simbiology: how to combine multiple species when plotting a graph?

hello,

I have some questions regarding to plotting a graph after simulating a model.

1. Is there a way to combine multiple species and consider them as one hypothetical specie? Let's say I created a model using the following reactions, and then run a simulation, and plot a graph.

ProteinA + Mg -> ProteinA_Mg

ProteinA_Mg + Mg -> ProteinA_Mg_Mg

If I want to plot a graph with only two species (Mg and ProteinA_with_any_number_of_Mg_molecules_attached), how could I accomplish this task?

2. Also, when creating a model w/out specifying the units (InitialAmountUnits and units for reaction rate constants), what unit is used by default?

Thanks in advance, Molly

[Fangjun Jiang]

You need to abstract your problem into a MATLAB programming problem and better provide some code and examples.

[Walter Roberson]

Notice the "simbiology" tag, Fangjun; the question is not a general modelling question. Still it would be easier for the specific function that produces the outputs to be posted, so that people could more easily research the matter.

Answer 1

[Arthur Goldsipe]

Hi Molly,

Regarding part 1:

Probably the easiest way to do what you want is to add an pseudo-species to represent the sum of all forms of ProteinA. Add a species to the model and then add a repeatedAssigment rule of the form "ProteinA_Total = ProteinA + ProteinA_Mg + ProteinA_Mg_Mg".

You can see an example of using a repeatedAssignment rule in the gprotein demo. In the SimBiology Desktop, you can open this demo project, located in <matlabroot>/toolbox/simbio/simbiodemos/gprotein.sbproj, or you can see the full demo by search the documentation for gprotein.

Regarding part 2:

Even if you supply units in the InitialAmountUnits property of species or the ValueUnits property of parameters, SimBiology will not do unit conversion during simulation unless you explicitly enable the UnitConversion setting. By default, this setting is off, it is up to the user to ensure that species and parameters are in consistent units. So, assuming your first sample reaction has mass action kinetics with a rate constant of k, SimBiology will calculate the initial rate of change of ProteinA_Mg as k*ProteinA_0*Mg_0, where "X_0" indicates the numeric value of the InitialAmount property of species X.

-Arthur