I am running a SimBiology project. I gave the model a vector that has several parameters and then when I ran this function:
[penny(i)] = sbiosimulate(dollars);
I got this error:
Warning: Reported from Dimensional Analysis:
Reaction rate dimension for reaction 'A -> null' must be either concentration/time or substance/time. Dimension substance/time is assumed.
I changed the unit for parameter using all existing unites, but I kept getting the error. May someone let me know how I could get rid of this error.
I am running a SimBiology project and I would like to get a table of species so:
dollar = out.m1;
get (dollar, 'species')
using get, I got this table, but when I used the get for parameter:
Regarding your first question, you need to check the units on everything in the reaction rate for the reaction "A -> null". For example, the reaction rate might be "k*A", with parameter k having units of 1/second and species A having units of mole/liter. In this case, the reaction rate has units of mole/liter/second, which has dimensions of concentration/time. It would also be valid for k to have units of liter/second, so that the reaction rate has units of mole/second, which would have dimensions of substance/time.
Regarding your second questions, parameters can either be stored (or "scoped") at the level of the model or at the level of the reaction. A model-scoped parameter can be used in multiple reactions, rules, or events. A reaction-scoped parameter can only be used in the reaction that contains it. Here's how to get all the parameters scoped to the first reaction in your model "dollar":
Or, if you want to get *all* parameters stored in a model, I recommend using the sbioselect command as follows:
sbioselect(dollar, 'Type', 'parameter')
This command will search the model and return all objects of type 'parameter'.
"Jerry " <firstname.lastname@example.org> wrote in message <email@example.com>...
> First question:
> I am running a SimBiology project. I gave the model a vector that has several parameters and then when I ran this function:
> [penny(i)] = sbiosimulate(dollars);
> I got this error:
> Warning: Reported from Dimensional Analysis:
> Reaction rate dimension for reaction 'A -> null' must be either concentration/time or substance/time. Dimension substance/time is assumed.
> I changed the unit for parameter using all existing unites, but I kept getting the error. May someone let me know how I could get rid of this error.
> Second question:
> I am running a SimBiology project and I would like to get a table of species so:
> dollar = out.m1;
> get (dollar, 'species')
> using get, I got this table, but when I used the get for parameter:
> get (dollar, 'parameters')
> I got this
> Empty matrix: 0-by-1
> Any idea how I could get the table of parameters.
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