Discover MakerZone

MATLAB and Simulink resources for Arduino, LEGO, and Raspberry Pi

Learn more

Discover what MATLAB® can do for your career.

Opportunities for recent engineering grads.

Apply Today

Thread Subject:
SimBiology Questions

Subject: SimBiology Questions

From: Jerry

Date: 17 Dec, 2012 17:50:23

Message: 1 of 2

Hello,

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.

Thanks,
Jerry

Subject: SimBiology Questions

From: Arthur Goldsipe

Date: 18 Dec, 2012 13:46:08

Message: 2 of 2

Hi Jerry,

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":

dollar.Reactions(1).KineticLaw.Parameters

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'.

-Arthur

"Jerry " <jerrycholo@gmail.com> wrote in message <kanm0v$fnn$1@newscl01ah.mathworks.com>...
> Hello,
>
> 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.
>
> Thanks,
> Jerry

Tags for this Thread

What are tags?

A tag is like a keyword or category label associated with each thread. Tags make it easier for you to find threads of interest.

Anyone can tag a thread. Tags are public and visible to everyone.

Contact us