Tutorial

This overarching tutorial of SBMLImporter covers how to import an SBML model into a JumpProblem for Gillespie simulations, a SDEProblem for chemical Langevin simulations, or an ODEProblem for deterministic simulations. It also covers how to change parameter and/or initial values for an imported model.

Input - a valid SBML model file

SBMLImporter only requires one input: a valid SBML file. SBML files can be created from various sources, such as the graphical interface of COPASI, by converting rule-based BioNetGen models, or by using any other SBML exporting tools. Additionally, a large collection of published SBML models are hosted on BioModels.

In this tutorial, we will use the Brusselator model, whose SBML file can be downloaded from here.

Importing a model

To import an SBML model use load_SBML:

using SBMLImporter
prn, cb = load_SBML(path; massaction=true)

Here, massaction=true informs the importer that the model follows chemical mass action kinetics. This is required for efficient jump (Gillespie type) simulations. Additional keyword arguments can be found in the API documentation.

load_SBML returns two outputs: a ParsedReactionSystem (prn) and a CallbackSet (cb). The CallbackSet holds any SBML events, as well as any piecewise functions parsed into events. The ParsedReactionSystem includes a Catalyst ReactionSystem (prn.rn), a map for the initial values of each species (prn.u0), and a map for setting the model parameter values (prn.p). Many modeling tasks can be performed with a Catalyst ReactionSystem, for example, the system reactions can be inspected by:

using Catalyst
reactions(prn.rn)

\[ \begin{align*} \varnothing &\xrightleftharpoons[C]{A C} \mathrm{X} \\ \mathrm{Y} + 2 \mathrm{X} &\xrightarrow{2 C} 3 \mathrm{X} \\ \mathrm{X} &\xrightarrow{B C} \mathrm{Y} \end{align*} \]

Note

The massaction keyword argument is only relevant for jump simulations. If you import the model as a SDEProblem or an ODEProblem, you can (and should) ignore this keyword argument.

Jump simulations

To perform jump simulations (e.g. using Gillespie's algorithm), convert the reaction system (prn.rn) into a JumpProblem (which requires first creating an intermediary DiscreteProblem).

using JumpProcesses
tspan = (0.0, 10.0)
dprob = DiscreteProblem(prn.rn, prn.u0, tspan, prn.p)
jprob = JumpProblem(prn.rn, dprob, Direct())

The JumpProblem can be simulated with any solver from the JumpProcesses.jl package, such as the SSAStepper:

using Plots
sol = solve(jprob, SSAStepper(), callback=cb)
plot(sol; xlabel = "Time [s]", ylabel = "Protein amount")

For more information on jump simulations, see JumpProcesses.jl's documentation. A guide to choosing a simulation algorithm can be found here.

SDE simulations

To perform chemical Langevin SDE simulations, convert the reaction-system prn.rn into a SDEProblem.

using StochasticDiffEq
tspan = (0.0, 10.0)
sprob = SDEProblem(prn.rn, prn.u0, tspan, prn.p)

Precompiling packages...
   2535.4 ms  ? LinearSolve → LinearSolveSparseArraysExt
   1817.1 ms  ? NonlinearSolveQuasiNewton
    763.2 ms  ? NonlinearSolveQuasiNewton → NonlinearSolveQuasiNewtonForwardDiffExt
   2821.7 ms  ? NonlinearSolveFirstOrder
   2927.7 ms  ? OrdinaryDiffEqDifferentiation
    574.1 ms  ? NonlinearSolve
   2098.1 ms  ? OrdinaryDiffEqDifferentiation → OrdinaryDiffEqDifferentiationSparseArraysExt
    826.7 ms  ? OrdinaryDiffEqNonlinearSolve
Info Given StochasticDiffEq was explicitly requested, output will be shown live 
┌ Warning: Module NonlinearSolve with build ID ffffffff-ffff-ffff-174b-2770ddeebc58 is missing from the cache.
│ This may mean NonlinearSolve [8913a72c-1f9b-4ce2-8d82-65094dcecaec] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2638
   2250.6 ms  ? StochasticDiffEq
┌ Warning: Module NonlinearSolve with build ID ffffffff-ffff-ffff-174b-2770ddeebc58 is missing from the cache.
│ This may mean NonlinearSolve [8913a72c-1f9b-4ce2-8d82-65094dcecaec] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2638
Precompiling packages...
   2459.3 ms  ? LinearSolve → LinearSolveSparseArraysExt
   1843.9 ms  ? OrdinaryDiffEqDifferentiation
   2883.2 ms  ? NonlinearSolveQuasiNewton
   2886.5 ms  ? NonlinearSolveFirstOrder
    773.2 ms  ? NonlinearSolveQuasiNewton → NonlinearSolveQuasiNewtonForwardDiffExt
   2153.8 ms  ? OrdinaryDiffEqDifferentiation → OrdinaryDiffEqDifferentiationSparseArraysExt
    567.7 ms  ? NonlinearSolve
Info Given OrdinaryDiffEqNonlinearSolve was explicitly requested, output will be shown live 
┌ Warning: Module NonlinearSolve with build ID ffffffff-ffff-ffff-174b-2770ddeebc58 is missing from the cache.
│ This may mean NonlinearSolve [8913a72c-1f9b-4ce2-8d82-65094dcecaec] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2638
    832.2 ms  ? OrdinaryDiffEqNonlinearSolve
┌ Warning: Module NonlinearSolve with build ID ffffffff-ffff-ffff-174b-2770ddeebc58 is missing from the cache.
│ This may mean NonlinearSolve [8913a72c-1f9b-4ce2-8d82-65094dcecaec] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2638
Precompiling packages...
   2459.0 ms  ? LinearSolve → LinearSolveSparseArraysExt
Info Given OrdinaryDiffEqDifferentiation was explicitly requested, output will be shown live 
┌ Warning: Module LinearSolveSparseArraysExt with build ID ffffffff-ffff-ffff-ce81-ff2eeeceb35a is missing from the cache.
│ This may mean LinearSolveSparseArraysExt [acf9803d-64eb-5f69-b965-a71e3e6e1ed4] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2638
   1832.5 ms  ? OrdinaryDiffEqDifferentiation
   2125.8 ms  ? OrdinaryDiffEqDifferentiation → OrdinaryDiffEqDifferentiationSparseArraysExt
┌ Warning: Module LinearSolveSparseArraysExt with build ID ffffffff-ffff-ffff-ce81-ff2eeeceb35a is missing from the cache.
│ This may mean LinearSolveSparseArraysExt [acf9803d-64eb-5f69-b965-a71e3e6e1ed4] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2638
Precompiling packages...
   2448.2 ms  ? LinearSolve → LinearSolveSparseArraysExt
   1858.5 ms  ? OrdinaryDiffEqDifferentiation
Info Given OrdinaryDiffEqDifferentiationSparseArraysExt was explicitly requested, output will be shown live 
┌ Warning: Module OrdinaryDiffEqDifferentiation with build ID ffffffff-ffff-ffff-8c8b-d967360a0e6c is missing from the cache.
│ This may mean OrdinaryDiffEqDifferentiation [4302a76b-040a-498a-8c04-15b101fed76b] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2638
    265.0 ms  ? OrdinaryDiffEqDifferentiation → OrdinaryDiffEqDifferentiationSparseArraysExt
┌ Warning: Module OrdinaryDiffEqDifferentiation with build ID ffffffff-ffff-ffff-8c8b-d967360a0e6c is missing from the cache.
│ This may mean OrdinaryDiffEqDifferentiation [4302a76b-040a-498a-8c04-15b101fed76b] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2638

The SDEProblem can be simulated with any solver from the StochasticDiffEq.jl package, such as the LambaEM solver:

sol = solve(sprob, LambaEM(), callback=cb)
plot(sol; xlabel = "Time [s]", ylabel = "Protein amount")

For more information on SDE simulations, see StochasticDiffEq.jl's documentation.

ODE simulations

To perform ODE simulations, first convert the reaction system (prn.rn) into an ODESystem.

using ModelingToolkit
sys = structural_simplify(convert(ODESystem, prn.rn))

Here we call structural_simplify to inline any potential assignment rules into the model equations. Given an ODESystem, a good sanity check is to inspect the generated ODEs:

equations(sys)

\[ \begin{align} \frac{\mathrm{d} X\left( t \right)}{\mathrm{d}t} &= A C - C X\left( t \right) - B C X\left( t \right) + \left( X\left( t \right) \right)^{2} C Y\left( t \right) \\ \frac{\mathrm{d} Y\left( t \right)}{\mathrm{d}t} &= B C X\left( t \right) - \left( X\left( t \right) \right)^{2} C Y\left( t \right) \end{align} \]

Once we have an ODESystem, we can build an ODEProblem:

using OrdinaryDiffEq
tspan = (0.0, 10.0)
oprob = ODEProblem(sys, prn.u0, tspan, prn.p, jac=true)

Precompiling packages...
   2546.2 ms  ? LinearSolve → LinearSolveSparseArraysExt
   1917.7 ms  ? OrdinaryDiffEqDifferentiation
    244.6 ms  ? OrdinaryDiffEqDifferentiation → OrdinaryDiffEqDifferentiationSparseArraysExt
   3099.5 ms  ? NonlinearSolveQuasiNewton
   3177.4 ms  ? NonlinearSolveFirstOrder
   1124.7 ms  ? NonlinearSolveQuasiNewton → NonlinearSolveQuasiNewtonForwardDiffExt
    821.1 ms  ? NonlinearSolve
   2940.0 ms  ? OrdinaryDiffEqExponentialRK
   3231.3 ms  ? OrdinaryDiffEqExtrapolation
   3279.2 ms  ? OrdinaryDiffEqRosenbrock
    950.8 ms  ? OrdinaryDiffEqNonlinearSolve
   1889.8 ms  ? OrdinaryDiffEqStabilizedIRK
   2000.0 ms  ? OrdinaryDiffEqIMEXMultistep
   2065.1 ms  ? OrdinaryDiffEqSDIRK
   2244.3 ms  ? OrdinaryDiffEqPDIRK
   2969.2 ms  ? OrdinaryDiffEqFIRK
   1829.5 ms  ? OrdinaryDiffEqBDF
   2866.2 ms  ? OrdinaryDiffEqDefault
Info Given OrdinaryDiffEq was explicitly requested, output will be shown live 
┌ Warning: Module OrdinaryDiffEqDifferentiation with build ID ffffffff-ffff-ffff-8c8b-d967360a0e6c is missing from the cache.
│ This may mean OrdinaryDiffEqDifferentiation [4302a76b-040a-498a-8c04-15b101fed76b] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2638
   1081.0 ms  ? OrdinaryDiffEq
┌ Warning: Module OrdinaryDiffEqDifferentiation with build ID ffffffff-ffff-ffff-8c8b-d967360a0e6c is missing from the cache.
│ This may mean OrdinaryDiffEqDifferentiation [4302a76b-040a-498a-8c04-15b101fed76b] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2638
Precompiling packages...
   2551.1 ms  ? LinearSolve → LinearSolveSparseArraysExt
   1944.3 ms  ? OrdinaryDiffEqDifferentiation
    262.7 ms  ? OrdinaryDiffEqDifferentiation → OrdinaryDiffEqDifferentiationSparseArraysExt
Info Given OrdinaryDiffEqExtrapolation was explicitly requested, output will be shown live 
┌ Warning: Module LinearSolveSparseArraysExt with build ID ffffffff-ffff-ffff-ce81-ff2eeeceb35a is missing from the cache.
│ This may mean LinearSolveSparseArraysExt [acf9803d-64eb-5f69-b965-a71e3e6e1ed4] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2638
   1917.7 ms  ? OrdinaryDiffEqExtrapolation
┌ Warning: Module LinearSolveSparseArraysExt with build ID ffffffff-ffff-ffff-ce81-ff2eeeceb35a is missing from the cache.
│ This may mean LinearSolveSparseArraysExt [acf9803d-64eb-5f69-b965-a71e3e6e1ed4] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2638
Precompiling packages...
   2562.3 ms  ? LinearSolve → LinearSolveSparseArraysExt
   1915.3 ms  ? OrdinaryDiffEqDifferentiation
    245.4 ms  ? OrdinaryDiffEqDifferentiation → OrdinaryDiffEqDifferentiationSparseArraysExt
   2638.0 ms  ? NonlinearSolveQuasiNewton
   2673.6 ms  ? NonlinearSolveFirstOrder
    773.7 ms  ? NonlinearSolveQuasiNewton → NonlinearSolveQuasiNewtonForwardDiffExt
    564.6 ms  ? NonlinearSolve
    846.0 ms  ? OrdinaryDiffEqNonlinearSolve
Info Given OrdinaryDiffEqStabilizedIRK was explicitly requested, output will be shown live 
┌ Warning: Module OrdinaryDiffEqDifferentiation with build ID ffffffff-ffff-ffff-8c8b-d967360a0e6c is missing from the cache.
│ This may mean OrdinaryDiffEqDifferentiation [4302a76b-040a-498a-8c04-15b101fed76b] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2638
   1037.5 ms  ? OrdinaryDiffEqStabilizedIRK
┌ Warning: Module OrdinaryDiffEqDifferentiation with build ID ffffffff-ffff-ffff-8c8b-d967360a0e6c is missing from the cache.
│ This may mean OrdinaryDiffEqDifferentiation [4302a76b-040a-498a-8c04-15b101fed76b] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2638
Precompiling packages...
   2483.2 ms  ? LinearSolve → LinearSolveSparseArraysExt
   1920.4 ms  ? OrdinaryDiffEqDifferentiation
    247.5 ms  ? OrdinaryDiffEqDifferentiation → OrdinaryDiffEqDifferentiationSparseArraysExt
   2647.7 ms  ? NonlinearSolveQuasiNewton
   2663.0 ms  ? NonlinearSolveFirstOrder
    824.2 ms  ? NonlinearSolveQuasiNewton → NonlinearSolveQuasiNewtonForwardDiffExt
    575.6 ms  ? NonlinearSolve
    837.6 ms  ? OrdinaryDiffEqNonlinearSolve
Info Given OrdinaryDiffEqSDIRK was explicitly requested, output will be shown live 
┌ Warning: Module OrdinaryDiffEqDifferentiation with build ID ffffffff-ffff-ffff-8c8b-d967360a0e6c is missing from the cache.
│ This may mean OrdinaryDiffEqDifferentiation [4302a76b-040a-498a-8c04-15b101fed76b] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2638
   1002.9 ms  ? OrdinaryDiffEqSDIRK
┌ Warning: Module OrdinaryDiffEqDifferentiation with build ID ffffffff-ffff-ffff-8c8b-d967360a0e6c is missing from the cache.
│ This may mean OrdinaryDiffEqDifferentiation [4302a76b-040a-498a-8c04-15b101fed76b] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2638
Precompiling packages...
   2563.9 ms  ? LinearSolve → LinearSolveSparseArraysExt
   1935.0 ms  ? OrdinaryDiffEqDifferentiation
    252.1 ms  ? OrdinaryDiffEqDifferentiation → OrdinaryDiffEqDifferentiationSparseArraysExt
   2702.2 ms  ? NonlinearSolveQuasiNewton
   2702.7 ms  ? NonlinearSolveFirstOrder
    779.2 ms  ? NonlinearSolveQuasiNewton → NonlinearSolveQuasiNewtonForwardDiffExt
    556.7 ms  ? NonlinearSolve
    830.3 ms  ? OrdinaryDiffEqNonlinearSolve
   1000.9 ms  ? OrdinaryDiffEqSDIRK
Info Given OrdinaryDiffEqBDF was explicitly requested, output will be shown live 
┌ Warning: Module OrdinaryDiffEqSDIRK with build ID ffffffff-ffff-ffff-c130-353e4a0b51b8 is missing from the cache.
│ This may mean OrdinaryDiffEqSDIRK [2d112036-d095-4a1e-ab9a-08536f3ecdbf] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2638
   1048.4 ms  ? OrdinaryDiffEqBDF
┌ Warning: Module OrdinaryDiffEqSDIRK with build ID ffffffff-ffff-ffff-c130-353e4a0b51b8 is missing from the cache.
│ This may mean OrdinaryDiffEqSDIRK [2d112036-d095-4a1e-ab9a-08536f3ecdbf] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2638
Precompiling packages...
   2512.4 ms  ? LinearSolve → LinearSolveSparseArraysExt
   1880.2 ms  ? OrdinaryDiffEqDifferentiation
    260.5 ms  ? OrdinaryDiffEqDifferentiation → OrdinaryDiffEqDifferentiationSparseArraysExt
Info Given OrdinaryDiffEqRosenbrock was explicitly requested, output will be shown live 
┌ Warning: Module LinearSolveSparseArraysExt with build ID ffffffff-ffff-ffff-ce81-ff2eeeceb35a is missing from the cache.
│ This may mean LinearSolveSparseArraysExt [acf9803d-64eb-5f69-b965-a71e3e6e1ed4] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2638
   1898.2 ms  ? OrdinaryDiffEqRosenbrock
┌ Warning: Module LinearSolveSparseArraysExt with build ID ffffffff-ffff-ffff-ce81-ff2eeeceb35a is missing from the cache.
│ This may mean LinearSolveSparseArraysExt [acf9803d-64eb-5f69-b965-a71e3e6e1ed4] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2638
Precompiling packages...
   2557.7 ms  ? LinearSolve → LinearSolveSparseArraysExt
   1827.1 ms  ? NonlinearSolveFirstOrder
   2548.2 ms  ? NonlinearSolveQuasiNewton
   2657.5 ms  ? OrdinaryDiffEqDifferentiation
    257.3 ms  ? OrdinaryDiffEqDifferentiation → OrdinaryDiffEqDifferentiationSparseArraysExt
    819.5 ms  ? NonlinearSolveQuasiNewton → NonlinearSolveQuasiNewtonForwardDiffExt
    607.7 ms  ? NonlinearSolve
    888.2 ms  ? OrdinaryDiffEqNonlinearSolve
   1973.0 ms  ? OrdinaryDiffEqRosenbrock
   1014.5 ms  ? OrdinaryDiffEqSDIRK
   1037.9 ms  ? OrdinaryDiffEqBDF
Info Given OrdinaryDiffEqDefault was explicitly requested, output will be shown live 
┌ Warning: Module OrdinaryDiffEqRosenbrock with build ID ffffffff-ffff-ffff-c99d-9d3b59a5d0a0 is missing from the cache.
│ This may mean OrdinaryDiffEqRosenbrock [43230ef6-c299-4910-a778-202eb28ce4ce] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2638
   1083.6 ms  ? OrdinaryDiffEqDefault
┌ Warning: Module OrdinaryDiffEqRosenbrock with build ID ffffffff-ffff-ffff-c99d-9d3b59a5d0a0 is missing from the cache.
│ This may mean OrdinaryDiffEqRosenbrock [43230ef6-c299-4910-a778-202eb28ce4ce] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2638
Precompiling packages...
   2549.2 ms  ? LinearSolve → LinearSolveSparseArraysExt
   1845.1 ms  ? NonlinearSolveFirstOrder
   2529.3 ms  ? NonlinearSolveQuasiNewton
   2642.9 ms  ? OrdinaryDiffEqDifferentiation
    244.7 ms  ? OrdinaryDiffEqDifferentiation → OrdinaryDiffEqDifferentiationSparseArraysExt
    808.3 ms  ? NonlinearSolveQuasiNewton → NonlinearSolveQuasiNewtonForwardDiffExt
    580.0 ms  ? NonlinearSolve
    831.2 ms  ? OrdinaryDiffEqNonlinearSolve
Info Given OrdinaryDiffEqFIRK was explicitly requested, output will be shown live 
┌ Warning: Module LinearSolveSparseArraysExt with build ID ffffffff-ffff-ffff-ce81-ff2eeeceb35a is missing from the cache.
│ This may mean LinearSolveSparseArraysExt [acf9803d-64eb-5f69-b965-a71e3e6e1ed4] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2638
   1873.2 ms  ? OrdinaryDiffEqFIRK
┌ Warning: Module LinearSolveSparseArraysExt with build ID ffffffff-ffff-ffff-ce81-ff2eeeceb35a is missing from the cache.
│ This may mean LinearSolveSparseArraysExt [acf9803d-64eb-5f69-b965-a71e3e6e1ed4] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2638
Precompiling packages...
   2425.7 ms  ? LinearSolve → LinearSolveSparseArraysExt
   1856.9 ms  ? OrdinaryDiffEqDifferentiation
    241.2 ms  ? OrdinaryDiffEqDifferentiation → OrdinaryDiffEqDifferentiationSparseArraysExt
   2626.1 ms  ? NonlinearSolveFirstOrder
   2629.9 ms  ? NonlinearSolveQuasiNewton
    809.9 ms  ? NonlinearSolveQuasiNewton → NonlinearSolveQuasiNewtonForwardDiffExt
    574.1 ms  ? NonlinearSolve
    873.6 ms  ? OrdinaryDiffEqNonlinearSolve
Info Given OrdinaryDiffEqPDIRK was explicitly requested, output will be shown live 
┌ Warning: Module OrdinaryDiffEqDifferentiation with build ID ffffffff-ffff-ffff-8c8b-d967360a0e6c is missing from the cache.
│ This may mean OrdinaryDiffEqDifferentiation [4302a76b-040a-498a-8c04-15b101fed76b] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2638
   1237.2 ms  ? OrdinaryDiffEqPDIRK
┌ Warning: Module OrdinaryDiffEqDifferentiation with build ID ffffffff-ffff-ffff-8c8b-d967360a0e6c is missing from the cache.
│ This may mean OrdinaryDiffEqDifferentiation [4302a76b-040a-498a-8c04-15b101fed76b] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2638
Precompiling packages...
   2542.0 ms  ? LinearSolve → LinearSolveSparseArraysExt
   1932.8 ms  ? OrdinaryDiffEqDifferentiation
    249.5 ms  ? OrdinaryDiffEqDifferentiation → OrdinaryDiffEqDifferentiationSparseArraysExt
   2675.8 ms  ? NonlinearSolveQuasiNewton
   2690.6 ms  ? NonlinearSolveFirstOrder
    770.4 ms  ? NonlinearSolveQuasiNewton → NonlinearSolveQuasiNewtonForwardDiffExt
    565.4 ms  ? NonlinearSolve
    876.0 ms  ? OrdinaryDiffEqNonlinearSolve
Info Given OrdinaryDiffEqIMEXMultistep was explicitly requested, output will be shown live 
┌ Warning: Module OrdinaryDiffEqDifferentiation with build ID ffffffff-ffff-ffff-8c8b-d967360a0e6c is missing from the cache.
│ This may mean OrdinaryDiffEqDifferentiation [4302a76b-040a-498a-8c04-15b101fed76b] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2638
   1045.1 ms  ? OrdinaryDiffEqIMEXMultistep
┌ Warning: Module OrdinaryDiffEqDifferentiation with build ID ffffffff-ffff-ffff-8c8b-d967360a0e6c is missing from the cache.
│ This may mean OrdinaryDiffEqDifferentiation [4302a76b-040a-498a-8c04-15b101fed76b] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2638
Precompiling packages...
   2549.0 ms  ? LinearSolve → LinearSolveSparseArraysExt
   1884.2 ms  ? OrdinaryDiffEqDifferentiation
    274.8 ms  ? OrdinaryDiffEqDifferentiation → OrdinaryDiffEqDifferentiationSparseArraysExt
Info Given OrdinaryDiffEqExponentialRK was explicitly requested, output will be shown live 
┌ Warning: Module OrdinaryDiffEqDifferentiation with build ID ffffffff-ffff-ffff-8c8b-d967360a0e6c is missing from the cache.
│ This may mean OrdinaryDiffEqDifferentiation [4302a76b-040a-498a-8c04-15b101fed76b] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2638
   1652.5 ms  ? OrdinaryDiffEqExponentialRK
┌ Warning: Module OrdinaryDiffEqDifferentiation with build ID ffffffff-ffff-ffff-8c8b-d967360a0e6c is missing from the cache.
│ This may mean OrdinaryDiffEqDifferentiation [4302a76b-040a-498a-8c04-15b101fed76b] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:2638

Setting jac=true means that the ODE Jacobian is computed symbolically, which often improves simulation performance. The ODEProblem can be simulated with any solver from the OrdinaryDiffEq.jl package, such as the Rodas5P solver:

sol = solve(oprob, Rodas5P(), callback=cb)
plot(sol; xlabel = "Time [s]", ylabel = "Protein amount")

For more information on ODE simulations, see OrdinaryDiffEq.jl's documentation. A guide to choosing an ODE solver can be found here.

Importing large models

For large models with more than 1000 species, constructing the Jacobian for the ODEProblem can be time-consuming. Therefore, if model load time is a problem, setting jac = false can help.

Changing Parameter Values and/or Initial Values

One of the most common modeling operations is to modify model parameter values and/or initial values. Because SBMLImporter imports models as a Catalyst ReactionSystem that supports the SymbolicIndexingInterface, these modifications are straightforward to perform at the ODEProblem, SDEProblem, or JumpProblem level.

Parameter values can be modified using prob.ps[:param_id]. For example, for the Brusselator imported as an ODEProblem above, the value of parameter A can be changed with:

oprob.ps[:A] = 2.0

Initial values can be modified with prob[:specie_id]. For example, to change the initial value of the species X to 2.0, do:

oprob[:X] = 2.0

Next Steps

For additional modeling tasks that can be carried out with a Catalyst ReactionSystem (e.g., bifurcation analysis, parameter estimation, etc.), see the Catalyst documentation. If you encounter any problems with importing an SBML model, first consult the FAQ. Additional details on importer options can be found in the API.