1.0.2: major components in separate *.mo files / MSL 3.2.3 (#13)

* Issue07 separate component (#11) * MSL version 3.2.3 * separate Interfaces/Substances/package.mo into separate components * separate the components within the package Interfaces.Compartments * Decompose the package BioChem.Interfaces.Nodes into separate components * Separate all components within Biochem/Interfaces/Reactions/package.mo into separate *.mo components * Decompose package BioChem/Interfaces/Reactions/Basics/package.mo into separate components * Separate BioChem/Interfaces/Reactions/Modifiers/package.mo into separate components * remove extra spaces from several modified package.mo * keep model declaration using partial or without partial identical to the original version * package.order files to be included in the repository * decompose BioChem/Compartments/package.mo into separate components * decompose BioChem/Substances/package.mo into separate components * Separate the Icons package within BioChem/package.mo into separate directory * Separate Biochem.Math package into a separate directory * Separate top models within the Biochem.Examples package * Separate all subpackages within Biochem.Examples into separate *.mo files. Each subpackage corresponds to a standalone example * Separate Biochem.Reactions.MichaelisMenten into separate components * separate Biochem.Reactions.MassAction.Reversible into separate components * decompose package Reactions.MassAction.Irreversible into separate components * Decompose Reactions.Inhibition into separate components * decompoase Reactions.FastEquilibrium into separate components * Decompose package Reactions into separate components * Develop 1.0.2 (#12) * MSL version 3.2.3 * separate Interfaces/Substances/package.mo into separate components * separate the components within the package Interfaces.Compartments * Decompose the package BioChem.Interfaces.Nodes into separate components * Separate all components within Biochem/Interfaces/Reactions/package.mo into separate *.mo components * Decompose package BioChem/Interfaces/Reactions/Basics/package.mo into separate components * Separate BioChem/Interfaces/Reactions/Modifiers/package.mo into separate components * remove extra spaces from several modified package.mo * keep model declaration using partial or without partial identical to the original version * package.order files to be included in the repository * decompose BioChem/Compartments/package.mo into separate components * decompose BioChem/Substances/package.mo into separate components * Separate the Icons package within BioChem/package.mo into separate directory * Separate Biochem.Math package into a separate directory * Separate top models within the Biochem.Examples package * Separate all subpackages within Biochem.Examples into separate *.mo files. Each subpackage corresponds to a standalone example * Separate Biochem.Reactions.MichaelisMenten into separate components * separate Biochem.Reactions.MassAction.Reversible into separate components * decompose package Reactions.MassAction.Irreversible into separate components * Decompose Reactions.Inhibition into separate components * decompoase Reactions.FastEquilibrium into separate components * Decompose package Reactions into separate components * ignore backup files * annotations for version 1.0.2 * Revert "ignore backup files" This reverts commit 898a667. * remove backup files * announcing version 1.0.2
OpenModelica · Jun 2, 2020 · b3131bf · b3131bf
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diff --git a/.gitignore b/.gitignore
@@ -19,3 +19,5 @@ dymosim.exe
 dymosim.exp
 
 dymosim.lib
+
+*.bak-mo
diff --git a/BioChem/Compartments/Compartment.mo b/BioChem/Compartments/Compartment.mo
@@ -0,0 +1,13 @@
+within BioChem.Compartments;
+
+model Compartment "Default compartment (constant volume)"
+  annotation(Documentation(info="<html>
+<h1>Compartment</h1>
+<p>
+Default compartment model.
+</p>
+</html>", revisions=""), Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}), graphics={Text(fillColor={0,85,0}, fillPattern=FillPattern.Solid, extent={{-100,-170},{100,-120}}, textString="%name", fontName="Arial"),Rectangle(lineColor={0,85,0}, fillColor={199,199,149}, fillPattern=FillPattern.Solid, lineThickness=10, extent={{-110,-110},{110,110}}, radius=20)}), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})));
+  extends BioChem.Interfaces.Compartments.Compartment(V(stateSelect=StateSelect.prefer));
+equation
+  der(V)=0 "Compartment volume is constant";
+end Compartment;
diff --git a/BioChem/Compartments/MainCompartment.mo b/BioChem/Compartments/MainCompartment.mo
@@ -0,0 +1,17 @@
+within BioChem.Compartments;
+
+model MainCompartment "Main compartment (constant volume)"
+  extends BioChem.Interfaces.Compartments.MainCompartment(V(stateSelect = StateSelect.prefer));
+equation
+  der(V) = 0 "Compartment volume is constant";
+  annotation(
+    Documentation(info = "<html>
+<h1>MainCompartment</h1>
+
+<p>
+Main compartment model.
+</p>
+</html>", revisions = ""),
+    Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}), graphics = {Text(fillColor = {0, 85, 0}, fillPattern = FillPattern.Solid, extent = {{-100, -170}, {100, -120}}, textString = "%name", fontName = "Arial"), Rectangle(lineColor = {0, 85, 0}, fillColor = {199, 199, 149}, fillPattern = FillPattern.Solid, lineThickness = 10, extent = {{-110, -110}, {110, 110}}, radius = 20), Text(fillPattern = FillPattern.Solid, extent = {{-82.12, -80}, {80, 80}}, textString = "main", fontName = "Arial", textStyle = {TextStyle.Bold})}),
+    Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})));
+end MainCompartment;
diff --git a/BioChem/Compartments/package.mo b/BioChem/Compartments/package.mo
@@ -1,7 +1,10 @@
 within BioChem;
+
 package Compartments "Different types of compartments used in the package"
   extends Icons.Library;
-  annotation(Documentation(info="<html>
+
+  annotation(
+    Documentation(info = "<html>
 <h1>Compartments</h1>
 
 
@@ -18,30 +21,7 @@ The classes in the package so far are illustrated in
 
 <a name=\"fig1\"></a>
 <img src=\"modelica://BioChem/Resources/Images/Compartment.png\" alt=\"Fig1: Compartments\">
- </html>", revisions=""), Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}), graphics={Rectangle(origin={5,-7.55952}, lineColor={0,85,0}, fillColor={199,199,149}, fillPattern=FillPattern.Solid, lineThickness=10, extent={{-70,-70},{40,30}}, radius=20)}), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})));
-  model Compartment "Default compartment (constant volume)"
-    annotation(Documentation(info="<html>
-<h1>Compartment</h1>
- <p>
- Default compartment model.
- </p>
- </html>", revisions=""), Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}), graphics={Text(fillColor={0,85,0}, fillPattern=FillPattern.Solid, extent={{-100,-170},{100,-120}}, textString="%name", fontName="Arial"),Rectangle(lineColor={0,85,0}, fillColor={199,199,149}, fillPattern=FillPattern.Solid, lineThickness=10, extent={{-110,-110},{110,110}}, radius=20)}), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})));
-    extends BioChem.Interfaces.Compartments.Compartment(V(stateSelect=StateSelect.prefer));
-  equation
-    der(V)=0 "Compartment volume is constant";
-  end Compartment;
-
-  model MainCompartment "Main compartment (constant volume)"
-    annotation(Documentation(info="<html>
-<h1>MainCompartment</h1>
-
- <p>
- Main compartment model.
- </p>
- </html>", revisions=""), Icon(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10}), graphics={Text(fillColor={0,85,0}, fillPattern=FillPattern.Solid, extent={{-100,-170},{100,-120}}, textString="%name", fontName="Arial"),Rectangle(lineColor={0,85,0}, fillColor={199,199,149}, fillPattern=FillPattern.Solid, lineThickness=10, extent={{-110,-110},{110,110}}, radius=20),Text(fillPattern=FillPattern.Solid, extent={{-82.12,-80},{80,80}}, textString="main", fontName="Arial", textStyle={TextStyle.Bold})}), Diagram(coordinateSystem(extent={{-100,100},{100,-100}}, preserveAspectRatio=true, grid={10,10})));
-    extends BioChem.Interfaces.Compartments.MainCompartment(V(stateSelect=StateSelect.prefer));
-  equation
-    der(V)=0 "Compartment volume is constant";
-  end MainCompartment;
-
+ </html>", revisions = ""),
+    Icon(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10}), graphics = {Rectangle(origin = {5, -7.55952}, lineColor = {0, 85, 0}, fillColor = {199, 199, 149}, fillPattern = FillPattern.Solid, lineThickness = 10, extent = {{-70, -70}, {40, 30}}, radius = 20)}),
+    Diagram(coordinateSystem(extent = {{-100, 100}, {100, -100}}, preserveAspectRatio = true, grid = {10, 10})));
 end Compartments;
diff --git a/BioChem/Compartments/package.order b/BioChem/Compartments/package.order
@@ -0,0 +1,2 @@
+Compartment
+MainCompartment
diff --git a/BioChem/Examples/CaOscillations.mo b/BioChem/Examples/CaOscillations.mo
@@ -0,0 +1,261 @@
+within BioChem.Examples;
+
+package CaOscillations "Oxhamre2005_Ca_oscillation"
+  extends BioChem.Icons.Example;
+
+  model Cytosol
+    extends BioChem.Compartments.MainCompartment(V(start = 1));
+    import BioChem.Math.*;
+    import BioChem.Constants.*;
+
+    model Ca_Cyt_
+      extends BioChem.Substances.Substance;
+      annotation(
+        __MathCore(RDF = "<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=\"#metaid_0000007\">
+      <bqbiol:isVersionOf>
+        <rdf:Bag>
+          <rdf:li rdf:resource=\"urn:miriam:obo.chebi:CHEBI%3A29108\"/>
+        </rdf:Bag>
+      </bqbiol:isVersionOf>
+    </rdf:Description>
+  </rdf:RDF>"));
+    end Ca_Cyt_;
+
+    model Jpump_
+      extends BioChem.Interfaces.Reactions.Uui;
+      parameter Real Fpump_0 = 2;
+      parameter Real Kpump = 0.1;
+    equation
+      rr = Fpump_0 * s1.c / (Kpump + s1.c);
+      annotation(
+        __MathCore(RDF = "<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=\"#metaid_0000029\">
+      <bqbiol:isVersionOf>
+        <rdf:Bag>
+          <rdf:li rdf:resource=\"urn:miriam:obo.go:GO%3A0051481\"/>
+          <rdf:li rdf:resource=\"urn:miriam:obo.go:GO%3A0006816\"/>
+        </rdf:Bag>
+      </bqbiol:isVersionOf>
+    </rdf:Description>
+  </rdf:RDF>"));
+    end Jpump_;
+
+    Endoplasmic_Reticulum endoplasmicReticulum(p1_sbml = p1_sbml, p2_sbml = p2_sbml, p3_sbml = p3_sbml) annotation(
+      Placement(transformation(origin = {-28.4357, 20.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}})));
+    inner Real Cytosol_V = V "Variable used to make the compartment volume accessible for inner components. Do not edit.";
+    inner Real Endoplasmic_Reticulum_V = endoplasmicReticulum.V "Variable used to make the compartment volume of inner compartments accessible. Do not edit.";
+    Cytosol.Ca_Cyt_ Ca_Cyt(c(start = 0)) annotation(
+      Placement(transformation(origin = {-10.0, -40.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}})));
+    Real n_sbml(start = 1);
+    parameter Real n0 = 1;
+    parameter Real kbN = 0.5;
+    parameter Real kappa = 5;
+    Real p1_sbml(start = 0);
+    parameter Real p11 = 0.2;
+    parameter Real p12 = 0.8;
+    parameter Real K1 = 5;
+    Real p2_sbml(start = 0);
+    parameter Real K2 = 0.7;
+    Real p3_sbml(start = 0.95);
+    parameter Real k31 = 0.5;
+    parameter Real K3 = 0.7;
+    Cytosol.Jpump_ Jpump annotation(
+      Placement(transformation(origin = {50.0, -10.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}, rotation = -270)));
+  equation
+    connect(Ca_Cyt.n1, endoplasmicReticulum.Ca_Cyt_node) annotation(
+      Line(origin = {-29.2619, -10.8}, points = {{19.2619, -29.2}, {19.2619, -16.2}, {-14.175, -16.2}, {-14.175, 30.8}, {-10.1738, 30.8}}, smooth = Smooth.Bezier));
+    connect(endoplasmicReticulum.CaER_node, Jpump.p1) annotation(
+      Line(origin = {27.5214, 13.75}, points = {{-44.9571, 6.25}, {22.4786, 6.25}, {22.4786, -12.5}}, smooth = Smooth.Bezier));
+    connect(Ca_Cyt.n1, Jpump.s1) annotation(
+      Line(origin = {30.0, -33.75}, points = {{-40.0, -6.25}, {20.0, -6.25}, {20.0, 12.5}}, smooth = Smooth.Bezier));
+    n_sbml = n0 * (exp((-kbN) * time) + kappa * (1 - exp((-kbN) * time)));
+    p1_sbml = p11 + p12 * n_sbml / (K1 + n_sbml);
+    p2_sbml = Ca_Cyt.c / (K2 + Ca_Cyt.c);
+    der(p3_sbml) = (-k31 * Ca_Cyt.c * p3_sbml) + k31 * K3 * (1 - p3_sbml);
+    annotation(
+      __MathCore(RDF = "<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=\"#metaid_0000004\">
+      <bqbiol:isVersionOf>
+        <rdf:Bag>
+          <rdf:li rdf:resource=\"urn:miriam:obo.go:GO%3A0005829\"/>
+        </rdf:Bag>
+      </bqbiol:isVersionOf>
+    </rdf:Description>
+  </rdf:RDF>"),
+      experiment(StartTime = 0.0, StopTime = 120, NumberOfIntervals = -1, Algorithm = "dassl", Tolerance = 1e-06),
+      Documentation(info = "<html>
+<h1>Ca Oscillations</h1>
+This example is a Modelica version of the model presented in <i>A Minimal Generic Model of Bacteria-Induced Intracellular Ca<sup>2+</sup>
+Oscillations in Epithelial Cells</i> by Camilla Oxhamre, Agneta Richter-Dahlfors, Vladimir P. Zhdanov, and Bengt Kasemoy. (Biophysical Journal Volume 88 April 2005 2976-2981)
+
+<h2>Abstract</h2>
+The toxin &alpha-hemolysin expressed by uropathogenic Escherichia coli bacteria was recently shown as the first
+pathophysiologically relevant protein to induce oscillations of the intracellular Ca<sup>2+</sup> concentration in target cells. Here, we
+propose a generic three-variable kinetic model describing the Ca<sup>2+</sup> oscillations induced in single rat renal epithelial cells by this
+toxin. Specifically, we take into account the interplay between 1), the cytosolic Ca<sup>2+</sup> concentration; 2), IP<sub>3</sub>-sensitive Ca<sup>2+</sup>
+channels located in the membrane separating the cytosol and endoplasmic reticulum; and 3), toxin-related activation of
+production of IP<sub>3</sub> by phospholipase C. With these ingredients, the predicted response of cells exposed to the toxin is in good
+agreement with the results of experiments.
+<h2>Simulations</h2>
+The simulation results are shown in the
+ <a href=\"#fig1\">Figure 1</a>. This plot corresponds to Fig 1C of the paper (Oxhamre 2005).
+<br>
+
+<a name=\"fig1\"></a>
+<img src=\"modelica://BioChem/Resources/Images/cytosol.png\" alt=\"Fig1: Simulation results\">
+</html>", revisions = ""));
+  end Cytosol;
+
+  model Endoplasmic_Reticulum
+    extends BioChem.Compartments.Compartment(V(start = 1));
+    import BioChem.Math.*;
+    import BioChem.Constants.*;
+
+    model CaER_
+      extends BioChem.Substances.Substance;
+      annotation(
+        __MathCore(RDF = "<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=\"#metaid_0000006\">
+      <bqbiol:isVersionOf>
+        <rdf:Bag>
+          <rdf:li rdf:resource=\"urn:miriam:obo.chebi:CHEBI%3A29108\"/>
+        </rdf:Bag>
+      </bqbiol:isVersionOf>
+    </rdf:Description>
+  </rdf:RDF>"));
+    end CaER_;
+
+    model Jch_
+      extends BioChem.Interfaces.Reactions.Uui;
+      parameter Real Fch_0 = 8;
+      input Real p1_sbml;
+      input Real p2_sbml;
+      input Real p3_sbml;
+    equation
+      rr = Fch_0 * p1_sbml * p2_sbml * p3_sbml;
+      annotation(
+        __MathCore(RDF = "<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=\"#metaid_0000027\">
+      <bqbiol:isVersionOf>
+        <rdf:Bag>
+          <rdf:li rdf:resource=\"urn:miriam:obo.go:GO%3A0051482\"/>
+          <rdf:li rdf:resource=\"urn:miriam:obo.go:GO%3A0006816\"/>
+        </rdf:Bag>
+      </bqbiol:isVersionOf>
+    </rdf:Description>
+  </rdf:RDF>"));
+    end Jch_;
+
+    model Jleak_
+      extends BioChem.Interfaces.Reactions.Uui;
+      parameter Real Fleak = 0.5;
+    equation
+      rr = Fleak;
+      annotation(
+        __MathCore(RDF = "<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=\"#metaid_0000028\">
+      <bqbiol:isVersionOf>
+        <rdf:Bag>
+          <rdf:li rdf:resource=\"urn:miriam:obo.go:GO%3A0006816\"/>
+          <rdf:li rdf:resource=\"urn:miriam:obo.go:GO%3A0007204\"/>
+        </rdf:Bag>
+      </bqbiol:isVersionOf>
+    </rdf:Description>
+  </rdf:RDF>"));
+    end Jleak_;
+
+    inner Real Endoplasmic_Reticulum_V = V "Variable used to make the compartment volume accessible for inner components. Do not edit.";
+    Endoplasmic_Reticulum.CaER_ CaER(c(start = 0)) annotation(
+      Placement(transformation(origin = {10.0, 10.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}, rotation = -540)));
+    input Real p1_sbml;
+    input Real p2_sbml;
+    input Real p3_sbml;
+    BioChem.Interfaces.Nodes.SubstanceConnector Ca_Cyt_node annotation(
+      Placement(transformation(origin = {-90.0, 10.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}), iconTransformation(origin = {-110.0, 0.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}})));
+    Endoplasmic_Reticulum.Jch_ Jch(p1_sbml = p1_sbml, p2_sbml = p2_sbml, p3_sbml = p3_sbml) annotation(
+      Placement(transformation(origin = {-80.0, -20.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}, rotation = -270)));
+    Endoplasmic_Reticulum.Jleak_ Jleak annotation(
+      Placement(transformation(origin = {-80.0, 43.7135}, extent = {{-10.0, -10.0}, {10.0, 10.0}}, rotation = -90)));
+    BioChem.Interfaces.Nodes.SubstanceConnector CaER_node annotation(
+      Placement(transformation(origin = {90.0, 0.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}}), iconTransformation(origin = {110.0, 0.0}, extent = {{-10.0, -10.0}, {10.0, 10.0}})));
+  equation
+    connect(Jleak.p1, Ca_Cyt_node) annotation(
+      Line(origin = {-85.0, 22.1159}, points = {{5.0, 10.3476}, {5.0, 0.8841}, {-5.0, 0.8841}, {-5.0, -12.1159}}, smooth = Smooth.Bezier));
+    connect(Jch.p1, Ca_Cyt_node) annotation(
+      Line(origin = {-85.0, -1.1875}, points = {{5.0, -7.5625}, {5.0, -1.8125}, {-5.0, -1.8125}, {-5.0, 11.1875}}, smooth = Smooth.Bezier));
+    connect(CaER.n1, CaER_node) annotation(
+      Line(origin = {63.5, 5.0}, points = {{-53.5, 5.0}, {13.5, 5.0}, {13.5, -5.0}, {26.5, -5.0}}, smooth = Smooth.Bezier));
+    connect(CaER.n1, Jleak.s1) annotation(
+      Line(origin = {-31.2, 38.6787}, points = {{41.2, -28.6787}, {28.2, -28.6787}, {28.2, 20.5363}, {-48.8, 20.5363}, {-48.8, 16.2848}}, smooth = Smooth.Bezier));
+    connect(CaER.n1, Jch.s1) annotation(
+      Line(origin = {-31.2, -16.4506}, points = {{41.2, 26.4506}, {28.2, 26.4506}, {28.2, -19.0509}, {-48.8, -19.0509}, {-48.8, -14.7994}}, smooth = Smooth.Bezier));
+    annotation(
+      __MathCore(RDF = "<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=\"#metaid_0000005\">
+      <bqbiol:isVersionOf>
+        <rdf:Bag>
+          <rdf:li rdf:resource=\"urn:miriam:obo.go:GO%3A0005790\"/>
+        </rdf:Bag>
+      </bqbiol:isVersionOf>
+    </rdf:Description>
+  </rdf:RDF>"));
+  end Endoplasmic_Reticulum;
+  annotation(
+    __MathCore(RDF = "<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=\"#metaid_0000030\">
+      <dc:creator rdf:parseType=\"Resource\">
+        <rdf:Bag>
+          <rdf:li rdf:parseType=\"Resource\">
+            <vCard:N rdf:parseType=\"Resource\">
+              <vCard:Family>Dharuri</vCard:Family>
+              <vCard:Given>Harish</vCard:Given>
+            </vCard:N>
+            <vCard:EMAIL>Harish_Dharuri@kgi.edu</vCard:EMAIL>
+            <vCard:ORG>
+              <vCard:Orgname>Keck Graduate Institute</vCard:Orgname>
+            </vCard:ORG>
+          </rdf:li>
+        </rdf:Bag>
+      </dc:creator>
+      <dcterms:created rdf:parseType=\"Resource\">
+        <dcterms:W3CDTF>2005-08-25T11:00:43Z</dcterms:W3CDTF>
+      </dcterms:created>
+      <dcterms:modified rdf:parseType=\"Resource\">
+        <dcterms:W3CDTF>2008-08-21T11:54:50Z</dcterms:W3CDTF>
+      </dcterms:modified>
+      <bqmodel:is>
+        <rdf:Bag>
+          <rdf:li rdf:resource=\"urn:miriam:biomodels.db:BIOMD0000000047\"/>
+        </rdf:Bag>
+      </bqmodel:is>
+      <bqmodel:isDescribedBy>
+        <rdf:Bag>
+          <rdf:li rdf:resource=\"urn:miriam:pubmed:15596518\"/>
+        </rdf:Bag>
+      </bqmodel:isDescribedBy>
+      <bqbiol:isVersionOf>
+        <rdf:Bag>
+          <rdf:li rdf:resource=\"urn:miriam:obo.go:GO%3A0019722\"/>
+          <rdf:li rdf:resource=\"urn:miriam:obo.go:GO%3A0048016\"/>
+        </rdf:Bag>
+      </bqbiol:isVersionOf>
+      <bqbiol:is>
+        <rdf:Bag>
+          <rdf:li rdf:resource=\"urn:miriam:taxonomy:10114\"/>
+          <rdf:li rdf:resource=\"urn:miriam:kegg.pathway:rno04020\"/>
+        </rdf:Bag>
+      </bqbiol:is>
+    </rdf:Description>
+  </rdf:RDF>"));
+  annotation(
+    Documentation(info = "<html>
+<h1>Ca Oscillations</h1>
+This example is a Modelica version of the model presented in <i>A Minimal Generic Model of Bacteria-Induced Intracellular Ca<sup>2+</sup>
+Oscillations in Epithelial Cells</i> by Camilla Oxhamre, Agneta Richter-Dahlfors, Vladimir P. Zhdanov, and Bengt Kasemoy. (Biophysical Journal Volume 88 April 2005 2976-2981).<br><br>
+
+See
+<a href=\"Modelica://BioChem.Examples.CaOscillations.Cytosol\">Cytosol</a>
+ for more documentation and simulation results.
+</html>", revisions = ""));
+end CaOscillations;