From 13442c9f824f125e0eb001ff6d3436558c94a985 Mon Sep 17 00:00:00 2001
From: bartjuw <barthj@uw.edu>
Date: Mon, 13 Nov 2023 16:14:47 -0800
Subject: [PATCH] Create OpenSystemThreeStep.xml

---
 models/OpenSystemThreeStep.xml | 99 ++++++++++++++++++++++++++++++++++
 1 file changed, 99 insertions(+)
 create mode 100644 models/OpenSystemThreeStep.xml

diff --git a/models/OpenSystemThreeStep.xml b/models/OpenSystemThreeStep.xml
new file mode 100644
index 0000000..12cd64c
--- /dev/null
+++ b/models/OpenSystemThreeStep.xml
@@ -0,0 +1,99 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- Created by libAntimony version v2.12.0.3 with libSBML version 5.18.1. -->
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
+  <model metaid="Open_system_three_step_model" id="Open_system_three_step_model">
+    <listOfCompartments>
+      <compartment sboTerm="SBO:0000410" id="default_compartment" spatialDimensions="3" size="1" constant="true"/>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species id="Xo" compartment="default_compartment" initialConcentration="10" hasOnlySubstanceUnits="false" boundaryCondition="true" constant="false"/>
+      <species id="S1" compartment="default_compartment" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+      <species id="S2" compartment="default_compartment" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter id="e1" value="1" constant="true"/>
+      <parameter id="k1" value="0.1" constant="true"/>
+      <parameter id="k2" value="0.04" constant="true"/>
+      <parameter id="e2" value="1" constant="true"/>
+      <parameter id="k3" value="0.14" constant="true"/>
+      <parameter id="k4" value="0.09" constant="true"/>
+      <parameter id="e3" value="1" constant="true"/>
+      <parameter id="k5" value="0.16" constant="true"/>
+    </listOfParameters>
+    <listOfReactions>
+      <reaction id="J1" reversible="true" fast="false">
+        <listOfReactants>
+          <speciesReference species="Xo" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="S1" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> e1 </ci>
+              <apply>
+                <minus/>
+                <apply>
+                  <times/>
+                  <ci> k1 </ci>
+                  <ci> Xo </ci>
+                </apply>
+                <apply>
+                  <times/>
+                  <ci> k2 </ci>
+                  <ci> S1 </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+        </kineticLaw>
+      </reaction>
+      <reaction id="J2" reversible="true" fast="false">
+        <listOfReactants>
+          <speciesReference species="S1" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="S2" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> e2 </ci>
+              <apply>
+                <minus/>
+                <apply>
+                  <times/>
+                  <ci> k3 </ci>
+                  <ci> S1 </ci>
+                </apply>
+                <apply>
+                  <times/>
+                  <ci> k4 </ci>
+                  <ci> S2 </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+        </kineticLaw>
+      </reaction>
+      <reaction id="J3" reversible="true" fast="false">
+        <listOfReactants>
+          <speciesReference species="S2" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> e3 </ci>
+              <ci> k5 </ci>
+              <ci> S2 </ci>
+            </apply>
+          </math>
+        </kineticLaw>
+      </reaction>
+    </listOfReactions>
+  </model>
+</sbml>