From f4842e8146bdf938ac82a5cfa8aa70df4c5d1e6d Mon Sep 17 00:00:00 2001 From: Torkel Date: Fri, 7 Jun 2024 15:14:43 -0400 Subject: [PATCH] init --- .../introduction_to_catalyst.md | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/docs/src/introduction_to_catalyst/introduction_to_catalyst.md b/docs/src/introduction_to_catalyst/introduction_to_catalyst.md index 40c2900988..94b36738ca 100644 --- a/docs/src/introduction_to_catalyst/introduction_to_catalyst.md +++ b/docs/src/introduction_to_catalyst/introduction_to_catalyst.md @@ -12,9 +12,9 @@ We first import the basic packages we'll need: ```@example tut1 # If not already installed, first hit "]" within a Julia REPL. Then type: -# add Catalyst DifferentialEquations Plots Latexify +# add Catalyst OrdinaryDiffEq Plots Latexify -using Catalyst, DifferentialEquations, Plots, Latexify +using Catalyst, OrdinaryDiffEq, Plots, Latexify ``` We now construct the reaction network. The basic types of arrows and predefined @@ -160,7 +160,7 @@ underlying problem. At this point we are all set to solve the ODEs. We can now use any ODE solver from within the -[DifferentialEquations.jl](https://docs.sciml.ai/DiffEqDocs/stable/solvers/ode_solve/) +[OrdinaryDiffEq.jl](https://docs.sciml.ai/DiffEqDocs/stable/solvers/ode_solve/) package. We'll use the recommended default explicit solver, `Tsit5()`, and then plot the solutions: @@ -169,7 +169,7 @@ sol = solve(oprob, Tsit5(), saveat=10.) plot(sol) ``` We see the well-known oscillatory behavior of the repressilator! For more on the -choices of ODE solvers, see the [DifferentialEquations.jl +choices of ODE solvers, see the [OrdinaryDiffEq.jl documentation](https://docs.sciml.ai/DiffEqDocs/stable/solvers/ode_solve/). --- @@ -182,6 +182,9 @@ Gillespie's `Direct` method, and then solve it to generate one realization of the jump process: ```@example tut1 +# imports the JumpProcesses packages +using JumpProcesses + # redefine the initial condition to be integer valued u₀map = [:m₁ => 0, :m₂ => 0, :m₃ => 0, :P₁ => 20, :P₂ => 0, :P₃ => 0] @@ -237,6 +240,9 @@ model by creating an `SDEProblem` and solving it similarly to what we did for OD above: ```@example tut1 +# imports the StochasticDiffEq package for SDE simulations +using StochasticDiffEq + # SDEProblem for CLE sprob = SDEProblem(bdp, u₀, tspan, p)