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TorkelETorkelE
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Merge branch 'master' into param_stoich
2 parents 56acc1f + 705d684 commit 297208f

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lines changed

‎.github/workflows/Documentation.yml

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- uses: actions/checkout@v4
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- uses: julia-actions/setup-julia@latest
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with:
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version: '1'
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version: '1.10.2'
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- name: Install dependencies
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run: julia --project=docs/ -e 'ENV["JULIA_PKG_SERVER"] = ""; using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
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- name: Build and deploy

‎Project.toml

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@@ -40,6 +40,7 @@ BifurcationKit = "0.3"
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DataStructures = "0.18"
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DiffEqBase = "6.83.0"
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DocStringExtensions = "0.8, 0.9"
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DynamicPolynomials = "0.5"
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DynamicQuantities = "0.13.2"
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Graphs = "1.4"
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HomotopyContinuation = "2.9"
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SymbolicUtils = "1.0.3"
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Symbolics = "5.27"
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Unitful = "1.12.4"
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julia = "1.9"
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julia = "1.10"
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[extras]
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BifurcationKit = "0f109fa4-8a5d-4b75-95aa-f515264e7665"

‎docs/Project.toml

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@@ -37,7 +37,7 @@ Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7"
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[compat]
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BenchmarkTools = "1.5"
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BifurcationKit = "0.3"
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BifurcationKit = "0.3.4"
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CairoMakie = "0.12"
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Catalyst = "13"
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DataFrames = "1.6"

‎docs/pages.jl

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@@ -9,30 +9,29 @@ pages = Any[
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"model_creation/dsl_basics.md",
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"model_creation/dsl_advanced.md",
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#"model_creation/programmatic_CRN_construction.md",
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#"model_creation/compositional_modeling.md",
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"model_creation/compositional_modeling.md",
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#"model_creation/constraint_equations.md",
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# Events.
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"model_creation/parametric_stoichiometry.md",# Distributed parameters, rates, and initial conditions.
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"model_creation/model_file_loading_and_export.md",# Distributed parameters, rates, and initial conditions.
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# Loading and writing models to files.
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"model_creation/model_visualisation.md",
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#"model_creation/network_analysis.md",
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"model_creation/chemistry_related_functionality.md",
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"Model creation examples" => Any[
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"model_creation/examples/basic_CRN_library.md",
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"model_creation/examples/programmatic_generative_linear_pathway.md",
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#"model_creation/examples/hodgkin_huxley_equation.md",
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"model_creation/examples/hodgkin_huxley_equation.md",
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#"model_creation/examples/smoluchowski_coagulation_equation.md"
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]
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],
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"Model simulation" => Any[
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"model_simulation/simulation_introduction.md",
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# Simulation introduction.
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"model_simulation/simulation_plotting.md",
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"model_simulation/simulation_structure_interfacing.md",
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"model_simulation/ensemble_simulations.md",
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# Stochastic simulation statistical analysis.
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"model_simulation/ode_simulation_performance.md",
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# ODE Performance considerations/advice.
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# SDE Performance considerations/advice.
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# Jump Performance considerations/advice.
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# Finite state projection
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# ODE parameter fitting using Turing.
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# SDE/Jump fitting.
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"inverse_problems/behaviour_optimisation.md",
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"inverse_problems/structural_identifiability.md",
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"inverse_problems/structural_identifiability.md", # Broken on Julia v1.10.3, requires v1.10.2 or 1.10.4.
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# Practical identifiability.
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"inverse_problems/global_sensitivity_analysis.md",
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"Inverse problem examples" => Any[
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# # Repository structure.
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# ],
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#"FAQs" => "faqs.md",
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#"API" => "api.md"
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]
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"API" => "api.md"
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]

‎docs/src/api.md

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models, and stochastic chemical kinetics jump process models.
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```@example ex1
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using Catalyst, DifferentialEquations, Plots
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using Catalyst, OrdinaryDiffEq, StochasticDiffEq, JumpProcesses, Plots
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t = default_t()
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@parameters β γ
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@species S(t) I(t) R(t)
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rxs = [Reaction(β, [S,I], [I], [1,1], [2])
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Reaction(γ, [I], [R])]
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@named rs = ReactionSystem(rxs, t)
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rs = complete(rs)
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u₀map = [S => 999.0, I => 1.0, R => 0.0]
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parammap = [β => 1/10000, γ => 0.01]
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tspan = (0.0, 250.0)
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# solve as ODEs
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odesys = convert(ODESystem, rs)
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odesys = complete(odesys)
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oprob = ODEProblem(odesys, u₀map, tspan, parammap)
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sol = solve(oprob, Tsit5())
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p1 = plot(sol, title = "ODE")
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# solve as SDEs
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sdesys = convert(SDESystem, rs)
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sdesys = complete(sdesys)
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sprob = SDEProblem(sdesys, u₀map, tspan, parammap)
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sol = solve(sprob, EM(), dt=.01)
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sol = solve(sprob, EM(), dt=.01, saveat = 2.0)
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p2 = plot(sol, title = "SDE")
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# solve as jump process
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jumpsys = convert(JumpSystem, rs)
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jumpsys = complete(jumpsys)
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u₀map = [S => 999, I => 1, R => 0]
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dprob = DiscreteProblem(jumpsys, u₀map, tspan, parammap)
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jprob = JumpProblem(jumpsys, dprob, Direct())
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sol = solve(jprob, SSAStepper())
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jprob = JumpProblem(jumpsys, dprob, Direct(); save_positions = (false,false))
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sol = solve(jprob, SSAStepper(), saveat = 2.0)
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p3 = plot(sol, title = "jump")
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plot(p1, p2, p3; layout = (3,1))

‎docs/src/assets/Project.toml

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Catalyst = "479239e8-5488-4da2-87a7-35f2df7eef83"
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DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
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DiffEqParamEstim = "1130ab10-4a5a-5621-a13d-e4788d82bd4c"
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DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa"
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Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
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Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
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DynamicalSystems = "61744808-ddfa-5f27-97ff-6e42cc95d634"

‎docs/src/assets/brusselator_sim_SBMLImporter.svg

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‎docs/src/assets/model_files/brusselator.xml

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<?xml version="1.0" encoding="UTF-8"?>
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<!-- Created by COPASI version 4.42 (Build 284) on 2024-01-10 09:22 with libSBML version 5.20.0. -->
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<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
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<model metaid="COPASI0" id="New_Model" name="New Model">
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<annotation>
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<copasi:COPASI xmlns:copasi="http://www.copasi.org/static/sbml">
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<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
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<rdf:Description rdf:about="#COPASI0">
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<dcterms:created>
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<rdf:Description>
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<dcterms:W3CDTF>2024-01-09T21:46:45Z</dcterms:W3CDTF>
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</rdf:Description>
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</dcterms:created>
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</rdf:Description>
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</rdf:RDF>
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</copasi:COPASI>
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
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<rdf:Description rdf:about="#COPASI0">
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<dcterms:created rdf:parseType="Resource">
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<dcterms:W3CDTF>2024-01-09T21:46:45Z</dcterms:W3CDTF>
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</dcterms:created>
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<dcterms:modified rdf:parseType="Resource">
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<dcterms:W3CDTF>2024-01-09T21:46:45Z</dcterms:W3CDTF>
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</dcterms:modified>
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</rdf:Description>
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</rdf:RDF>
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</annotation>
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<listOfFunctionDefinitions>
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<functionDefinition id="Constant_flux__irreversible" name="Constant flux (irreversible)">
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<lambda>
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<bvar>
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<ci> v </ci>
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</bvar>
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<ci> v </ci>
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</lambda>
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</math>
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</functionDefinition>
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</listOfFunctionDefinitions>
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<listOfUnitDefinitions>
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<unitDefinition id="length" name="length">
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<listOfUnits>
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<unit kind="metre" exponent="1" scale="0" multiplier="1"/>
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</listOfUnits>
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</unitDefinition>
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<unitDefinition id="area" name="area">
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<listOfUnits>
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<unit kind="metre" exponent="2" scale="0" multiplier="1"/>
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</listOfUnits>
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</unitDefinition>
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<unitDefinition id="volume" name="volume">
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<listOfUnits>
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<unit kind="litre" exponent="1" scale="0" multiplier="1"/>
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</listOfUnits>
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</unitDefinition>
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<unitDefinition id="time" name="time">
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<listOfUnits>
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<unit kind="second" exponent="1" scale="0" multiplier="1"/>
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</listOfUnits>
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</unitDefinition>
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<unitDefinition id="substance" name="substance">
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<listOfUnits>
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<unit kind="mole" exponent="1" scale="0" multiplier="1"/>
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</listOfUnits>
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</unitDefinition>
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</listOfUnitDefinitions>
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<listOfCompartments>
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<compartment id="compartment" name="compartment" spatialDimensions="3" size="1" constant="true"/>
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</listOfCompartments>
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<listOfSpecies>
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<species id="X" name="X" compartment="compartment" hasOnlySubstanceUnits="true" initialAmount="2" boundaryCondition="false" constant="false"/>
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<species id="Y" name="Y" compartment="compartment" hasOnlySubstanceUnits="true" initialAmount="10" boundaryCondition="false" constant="false"/>
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</listOfSpecies>
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<listOfParameters>
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<parameter id="A" name="A" value="1" constant="true"/>
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<parameter id="B" name="B" value="4" constant="true"/>
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</listOfParameters>
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<listOfReactions>
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<reaction id="r2" name="r2" reversible="false">
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<listOfReactants>
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<speciesReference species="Y" stoichiometry="1"/>
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<speciesReference species="X" stoichiometry="2"/>
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</listOfReactants>
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<listOfProducts>
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<speciesReference species="X" stoichiometry="3"/>
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</listOfProducts>
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<kineticLaw>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<apply>
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<times/>
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<ci> compartment </ci>
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<ci> k1 </ci>
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<apply>
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<power/>
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<ci> X </ci>
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<cn> 2 </cn>
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</apply>
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<ci> Y </ci>
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</apply>
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</math>
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<listOfParameters>
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<parameter id="k1" name="k1" value="1"/>
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</listOfParameters>
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</kineticLaw>
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</reaction>
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<reaction id="r3" name="r3" reversible="false">
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<listOfReactants>
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<speciesReference species="X" stoichiometry="1"/>
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</listOfReactants>
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<listOfProducts>
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<speciesReference species="Y" stoichiometry="1"/>
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</listOfProducts>
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<kineticLaw>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<apply>
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<times/>
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<ci> compartment </ci>
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<ci> B </ci>
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<ci> X </ci>
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</apply>
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</math>
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</kineticLaw>
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</reaction>
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<reaction id="r4" name="r4" reversible="false">
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<listOfReactants>
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<speciesReference species="X" stoichiometry="1"/>
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</listOfReactants>
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<kineticLaw>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<apply>
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<times/>
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<ci> compartment </ci>
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<ci> k1 </ci>
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<ci> X </ci>
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</apply>
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</math>
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<listOfParameters>
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<parameter id="k1" name="k1" value="1"/>
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</listOfParameters>
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</kineticLaw>
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</reaction>
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<reaction id="r1" name="r1" reversible="false">
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<listOfProducts>
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<speciesReference species="X" stoichiometry="1"/>
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</listOfProducts>
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<kineticLaw>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<apply>
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<times/>
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<ci> compartment </ci>
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<apply>
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<ci> Constant_flux__irreversible </ci>
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<ci> A </ci>
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</apply>
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</apply>
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</math>
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</kineticLaw>
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</reaction>
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</listOfReactions>
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</model>
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</sbml>

‎docs/src/assets/model_files/repressilator.net

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# Created by BioNetGen 2.3.1
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begin parameters
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1 Na 6.022e23 # Constant
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2 V 1.4e-15 # Constant
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3 c0 1e9 # Constant
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4 c1 224 # Constant
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5 c2 9 # Constant
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6 c3 0.5 # Constant
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7 c4 5e-4 # Constant
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8 c5 0.167 # Constant
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9 c6 ln(2)/120 # Constant
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10 c7 ln(2)/600 # Constant
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11 tF 1e-4 # Constant
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12 rF 1000 # Constant
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13 pF 1000 # Constant
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14 _rateLaw1 (((c0/Na)/V)*tF)/pF # ConstantExpression
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15 _rateLaw2 c1*tF # ConstantExpression
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16 _rateLaw3 (((c0/Na)/V)*tF)/pF # ConstantExpression
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17 _rateLaw4 c2*tF # ConstantExpression
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18 _rateLaw5 c3*rF # ConstantExpression
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19 _rateLaw6 c4*rF # ConstantExpression
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20 _rateLaw7 (c5/rF)*pF # ConstantExpression
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21 _rateLaw8 (((c0/Na)/V)*tF)/pF # ConstantExpression
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22 _rateLaw9 c1*tF # ConstantExpression
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23 _rateLaw10 (((c0/Na)/V)*tF)/pF # ConstantExpression
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24 _rateLaw11 c2*tF # ConstantExpression
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25 _rateLaw12 c3*rF # ConstantExpression
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26 _rateLaw13 c4*rF # ConstantExpression
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27 _rateLaw14 (c5/rF)*pF # ConstantExpression
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28 _rateLaw15 (((c0/Na)/V)*tF)/pF # ConstantExpression
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29 _rateLaw16 c1*tF # ConstantExpression
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30 _rateLaw17 (((c0/Na)/V)*tF)/pF # ConstantExpression
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31 _rateLaw18 c2*tF # ConstantExpression
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32 _rateLaw19 c3*rF # ConstantExpression
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33 _rateLaw20 c4*rF # ConstantExpression
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34 _rateLaw21 (c5/rF)*pF # ConstantExpression
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end parameters
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begin species
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1 Null() 1
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2 gTetR(lac!1,lac!2).pLacI(tet!1).pLacI(tet!2) 1
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3 gCI(tet!1,tet!2).pTetR(cI!1).pTetR(cI!2) 1
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4 gLacI(cI!1,cI!2).pCI(lac!1).pCI(lac!2) 1
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5 mTetR() 3163
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6 mCI() 6819
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7 mLacI() 129
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8 pTetR(cI) 183453
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9 pCI(lac) 2006198
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10 pLacI(tet) 165670
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11 gTetR(lac!1,lac).pLacI(tet!1) 0
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12 gCI(tet!1,tet).pTetR(cI!1) 0
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13 gLacI(cI!1,cI).pCI(lac!1) 0
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14 gTetR(lac,lac) 0
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15 gCI(tet,tet) 0
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16 gLacI(cI,cI) 0
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end species
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begin reactions
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1 2 10,11 2*_rateLaw4 #_reverse__R2
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2 2 2,5 _rateLaw6 #_R4
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3 5 5,8 _rateLaw7 #_R5
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4 1,5 1 c6 #_R6
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5 1,8 1 c7 #_R7
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6 3 8,12 2*_rateLaw11 #_reverse__R9
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7 3 3,6 _rateLaw13 #_R11
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8 6 6,9 _rateLaw14 #_R12
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9 1,6 1 c6 #_R13
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10 1,9 1 c7 #_R14
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11 4 9,13 2*_rateLaw18 #_reverse__R16
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12 4 4,7 _rateLaw20 #_R18
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13 7 7,10 _rateLaw21 #_R19
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14 1,7 1 c6 #_R20
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15 1,10 1 c7 #_R21
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16 11 10,14 _rateLaw2 #_reverse__R1
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17 10,11 2 _rateLaw3 #_R2
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18 11 5,11 _rateLaw6 #_R4
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19 12 8,15 _rateLaw9 #_reverse__R8
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20 8,12 3 _rateLaw10 #_R9
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21 12 6,12 _rateLaw13 #_R11
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22 13 9,16 _rateLaw16 #_reverse__R15
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23 9,13 4 _rateLaw17 #_R16
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24 13 7,13 _rateLaw20 #_R18
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25 10,14 11 2*_rateLaw1 #_R1
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26 14 5,14 _rateLaw5 #_R3
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27 8,15 12 2*_rateLaw8 #_R8
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28 15 6,15 _rateLaw12 #_R10
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29 9,16 13 2*_rateLaw15 #_R15
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30 16 7,16 _rateLaw19 #_R17
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end reactions
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begin groups
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1 pTetR 8
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2 pCI 9
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3 pLacI 10
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4 NULL 1
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end groups

‎docs/src/assets/network_graphs/brusselator_graph.png

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