glycolysis.jl's Introduction

Glycolysis

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