Negative Feedback Marchetti Model

Samuel Isaacson, Chris Rackauckas
using DiffEqBase, OrdinaryDiffEq, DiffEqBiological, DiffEqJump, DiffEqProblemLibrary.JumpProblemLibrary, Plots, Statistics
gr()
fmt = :png
JumpProblemLibrary.importjumpproblems()

Model and example solutions

Here we implement the gene expression model from appendix A.6 of Marchetti, Priami and Thanh, Simulation Algorithms for Comptuational Systems Biology, Springer (2017).

jprob = prob_jump_dnadimer_repressor
rn = jprob.network
rnpar = jprob.rates
varlabels = jprob.prob_data["specs_names"]
u0 = jprob.u0
tf = jprob.tstop
4000.0
u0f = [1000., 0., 0., 0.,0.]
odeprob = ODEProblem(rn, u0f, (0.,tf),rnpar)
sol = solve(odeprob,Tsit5())
plot(sol, format=:png, label=varlabels)