferase (CAT) over 3h. It can be modified and interrogated as required.
With a working local installation of Julia, start up the REPL by running julia on the command line. Use the following two commands to call up the package manager and activating the environment: ] activate . (don't forget the dot). Exit the package manager by pressing Backspace, and then run the model by calling include("run.jl"). This solves the model for the best fit parameter set; a specific parameter set (or multiple sets) can be selected in the script.
Alternatively, run the scripts on our lab Julia Docker container according to the instructions here.
The model is generated from a network stoichiometry ("./model/network/Network.dat" file) obtained by modifying an iAF1260 model for K12-MG1655 E. coli, in order to more closely approximate cell-free lysate conditions. ODEs are generated from the network, and encoded in "./model/scripts/Kinetics.jl".
There are a total of 148 metabolites, which take part in 204 enzyme-catalysed reactions. Each reaction is associated with a Vmax rate constant, a Km saturation constant, and if applicable, control constants. These parameters, and the initial conditions for all species, are found in "./model/params". An ensemble of 100 parameter sets was obtained by MCMC fitting to HPLC time-series data for 37 metabolites.