Package for modeling mammalian glycolysis activity.
See our bioRxiv preprint for examples of how to use this package to study glycolysis regulation.
Code to reproduce all figures in the preprint is in examples/biorxiv figures folder.
You can use it to simulate glycolysis using the following code:
using Glycolysis, DifferentialEquations, CairoMakie # Set ATPase rate to be equal to 10% of glycolysis Vmax which is set by HK1 Vmax glycolysis_params.ATPase_Vmax = 0.1 * 2 * glycolysis_params.HK1_Vmax * glycolysis_params.HK1_Conc prob = ODEProblem(glycolysis_ODEs, glycolysis_init_conc, (0, 100), glycolysis_params) #Simulate glycolysis activity sol = solve(prob, Rodas4(), abstol = 1e-12, reltol = 1e-5) #List of all metabolites in the model can be found by running propertynames(glycolysis_init_conc) #Plot all [Metabolite] over time fig = Figure() ax = Axis(fig[1, 1], yscale = log10, xlabel = "Time, min", ylabel = "[Metabolite], M") #Substitute :ATP, :ADP, :Phosphate for any metabolite(s) from propertynames(glycolysis_init_conc) for metabolite in [:ATP, :ADP, :Phosphate] lines!(ax, sol.t, [u[metabolite] for u in sol.u], label = String(metabolite)) end Legend(fig[1, 2], ax) fig
