MATLAB: Synax for species generation in SimBiology.

biologymodellingSimBiology

In other modelling software I can simple use:

' -> protein'

for fist order production of a protein however this doesn't seem to be excepted in SimBiology. I have also tried:

'null -> protein' but this also does not work.

What is the syntax for producing a species out of nothing in simbiolgy?

Thanks

Best Answer

Hi Ciaran,

'null -> protein' is the syntax used in SimBiology. However, you will also need to specify the reaction rate.

When you say that this syntax didn't work, what error did you get? Can you post sample code or attach a model?

-Arthur

Related Solutions

MATLAB: Creating a cell growth model using SimBiology.

Hi,

The capacity of a compartment can vary during the course of a simulation. To do this, you must set the Constant property to false (or the ConstantCapacity property in SimBiology versions before R2019b). Then, you can change the compartment capacity using things like repeated assignment rules, rate rules, and events.

You cannot add additional components of any time (compartments, species, parameters, reactions, etc.) during the course of a simulation. So you cannot directly simulate an increasing number of cells if you need to treat each of them as distinct entitites in your model.

However, you may still be able to model cell growth in SimBiology. The feasibility and exact approach will depend on your goals, but let me offer an example:

Create a SimBiology model of a single growing cell and add a parameter to the model that counts the number of times the cell has divided. Add an event to implement cell division. This event divides each compartment volume and the amount of each species by 2, and increments the counter for the number of cell divisions. Then, simulate your model for the desired time and analyze the results.

MATLAB: Get initial amounts of some species

As of R2011a, you can use sbioparamestim to estimate the initial amount of a species. If you can't easily upgrade to R2011a, you can either try another estimation function (e.g., sbionlinfit) or work around the limitation by estimating a parameter that controls the initial amount via an initialAssignment rule.

-Arthur

P.S. Here's a simple example to estimate the initial amount of x in the radiodecay model:

% Create a parameter and initial assignment rule
sbioloadproject radiodecay.sbproj m1
x = sbioselect(m1, 'Name', 'x');
x0 = m1.addparameter('x0', 1000, 'ValueUnits', 'molecule');
m1.addrule('x = x0', 'initialAssignment');
% Create synthetic data
c = sbioselect(m1, 'Name', 'c');
t = [1:10]'; y = 2000*exp(-c.Value*t);
% Fit the data, simulate, and plot
[x0Estimate, result] = sbioparamestim(m1, t, y, x, x0)
x0.Value = x0Estimate;
sd = sbiosimulate(m1);
plot(sd.Time, sd.Data, '-', t, y, 'x')

Best Answer

Related Solutions

MATLAB: Creating a cell growth model using SimBiology.

MATLAB: Get initial amounts of some species

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