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April 16, 2021 17:18
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[Catalyst Julia Usage] Basic Usage Of Catalyst.jl #julia #kinetics #reactions
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| repressilator = @reaction_network begin | |
| hillr(P₃,α,K,n), ∅ --> m₁ | |
| hillr(P₁,α,K,n), ∅ --> m₂ | |
| hillr(P₂,α,K,n), ∅ --> m₃ | |
| (δ,γ), m₁ ↔ ∅ | |
| (δ,γ), m₂ ↔ ∅ | |
| (δ,γ), m₃ ↔ ∅ | |
| β, m₁ --> m₁ + P₁ | |
| β, m₂ --> m₂ + P₂ | |
| β, m₃ --> m₃ + P₃ | |
| μ, P₁ --> ∅ | |
| μ, P₂ --> ∅ | |
| μ, P₃ --> ∅ | |
| end α K n δ γ β μ; | |
| latexify(repressilator) | |
| g = Graph(repressilator) | |
| odesys = convert(ODESystem, repressilator) | |
| latexify(odesys) | |
| speciesmap(repressilator) | |
| paramsmap(repressilator) | |
| species(repressilator) | |
| params(repressilator) | |
| # parameters [α,K,n,δ,γ,β,μ] | |
| p = (.5, 40, 2, log(2)/120, 5e-3, 20*log(2)/120, log(2)/60) | |
| # initial condition [m₁,m₂,m₃,P₁,P₂,P₃] | |
| u₀ = [0.,0.,0.,20.,0.,0.] | |
| # time interval to solve on | |
| tspan = (0., 10000.) | |
| # create the ODEProblem we want to solve | |
| oprob = ODEProblem(repressilator, u₀, tspan, p) | |
| sol = solve(oprob, Tsit5(), saveat=10.) | |
| plot(sol) |
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