# Simple Test Model
# root = "roadRunnerTest_1";
[SBML]
<?xml version="1.0" encoding="UTF-8"?>
<!-- Created by XMLPrettyPrinter on 1/1/2013 from  -->
<sbml xmlns = "http://www.sbml.org/sbml/level2/version4" level = "2" version = "4">
   <model id = "cell">
      <listOfCompartments>
         <compartment id = "compartment" size = "1"/>
      </listOfCompartments>
      <listOfSpecies>
         <species id = "src" boundaryCondition = "true" initialConcentration = "0" compartment = "compartment"/>
         <species id = "waste" boundaryCondition = "true" initialConcentration = "0" compartment = "compartment"/>
         <species id = "Xo" boundaryCondition = "true" initialConcentration = "1" compartment = "compartment"/>
         <species id = "X1" boundaryCondition = "true" initialConcentration = "0" compartment = "compartment"/>
         <species id = "S1" boundaryCondition = "false" initialConcentration = "0.1" compartment = "compartment"/>
         <species id = "S2" boundaryCondition = "false" initialConcentration = "0.25" compartment = "compartment"/>
         <species id = "S3" boundaryCondition = "false" initialConcentration = "0.1" compartment = "compartment"/>
      </listOfSpecies>
      <listOfParameters>
         <parameter id = "kk1" value = "1"/>
         <parameter id = "k1" value = "0.1"/>
         <parameter id = "k_1" value = "0.05"/>
         <parameter id = "kk2" value = "1"/>
         <parameter id = "k2" value = "0.15"/>
         <parameter id = "k_2" value = "0.067"/>
         <parameter id = "kk3" value = "1"/>
         <parameter id = "k3" value = "0.4"/>
         <parameter id = "k_3" value = "0.09"/>
         <parameter id = "kk4" value = "1"/>
         <parameter id = "k4" value = "0.55"/>
         <parameter id = "k_4" value = "0.01"/>
      </listOfParameters>
      <listOfReactions>
         <reaction id = "J1" reversible = "false">
            <listOfReactants>
               <speciesReference species = "Xo" stoichiometry = "1"/>
            </listOfReactants>
            <listOfProducts>
               <speciesReference species = "S1" stoichiometry = "1"/>
            </listOfProducts>
            <kineticLaw>
               <math xmlns = "http://www.w3.org/1998/Math/MathML">
                  <apply>
                     <times/>
                     <ci>
                           kk1
                     </ci>
                     <apply>
                        <minus/>
                        <apply>
                           <times/>
                           <ci>
                                 k1
                           </ci>
                           <ci>
                                 Xo
                           </ci>
                        </apply>
                        <apply>
                           <times/>
                           <ci>
                                 k_1
                           </ci>
                           <ci>
                                 S1
                           </ci>
                        </apply>
                     </apply>
                  </apply>
               </math>
            </kineticLaw>
         </reaction>
         <reaction id = "J2" reversible = "false">
            <listOfReactants>
               <speciesReference species = "S1" stoichiometry = "1"/>
            </listOfReactants>
            <listOfProducts>
               <speciesReference species = "S2" stoichiometry = "1"/>
            </listOfProducts>
            <kineticLaw>
               <math xmlns = "http://www.w3.org/1998/Math/MathML">
                  <apply>
                     <times/>
                     <ci>
                           kk2
                     </ci>
                     <apply>
                        <minus/>
                        <apply>
                           <times/>
                           <ci>
                                 k2
                           </ci>
                           <ci>
                                 S1
                           </ci>
                        </apply>
                        <apply>
                           <times/>
                           <ci>
                                 k_2
                           </ci>
                           <ci>
                                 S2
                           </ci>
                        </apply>
                     </apply>
                  </apply>
               </math>
            </kineticLaw>
         </reaction>
         <reaction id = "J3" reversible = "false">
            <listOfReactants>
               <speciesReference species = "S2" stoichiometry = "1"/>
            </listOfReactants>
            <listOfProducts>
               <speciesReference species = "S3" stoichiometry = "1"/>
            </listOfProducts>
            <kineticLaw>
               <math xmlns = "http://www.w3.org/1998/Math/MathML">
                  <apply>
                     <times/>
                     <ci>
                           kk3
                     </ci>
                     <apply>
                        <minus/>
                        <apply>
                           <times/>
                           <ci>
                                 k3
                           </ci>
                           <ci>
                                 S2
                           </ci>
                        </apply>
                        <apply>
                           <times/>
                           <ci>
                                 k_3
                           </ci>
                           <ci>
                                 S3
                           </ci>
                        </apply>
                     </apply>
                  </apply>
               </math>
            </kineticLaw>
         </reaction>
         <reaction id = "J4" reversible = "false">
            <listOfReactants>
               <speciesReference species = "S3" stoichiometry = "1"/>
            </listOfReactants>
            <listOfProducts>
               <speciesReference species = "X1" stoichiometry = "1"/>
            </listOfProducts>
            <kineticLaw>
               <math xmlns = "http://www.w3.org/1998/Math/MathML">
                  <apply>
                     <times/>
                     <ci>
                           kk4
                     </ci>
                     <apply>
                        <minus/>
                        <apply>
                           <times/>
                           <ci>
                                 k4
                           </ci>
                           <ci>
                                 S3
                           </ci>
                        </apply>
                        <apply>
                           <times/>
                           <ci>
                                 k_4
                           </ci>
                           <ci>
                                 X1
                           </ci>
                        </apply>
                     </apply>
                  </apply>
               </math>
            </kineticLaw>
         </reaction>
      </listOfReactions>
   </model>
</sbml>
[END_MODEL]

[JARNAC]
p = defn cell
      var S1, S2, S3;
      ext src, waste;
      ext Xo, X1;

      J1: Xo -> S1; k1*Xo - k_1*S1;
      J2: S1 -> S2; k2*S1 - k_2*S2;
      J3: S2 -> S3; k3*S2 - k_3*S3;
      J4: S3 -> X1; k4*S3 - k_4*X1;
  end;

p.Xo = 1;
p.X1 = 0;
p.S1 = 0.5;
p.S2 = 0.2;
p.S3 = 0.1;
p.k1 = 0.1;  p.k_1 = 0.05;
p.k2 = 0.15; p.k_2 = 0.067;
p.k3 = 0.4;  p.k_3 = 0.09;
p.k4 = 0.55; p.k_4 = 0.01;
[END_MODEL]

[INITIALIZATION]
[Conservation Laws]
False
[END_INITIALIZATION]

[START_TESTS]
[Set Steady State Selection List]
S1 S2 S3

[Compute Steady State]
True

[Species Concentrations]
S1 0.569694868238558
S2 0.208044382801664
S3 0.13002773925104

[Fluxes]
J1 0.0715152565880721
J2 0.0715152565880721
J3 0.0715152565880721
J4 0.0715152565880721

[Full Jacobian]
      -0.2      0.067       0
      0.15     -0.467       0.09
         0      0.4        -0.64

[Individual Eigenvalues]
S1 -0.15726345 0
S2 -0.38237134 0
S3 -0.76736521 0
[Eigenvalue Matrix]
-0.15726345 0
-0.38237134 0
-0.76736521 0


[Stoichiometry Matrix]
         1         -1          0          0
         0          1         -1          0
         0          0          1         -1

[Link Matrix]
         1          0          0
         0          1          0
         0          0          1

[Unscaled Elasticity Matrix]
     -0.05          0          0
      0.15        -0.067       0
         0        0.4       -0.09
         0       0            0.55

[Scaled Elasticity Matrix]
-0.39830303      0             0
 1.1949091      -0.19490909    0
         0       1.1636364    -0.16363636
         0                     1

[Unscaled Concentration Control Matrix]
 5.6969487 -4.7676838 -0.79858703 -0.13067788
 2.0804438 0.69348128 -2.3838419 -0.39008322
 1.3002774  0.4334258 0.072598821  -1.806302

[Scaled Concentration Control Matrix]
0.715152565880724 -0.598499560612292 -0.100248676402559 -0.0164043288658731
0.715152565880721 0.238384188626906 -0.819445648404993 -0.134091106102633
0.715152565880721 0.238384188626906 0.039929351595007 -0.993466106102634

[Unscaled Flux Control Matrix]
0.71515257 0.23838419 0.039929352 0.0065338939
0.71515257 0.23838419 0.039929352 0.0065338939
0.71515257 0.23838419 0.039929352 0.0065338939
0.71515257 0.23838419 0.039929352 0.0065338939

[Scaled Flux Control Matrix]
0.715152565880722 0.238384188626906 0.0399293515950069 0.00653389389736468
0.715152565880722 0.238384188626906 0.0399293515950069 0.00653389389736467
0.715152565880722 0.238384188626906 0.039929351595007 0.00653389389736467
0.715152565880722 0.238384188626906 0.0399293515950071 0.0065338938973647

#[Individual Unscaled Flux Control Coefficients]


[Floating Species Ids]
S1 S2 S3
[Boundary Species Ids]
src waste Xo X1
[Global Parameter Ids]
kk1 k1 k_1 kk2 k2 k_2 kk3 k3 k_3 kk4 k4 k_4
[Compartment Ids]
compartment
[Reaction Ids]
J1 J2 J3 J4
[Species Initial Condition Ids]
init(S1) init(S2) init(S3)
[Get Eigenvalue Ids]
eigen(S1) eigen(S2) eigen(S3)
[Get Rates Of Change Ids]
S1' S2' S3'
[Set Steady State Selection List]
S2 S3
[Get Steady State Selection List]
S2 S3
[Set Time Course Selection List]
time S2 S3
[Get Time Course Selection List]
time S2 S3
[Compute Steady State Values]
0.20804438 0.1300277392
[Floating Species Concentrations]
0.56969487  0.20804438 0.13002774
[Boundary Species Concentrations]
0 0 1 0
[Get Global Parameter Values]
   1    0.1   0.05    1   0.15   0.067    1    0.4    0.09    1   0.55   0.01
[Get Initial Floating Species Concs]
0.1   0.25  0.1
[Get Reaction Rates]
0.07151526 0.07151526 0.07151526 0.07151526
[Get Reaction Rate By Index]
0.07151526 0.07151526 0.07151526 0.07151526
[Number of Dependent Species]
0
[Number of Independent Species]
3
[Number Of Rules]
0
[Get Rates Of Change]
0 0 0
[Get Reaction Rates Ex]
1 2 3
0.05 0.016 1.53 1.65
[Get Rates of Change Ex]
1 2 3
0.034 -0.514 -1.12
[Get Rate of Change by Index]
1 2 3
0.034 -0.514 -1.12
[END_TESTS]