MathSBML Model Builder: Model Construction

The Model Builder maintains an internal database consisting of a single model that can be manipulated by the user.

The functions add_, remove_, and modify_ where "_" can be replaced by any of the following Compartment, Event, Function, Parameter, Reaction, Rule, Species, Unit allow one to add, remove, or modify contents of the database.

The add_ and remove_ functions are new in MathSBML version 2.1.5. The modify_ functions are new in Version 2.2.0.

Format of the add_ functions

In the following table, options is an option list; id is a valid id for the given SBML field (metaid for rules); and SSBML is a symbolic SBML version of the entity (i.e., XMLElement["entity name",...])

add_ Function	Options	Description
addCompartment[options]	Any valid options for compartmentToSBML	Adds a compartment to the model. Click here for more information
addCompartment[id,options]	Any valid options for compartmentToSBML
addCompartment[SSBML]	no options
addEvent[options]	Any valid options for eventToSBML	Adds an event to the model. Click here for more information
addEvent[id,options]	Any valid options for eventToSBML
addEvent[SSBML]	no options
addFunction[options]	Any valid options for functionToSBML	Adds a function to the model
addFunction[id,options]	Any valid options for functionToSBML
addFunction[SSBML]	no options
addParameter[options]	Any valid options for parameterToSBML	Adds a parameter to the model
addParameter[id,options]	Any valid options for parameterToSBML
addParameter[SSBML]	no options
addReaction[options]	Any valid options for reactionToSBML	Adds a reaction to the model
addReaction[reaction,options]	Any valid options for reactionToSBML
addReaction[SSBML]	no options
addRule[options]	Any valid options for ruleToSBML	Adds a rule to the model
addRule[metaid,options]	Any valid options for ruleToSBML
addRule[SSBML]	no options
addSpecies[options]	Any valid options for speciesToSBML	Adds a species to the model
addSpecies[id,options]	Any valid options for speciesToSBML
addSpecies[SSBML]	no options

Format of the remove_ functions

remove_ Function	Description
removeCompartment[id]	Removes the specified compartment from the model.
removeEvent[id]	Removes the specified event from the model.
removeFunction[id]	Removes the specified function from the model.
removeParameter[id]	Removes the specified parameter from the model.
removeReaction[id]	Removes the specified reaction from the model.
removeRule[metaid]	Removes the specified rule from the model.
removeSpecies[id]	Removes the specified species from the model.

Additional Functions

Function Name	Description
newModel[options]	Reinitializes the database and removes its currentcontents. Options are id and name. (in MathSBML 2.1.4)
createModel[]	Generates text SBML (Level 2) based on the current contents of the model. (in MathSBML 2.1.5)
createModel[filename]	Writes a text SBML file (Level 2) based on the current contents of the model. (in MathSBML 2.1.5)
createSymbolicModel[]	Generates a Symbolic XML version of theLevel 2 SBML corresponding to the current model. (in MathSBML 2.1.5)
showModel[]	Generates a verbose listing like the one generated by SBMLRead. (in MathSBML 2.1.5)
loadSimulator[]	Takes the current model and returns it in a format readable by the simulator functions such as SBMLNDSolve (in MathSBML 2.1.5)
loadModelBuilder[file,options]	Equivalent to SBMLRead[file, loadModelBuilder->True, EchoLoad->True] in that it will read an SBML file into the model builder. Any valid option for SBMLRead may be used as well. (in MathSBML 2.1.5)
SBMLRead	Will automatically load the file it reads into the model builder, replacing any model that was previously there.This action can be overridden by setting the option LoadModelBuilder->False in SBMLRead

Example

Both the input needed to build a simple model with a single enzymatic reaction, as well as the output produced by Mathematica, are shown in the following dialog.


Input:   newModel["EnzymaticReaction"];

Input:   addSpecies[S, compartment -> "Cell", initialConcentration -> 1];
Output:  Compartment Cell  added.
         Species S added to compartment Cell

Input:   addSpecies[P, compartment -> "Cell", initialConcentration -> 0];
Output:  Species P added to compartment Cell

Input:   addSpecies[Enz, compartment -> "Cell", initialConcentration -> .1];
Output:  Species Enz added to compartment Cell

Input:   addSpecies[X, compartment -> "Cell", initialConcentration -> 0];
Output:  Species X added to compartment Cell

Input:   addReaction[S + Enz -> X, id -> r1, kineticLaw -> k1*S*Enz, parameters -> { k1 -> 0.5}];
Output:  Reaction r1 added.

Input:   addReaction[X -> S + Enz, id -> r2, kineticLaw -> k2*X, parameters -> {k2 -> 0.01}];
Output:  Reaction r2 added.

Input:   addReaction[X -> P + Enz, id -> r3, kineticLaw -> k3*X, parameters -> {k3 -> 0.5}];
Output:  Reaction r3 added.


Input:   createModel[];

Output:  <?xml version="1.0" encoding="UTF-8"?>
         <!-- Generated 23-September-2003 10:28:11.369320 -->
         <!-- Generated by MathSBML 2.1.5b10 (23 Sept 2003) -->
         <sbml xmlns="http://www.sbml.org/sbml/level2"
             level="2"
             version="1">
          <model id="enzymaticReaction"
              name="enzymaticReaction">
           <listOfFunctionDefinitions/>
           <listOfUnitDefinitions/>
           <listOfCompartments>
            <compartment id="Cell"
                name="Cell"/>
           </listOfCompartments>
           <listOfSpecies>
            <species id="S"
                name="S"
                compartment="Cell"
                boundaryCondition="false"
                constant="false"
                initialConcentration="1"/>
            <species id="P"
                name="P"
                compartment="Cell"
                boundaryCondition="false"
                constant="false"
                initialConcentration="0"/>
            <species id="Enz"
                name="Enz"
                compartment="Cell"
                boundaryCondition="false"
                constant="false"
                initialConcentration="0.1"/>
            <species id="X"
                name="X"
                compartment="Cell"
                boundaryCondition="false"
                constant="false"
                initialConcentration="0"/>
           </listOfSpecies>
           <listOfParameters/>
           <listOfRules/>
           <listOfReactions>
            <reaction id="r1"
                name="r1"
                reversible="true"
                fast="false">
             <listOfReactants>
              <speciesReference species="Enz"/>
              <speciesReference species="S"/>
             </listOfReactants>
             <listOfProducts>
              <speciesReference species="X"/>
             </listOfProducts>
             <listOfModifiers/>
             <kineticLaw timeUnits="time"
                 substanceUnits="substance">
              <math xmlns="http://www.w3.org/1998/Math/MathML">
               <apply>
                <times/>
                <ci>Enz</ci>
                <ci>k1</ci>
                <ci>S</ci>
               </apply>
              </math>
              <listOfParameters>
               <parameter id="k1"
                   value="0.5"/>
              </listOfParameters>
             </kineticLaw>
            </reaction>
            <reaction id="r2"
                name="r2"
                reversible="true"
                fast="false">
             <listOfReactants>
              <speciesReference species="X"/>
             </listOfReactants>
             <listOfProducts>
              <speciesReference species="Enz"/>
              <speciesReference species="S"/>
             </listOfProducts>
             <listOfModifiers/>
             <kineticLaw timeUnits="time"
                 substanceUnits="substance">
              <math xmlns="http://www.w3.org/1998/Math/MathML">
               <apply>
                <times/>
                <ci>k2</ci>
                <ci>X</ci>
               </apply>
              </math>
              <listOfParameters>
               <parameter id="k2"
                   value="0.01"/>
              </listOfParameters>
             </kineticLaw>
            </reaction>
            <reaction id="r3"
                name="r3"
                reversible="true"
                fast="false">
             <listOfReactants>
              <speciesReference species="X"/>
             </listOfReactants>
             <listOfProducts>
              <speciesReference species="Enz"/>
              <speciesReference species="P"/>
             </listOfProducts>
             <listOfModifiers/>
             <kineticLaw timeUnits="time"
                 substanceUnits="substance">
              <math xmlns="http://www.w3.org/1998/Math/MathML">
               <apply>
                <times/>
                <ci>k3</ci>
                <ci>X</ci>
               </apply>
              </math>
              <listOfParameters>
               <parameter id="k3"
                   value="0.5"/>
              </listOfParameters>
             </kineticLaw>
            </reaction>
           </listOfReactions>
           <listOfEvents/>
          </model>
         </sbml>

Input:   m = loadSimulator[];


Input:   n = SBMLNDSolve[m, 5]
Output:  {{enzymaticReaction`S[t] -> InterpolatingFunction[{{0., 5.}}, <>][t], 
           enzymaticReaction`P[t] ->InterpolatingFunction[{{0., 5.}}, <>][t], 
           enzymaticReaction`Enz[t]->InterpolatingFunction[{{0., 5.}}, <>][t], 
           enzymaticReaction`X[t]->InterpolatingFunction[{{0., 5.}}, <>][t]}}


Input:   SBMLGridPlot[n, PlotRange -> All];
Output:  
        
Input:   SBMLPlot[n];
Output:

returns the string

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