MATLAB: Adding parameters while programmatically setting up a SimBiology model

addparameteraddreactionkineticlawMATLABscopeSimBiology

I am setting up a SimBiology model programmatically, but am running into errors adding parameters and setting up reactions. The documentation suggests that parameters can be scoped to specific kinetic laws or to the model (in which case they are available to all kinetic laws and reactions). Since some of my parameters are used in several reactions, I figured it would be good to scope them to the model. However, I get the following error among others:
Error using SBCompiler.SimulationObject/simulate
--> Error reported from KineticLaw Validation:
Cannot find parameter with name ''.
To me this reads as if there is a scoping problem – the kinetic law can't find my parameter. I made the stripped down version of my model below:
%%Model
test=sbiomodel('test');
%%Compartments
Acell=addcompartment(test,'Acell',30,'CapacityUnits','picoliter','ConstantCapacity',false);
cytoplasm=addcompartment(Acell,'cytoplasm',15,'CapacityUnits','picoliter','ConstantCapacity',false);
nucleus=addcompartment(Acell,'nucleus',15,'CapacityUnits','picoliter','ConstantCapacity',false);
%%Species
B=addspecies(cytoplasm,'B',0,'InitialAmountUnits','molecule');
A=addspecies(nucleus,'A',1943,'InitialAmountUnits','molecule');
gB=addspecies(nucleus,'gB',4,'InitialAmountUnits','molecule');
gB_A=addspecies(nucleus,'gB_A',0,'InitialAmountUnits','molecule');
%%Parameters
bB_A=addparameter(test,'bB_A',.1,'ValueUnits','1/(molecule*second)');
ubB_A=addparameter(test,'ubB_A',1.0,'ValueUnits','1/(second)');
deg_A=addparameter(test,'deg_A',0.05,'ValueUnits','1/(second)');
deg_B=addparameter(test,'deg_B',0.005,'ValueUnits','1/(second)');
synth_B=addparameter(test,'synth_B',2,'ValueUnits','1/(second)');
%%Reactions
PRODB_A=addreaction(test,'nucleus.gB_A -> cytoplasm.B + nucleus.gB_A','ReactionRate','synth_B*nucleus.gB_A');
BINDgB_A=addreaction(test,'nucleus.gB + nucleus.A <-> nucleus.gB_A','ReactionRate','bB_A*nucleus.gB*nucleus.A - ubB_A*nucleus.gB_A');
DEGA=addreaction(test,'nucleus.A -> null','ReactionRate','deg_A*nucleus.A');
DEGB=addreaction(test,'cytoplasm.B -> null','ReactionRate','deg_B*cytoplasm.B');
%%Kinetic Laws
kPRODB_A=addkineticlaw(PRODB_A,'MassAction');
kBINDgB_A=addkineticlaw(BINDgB_A,'MassAction');
kDEGA=addkineticlaw(DEGA,'MassAction');
kDEGB=addkineticlaw(DEGB,'MassAction');
%%Configuration
cs=getconfigset(test,'active');
cs.SolverType = 'ssa';
cs.StopTime = 50*60;
solver = cs.SolverOptions;
solver.LogDecimation = 10;
cs.CompileOptions.DimensionalAnalysis = false;
When I run this I get several errors:
>> [time,x,names]=sbiosimulate(test);
Error using SBCompiler.SimulationObject/simulate
--> Error reported from KineticLaw Validation:
Cannot find parameter with name ''.
--> Error reported from KineticLaw Validation:
Cannot find parameter with name ''.
--> Error reported from KineticLaw Validation:
Cannot find parameter with name ''.
--> Error reported from KineticLaw Validation:
Cannot find parameter with name ''.
--> Error reported from Expression Validation:
Invalid reaction rate '' for reaction 'nucleus.gB_A -> cytoplasm.B + nucleus.gB_A'. Reaction rates must be valid MATLAB expressions and
cannot end in semicolons, commas, comments ('%' and optional text), or line continuations ('...' and optional text).
--> Error reported from Expression Validation:
Invalid reaction rate '' for reaction 'nucleus.gB + nucleus.A <-> nucleus.geB_A'. Reaction rates must be valid MATLAB expressions and
cannot end in semicolons, commas, comments ('%' and optional text), or line continuations ('...' and optional text).
--> Error reported from Expression Validation:
Invalid reaction rate '' for reaction 'nucleus.A -> null'. Reaction rates must be valid MATLAB expressions and cannot end in semicolons,
commas, comments ('%' and optional text), or line continuations ('...' and optional text).
--> Error reported from Expression Validation:
Invalid reaction rate '' for reaction 'cytoplasm.B -> null'. Reaction rates must be valid MATLAB expressions and cannot end in semicolons,
commas, comments ('%' and optional text), or line continuations ('...' and optional text).
Error in sbiosimulate (line 143)
[t, x] = simobj.simulate(mobj, cs, variants, doses);
I'm quite puzzled as to why the model is incorrectly specified.
One solution is to reorganize everything so that I add a reaction, add a kinetic law, add parameter scoped to that kinetic law, then set the kinetic law constants. But if I do this, how do share a parameter between reactions (not in the stripped down example above, but in my larger model)?

Best Answer

I solved my problem and leave the question up in case it is useful to anyone else.
Each kinetic law just needs to have the parameters it uses specified:
So after the kinetic law statement block above:
%%Add kinetic law constants for each kinetic law
kPRODB_A.ParameterVariableNames={'synth_B'};
kBINDgB_A.ParameterVariableNames={'bB_A','ubB_A'};
kDEGA.ParameterVariableNames={'deg_A'};
kDEGB.ParameterVariableNames={'deg_B'};
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