Adding the Reaction for Transcription

A simple model of transcription shows only the DNA and mRNA. For more details, see Transcription.

  1. Add the reaction DNA -> DNA + mRNA to the model.

    Robj1 = addreaction(Mobj, 'DNA -> DNA + mRNA');

    The species DNA and mRNA are automatically added to the model.

      Note:   Because this example has only one compartment, you need not specify the compartment to which each species belongs. If there are multiple compartments, here is an example of the reaction syntax:

      Robj1 = addreaction(Mobj, 'nucleus.DNA -> nucleus.DNA + cytoplasm.mRNA');

      nucleus and cytoplasm are the names of the compartments.

  2. Specify the kinetics of the reaction to be Mass Action by creating a kinetic law object, Kobj1, and setting its KineticLawName property to MassAction.

    Kobj1 = addkineticlaw(Robj1,'MassAction');

    For a nonreversible reaction, MassAction kinetics defines the reaction rate expression as forward rate constant * reactants.

  3. The kinetic law serves as a map between parameters and species needed by the reaction rate expression and parameters and species in the model. To see the parameters and species that must be mapped, retrieve the ParameterVariables and SpeciesVariables properties of Kobj1.

    get(Kobj1, 'ParameterVariables')
    get(Kobj1, 'SpeciesVariables')
    ans = 
        'Forward Rate Parameter'
    ans = 
        'MassAction Species'
  4. Because the kinetic law requires a forward rate parameter, create a parameter, k1, and set its value to 0.2. Map the parameter k1 to the forward rate parameter, by setting the ParameterVariablesNames property of Kobj1 to k1.

    Pobj1 = addparameter(Kobj1, 'k1', 0.2);
    set(Kobj1, 'ParameterVariableNames', 'k1');
  5. For Mass Action kinetics, the SpeciesVariables are automatically assigned to the reactants. Therefore, the SpeciesVariablesNames property of Kobj1 is automatically set to DNA. To confirm this, retrieve the SpeciesVariableNames property of Kobj1.

    get(Kobj1, 'SpeciesVariableNames')
    ans = 

    The reaction rate expression is now defined as k1 * DNA.

  6. Set the initial amount for the species DNA to 50 and mRNA to 0. Select the species using the function sbioselect, which returns an object.

    Sobj1 = sbioselect(Mobj, 'Type', 'species', 'Name', 'DNA');
    set(Sobj1, 'InitialAmount', 50);

    The value for mRNA defaults to 0.

  7. Check the initial amounts for the species.


    MATLAB® displays a summary list.

    SimBiology Species Array
       Index:  Compartment:  Name:  InitialAmount: InitialAmountUnits:
       1       contents       DNA    50                 
       2       contents       mRNA   0   
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