Merge branch 'master' into proposed_constraint_eqs_doc_up

SciML · Jun 4, 2024 · 6f4fc6d · 6f4fc6d
2 parents ffb230e + 940861e
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diff --git a/.github/workflows/Documentation.yml b/.github/workflows/Documentation.yml
@@ -14,7 +14,7 @@ jobs:
       - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@latest
         with:
-          version: '1'
+          version: '1.10.2'
       - name: Install dependencies
         run: julia --project=docs/ -e 'ENV["JULIA_PKG_SERVER"] = ""; using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
       - name: Build and deploy

diff --git a/Project.toml b/Project.toml
@@ -40,6 +40,7 @@ BifurcationKit = "0.3"
 DataStructures = "0.18"
 DiffEqBase = "6.83.0"
 DocStringExtensions = "0.8, 0.9"
+DynamicPolynomials = "0.5"
 DynamicQuantities = "0.13.2"
 Graphs = "1.4"
 HomotopyContinuation = "2.9"
@@ -57,7 +58,7 @@ StructuralIdentifiability = "0.5.1"
 SymbolicUtils = "1.0.3"
 Symbolics = "5.27"
 Unitful = "1.12.4"
-julia = "1.9"
+julia = "1.10"
 
 [extras]
 BifurcationKit = "0f109fa4-8a5d-4b75-95aa-f515264e7665"

diff --git a/docs/Project.toml b/docs/Project.toml
@@ -37,7 +37,7 @@ Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7"
 
 [compat]
 BenchmarkTools = "1.5"
-BifurcationKit = "0.3"
+BifurcationKit = "0.3.4"
 CairoMakie = "0.12"
 Catalyst = "13"
 DataFrames = "1.6"

diff --git a/docs/pages.jl b/docs/pages.jl
@@ -9,30 +9,29 @@ pages = Any[
         "model_creation/dsl_basics.md",
         "model_creation/dsl_advanced.md",
         #"model_creation/programmatic_CRN_construction.md",
-        #"model_creation/compositional_modeling.md",
+        "model_creation/compositional_modeling.md",
         "model_creation/constraint_equations.md",
         # Events.
-        #"model_creation/parametric_stoichiometry.md",# Distributed parameters, rates, and initial conditions.
+        "model_creation/parametric_stoichiometry.md",# Distributed parameters, rates, and initial conditions.
+        "model_creation/model_file_loading_and_export.md",# Distributed parameters, rates, and initial conditions.
         # Loading and writing models to files.
         "model_creation/model_visualisation.md",
         #"model_creation/network_analysis.md",
         "model_creation/chemistry_related_functionality.md",
         "Model creation examples" => Any[
             "model_creation/examples/basic_CRN_library.md",
             "model_creation/examples/programmatic_generative_linear_pathway.md",
-            #"model_creation/examples/hodgkin_huxley_equation.md",
+            "model_creation/examples/hodgkin_huxley_equation.md",
             #"model_creation/examples/smoluchowski_coagulation_equation.md"
         ]
     ],
     "Model simulation" => Any[
         "model_simulation/simulation_introduction.md",
-        # Simulation introduction.
         "model_simulation/simulation_plotting.md",
         "model_simulation/simulation_structure_interfacing.md",
         "model_simulation/ensemble_simulations.md",
         # Stochastic simulation statistical analysis.
         "model_simulation/ode_simulation_performance.md",
-        # ODE Performance considerations/advice.
         # SDE Performance considerations/advice.
         # Jump Performance considerations/advice.
         # Finite state projection
@@ -51,7 +50,7 @@ pages = Any[
         # ODE parameter fitting using Turing.
         # SDE/Jump fitting.
         "inverse_problems/behaviour_optimisation.md",
-        "inverse_problems/structural_identifiability.md",
+        "inverse_problems/structural_identifiability.md", # Broken on Julia v1.10.3, requires v1.10.2 or 1.10.4.
         # Practical identifiability.
         "inverse_problems/global_sensitivity_analysis.md",
         "Inverse problem examples" => Any[
@@ -68,5 +67,5 @@ pages = Any[
     #     # Repository structure.
     # ],
     #"FAQs" => "faqs.md",
-    #"API" => "api.md"
-]
+    "API" => "api.md"
+]
diff --git a/docs/src/api.md b/docs/src/api.md
@@ -35,37 +35,41 @@ corresponding chemical reaction ODE models, chemical Langevin equation SDE
 models, and stochastic chemical kinetics jump process models.
 
 ```@example ex1
-using Catalyst, DifferentialEquations, Plots
+using Catalyst, OrdinaryDiffEq, StochasticDiffEq, JumpProcesses, Plots
 t = default_t()
 @parameters β γ
 @species S(t) I(t) R(t)
 
 rxs = [Reaction(β, [S,I], [I], [1,1], [2])
        Reaction(γ, [I], [R])]
 @named rs = ReactionSystem(rxs, t)
+rs = complete(rs)
 
 u₀map    = [S => 999.0, I => 1.0, R => 0.0]
 parammap = [β => 1/10000, γ => 0.01]
 tspan    = (0.0, 250.0)
 
 # solve as ODEs
 odesys = convert(ODESystem, rs)
+odesys = complete(odesys)
 oprob = ODEProblem(odesys, u₀map, tspan, parammap)
 sol = solve(oprob, Tsit5())
 p1 = plot(sol, title = "ODE")
 
 # solve as SDEs
 sdesys = convert(SDESystem, rs)
+sdesys = complete(sdesys)
 sprob = SDEProblem(sdesys, u₀map, tspan, parammap)
-sol = solve(sprob, EM(), dt=.01)
+sol = solve(sprob, EM(), dt=.01, saveat = 2.0)
 p2 = plot(sol, title = "SDE")
 
 # solve as jump process
 jumpsys = convert(JumpSystem, rs)
+jumpsys = complete(jumpsys)
 u₀map    = [S => 999, I => 1, R => 0]
 dprob = DiscreteProblem(jumpsys, u₀map, tspan, parammap)
-jprob = JumpProblem(jumpsys, dprob, Direct())
-sol = solve(jprob, SSAStepper())
+jprob = JumpProblem(jumpsys, dprob, Direct(); save_positions = (false,false))
+sol = solve(jprob, SSAStepper(), saveat = 2.0)
 p3 = plot(sol, title = "jump")
 
 plot(p1, p2, p3; layout = (3,1))

diff --git a/docs/src/assets/Project.toml b/docs/src/assets/Project.toml
@@ -5,6 +5,7 @@ CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
 Catalyst = "479239e8-5488-4da2-87a7-35f2df7eef83"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 DiffEqParamEstim = "1130ab10-4a5a-5621-a13d-e4788d82bd4c"
+DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 DynamicalSystems = "61744808-ddfa-5f27-97ff-6e42cc95d634"

diff --git a/docs/src/assets/brusselator_sim_SBMLImporter.svg b/docs/src/assets/brusselator_sim_SBMLImporter.svg
diff --git a/docs/src/assets/model_files/brusselator.xml b/docs/src/assets/model_files/brusselator.xml
@@ -0,0 +1,161 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- Created by COPASI version 4.42 (Build 284) on 2024-01-10 09:22 with libSBML version 5.20.0. -->
+<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
+  <model metaid="COPASI0" id="New_Model" name="New Model">
+    <annotation>
+      <copasi:COPASI xmlns:copasi="http://www.copasi.org/static/sbml">
+        <rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+          <rdf:Description rdf:about="#COPASI0">
+            <dcterms:created>
+              <rdf:Description>
+                <dcterms:W3CDTF>2024-01-09T21:46:45Z</dcterms:W3CDTF>
+              </rdf:Description>
+            </dcterms:created>
+          </rdf:Description>
+        </rdf:RDF>
+      </copasi:COPASI>
+      <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/">
+        <rdf:Description rdf:about="#COPASI0">
+          <dcterms:created rdf:parseType="Resource">
+            <dcterms:W3CDTF>2024-01-09T21:46:45Z</dcterms:W3CDTF>
+          </dcterms:created>
+          <dcterms:modified rdf:parseType="Resource">
+            <dcterms:W3CDTF>2024-01-09T21:46:45Z</dcterms:W3CDTF>
+          </dcterms:modified>
+        </rdf:Description>
+      </rdf:RDF>
+    </annotation>
+    <listOfFunctionDefinitions>
+      <functionDefinition id="Constant_flux__irreversible" name="Constant flux (irreversible)">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <lambda>
+            <bvar>
+              <ci> v </ci>
+            </bvar>
+            <ci> v </ci>
+          </lambda>
+        </math>
+      </functionDefinition>
+    </listOfFunctionDefinitions>
+    <listOfUnitDefinitions>
+      <unitDefinition id="length" name="length">
+        <listOfUnits>
+          <unit kind="metre" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="area" name="area">
+        <listOfUnits>
+          <unit kind="metre" exponent="2" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="volume" name="volume">
+        <listOfUnits>
+          <unit kind="litre" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="time" name="time">
+        <listOfUnits>
+          <unit kind="second" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+      <unitDefinition id="substance" name="substance">
+        <listOfUnits>
+          <unit kind="mole" exponent="1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+    </listOfUnitDefinitions>
+    <listOfCompartments>
+      <compartment id="compartment" name="compartment" spatialDimensions="3" size="1" constant="true"/>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species id="X" name="X" compartment="compartment" hasOnlySubstanceUnits="true" initialAmount="2" boundaryCondition="false" constant="false"/>
+      <species id="Y" name="Y" compartment="compartment" hasOnlySubstanceUnits="true" initialAmount="10" boundaryCondition="false" constant="false"/>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter id="A" name="A" value="1" constant="true"/>
+      <parameter id="B" name="B" value="4" constant="true"/>
+    </listOfParameters>
+    <listOfReactions>
+      <reaction id="r2" name="r2" reversible="false">
+        <listOfReactants>
+          <speciesReference species="Y" stoichiometry="1"/>
+          <speciesReference species="X" stoichiometry="2"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="X" stoichiometry="3"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> compartment </ci>
+              <ci> k1 </ci>
+              <apply>
+                <power/>
+                <ci> X </ci>
+                <cn> 2 </cn>
+              </apply>
+              <ci> Y </ci>
+            </apply>
+          </math>
+          <listOfParameters>
+            <parameter id="k1" name="k1" value="1"/>
+          </listOfParameters>
+        </kineticLaw>
+      </reaction>
+      <reaction id="r3" name="r3" reversible="false">
+        <listOfReactants>
+          <speciesReference species="X" stoichiometry="1"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="Y" stoichiometry="1"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> compartment </ci>
+              <ci> B </ci>
+              <ci> X </ci>
+            </apply>
+          </math>
+        </kineticLaw>
+      </reaction>
+      <reaction id="r4" name="r4" reversible="false">
+        <listOfReactants>
+          <speciesReference species="X" stoichiometry="1"/>
+        </listOfReactants>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> compartment </ci>
+              <ci> k1 </ci>
+              <ci> X </ci>
+            </apply>
+          </math>
+          <listOfParameters>
+            <parameter id="k1" name="k1" value="1"/>
+          </listOfParameters>
+        </kineticLaw>
+      </reaction>
+      <reaction id="r1" name="r1" reversible="false">
+        <listOfProducts>
+          <speciesReference species="X" stoichiometry="1"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> compartment </ci>
+              <apply>
+                <ci> Constant_flux__irreversible </ci>
+                <ci> A </ci>
+              </apply>
+            </apply>
+          </math>
+        </kineticLaw>
+      </reaction>
+    </listOfReactions>
+  </model>
+</sbml>
diff --git a/docs/src/assets/model_files/repressilator.net b/docs/src/assets/model_files/repressilator.net
@@ -0,0 +1,93 @@
+# Created by BioNetGen 2.3.1
+begin parameters
+    1 Na          6.022e23  # Constant
+    2 V           1.4e-15  # Constant
+    3 c0          1e9  # Constant
+    4 c1          224  # Constant
+    5 c2          9  # Constant
+    6 c3          0.5  # Constant
+    7 c4          5e-4  # Constant
+    8 c5          0.167  # Constant
+    9 c6          ln(2)/120  # Constant
+   10 c7          ln(2)/600  # Constant
+   11 tF          1e-4  # Constant
+   12 rF          1000  # Constant
+   13 pF          1000  # Constant
+   14 _rateLaw1   (((c0/Na)/V)*tF)/pF  # ConstantExpression
+   15 _rateLaw2   c1*tF  # ConstantExpression
+   16 _rateLaw3   (((c0/Na)/V)*tF)/pF  # ConstantExpression
+   17 _rateLaw4   c2*tF  # ConstantExpression
+   18 _rateLaw5   c3*rF  # ConstantExpression
+   19 _rateLaw6   c4*rF  # ConstantExpression
+   20 _rateLaw7   (c5/rF)*pF  # ConstantExpression
+   21 _rateLaw8   (((c0/Na)/V)*tF)/pF  # ConstantExpression
+   22 _rateLaw9   c1*tF  # ConstantExpression
+   23 _rateLaw10  (((c0/Na)/V)*tF)/pF  # ConstantExpression
+   24 _rateLaw11  c2*tF  # ConstantExpression
+   25 _rateLaw12  c3*rF  # ConstantExpression
+   26 _rateLaw13  c4*rF  # ConstantExpression
+   27 _rateLaw14  (c5/rF)*pF  # ConstantExpression
+   28 _rateLaw15  (((c0/Na)/V)*tF)/pF  # ConstantExpression
+   29 _rateLaw16  c1*tF  # ConstantExpression
+   30 _rateLaw17  (((c0/Na)/V)*tF)/pF  # ConstantExpression
+   31 _rateLaw18  c2*tF  # ConstantExpression
+   32 _rateLaw19  c3*rF  # ConstantExpression
+   33 _rateLaw20  c4*rF  # ConstantExpression
+   34 _rateLaw21  (c5/rF)*pF  # ConstantExpression
+end parameters
+begin species
+    1 Null() 1
+    2 gTetR(lac!1,lac!2).pLacI(tet!1).pLacI(tet!2) 1
+    3 gCI(tet!1,tet!2).pTetR(cI!1).pTetR(cI!2) 1
+    4 gLacI(cI!1,cI!2).pCI(lac!1).pCI(lac!2) 1
+    5 mTetR() 3163
+    6 mCI() 6819
+    7 mLacI() 129
+    8 pTetR(cI) 183453
+    9 pCI(lac) 2006198
+   10 pLacI(tet) 165670
+   11 gTetR(lac!1,lac).pLacI(tet!1) 0
+   12 gCI(tet!1,tet).pTetR(cI!1) 0
+   13 gLacI(cI!1,cI).pCI(lac!1) 0
+   14 gTetR(lac,lac) 0
+   15 gCI(tet,tet) 0
+   16 gLacI(cI,cI) 0
+end species
+begin reactions
+    1 2 10,11 2*_rateLaw4 #_reverse__R2
+    2 2 2,5 _rateLaw6 #_R4
+    3 5 5,8 _rateLaw7 #_R5
+    4 1,5 1 c6 #_R6
+    5 1,8 1 c7 #_R7
+    6 3 8,12 2*_rateLaw11 #_reverse__R9
+    7 3 3,6 _rateLaw13 #_R11
+    8 6 6,9 _rateLaw14 #_R12
+    9 1,6 1 c6 #_R13
+   10 1,9 1 c7 #_R14
+   11 4 9,13 2*_rateLaw18 #_reverse__R16
+   12 4 4,7 _rateLaw20 #_R18
+   13 7 7,10 _rateLaw21 #_R19
+   14 1,7 1 c6 #_R20
+   15 1,10 1 c7 #_R21
+   16 11 10,14 _rateLaw2 #_reverse__R1
+   17 10,11 2 _rateLaw3 #_R2
+   18 11 5,11 _rateLaw6 #_R4
+   19 12 8,15 _rateLaw9 #_reverse__R8
+   20 8,12 3 _rateLaw10 #_R9
+   21 12 6,12 _rateLaw13 #_R11
+   22 13 9,16 _rateLaw16 #_reverse__R15
+   23 9,13 4 _rateLaw17 #_R16
+   24 13 7,13 _rateLaw20 #_R18
+   25 10,14 11 2*_rateLaw1 #_R1
+   26 14 5,14 _rateLaw5 #_R3
+   27 8,15 12 2*_rateLaw8 #_R8
+   28 15 6,15 _rateLaw12 #_R10
+   29 9,16 13 2*_rateLaw15 #_R15
+   30 16 7,16 _rateLaw19 #_R17
+end reactions
+begin groups
+    1 pTetR                8
+    2 pCI                  9
+    3 pLacI                10
+    4 NULL                 1
+end groups
diff --git a/docs/src/assets/network_graphs/brusselator_graph.png b/docs/src/assets/network_graphs/brusselator_graph.png
diff --git a/docs/src/assets/network_graphs/repressilator_complex_graph.png b/docs/src/assets/network_graphs/repressilator_complex_graph.png
diff --git a/docs/src/assets/network_graphs/repressilator_graph.png b/docs/src/assets/network_graphs/repressilator_graph.png