does anybody please explain how to use 'tomlab' in Simbiology?

Hello, does anybody please explain how to use 'tomlab' in Simbiology? previously I used sundial, ode15s etc. Now I want to use tomlab instead of those.

Thanks in advance.

Emran

Answer 1

[protein]

Hi Arthur,

Thanks a lot. I use the same outline as you have given. Now I only want to use the 'solvers of tomlab'.

In Simbiology normally I use:

                     configsetObj = getconfigset(model);

                     set(configsetObj, 'StopTime', 86400, 'SolverType', 'ode15s');   % for 'ode15s'solver

now is it possible to follow same procedure:??

                     set(configsetObj, 'StopTime', 86400, 'SolverType', *'SNOPT'*);  %  a TOMLAb solver

or, what will be the actual code for 'SNOPT' , 'NPSOL' etc.

Regards,

Emran

Answer 2

[Arthur Goldsipe]

Hi Emran,

TOMLAB and SimBiology are two separate products and are not integrated. Furthermore, TOMLAB is used for optimizing some objective function, while the SimBiology solvers ode15s and sundials are used for solving ordinary differential equations. Therefore, it does not really make sense to replace sundials with TOMLAB.

Perhaps you mean that you want to use TOMLAB for optimization of a SimBiology model? For example, you might want to determine the set of model parameters that best fit some experimental data. You should be able to do this by writing your own objective function to pass to TOMLAB. Here's a brief outline of what that function might look like:

• Accept parameter values as inputs
• Apply these parameter values to your SimBiology model
• Set the OutputTimes of the model's configset to the experimental times
• Simulate your model
• Calculate the sum of the squares of the errors (the difference between simulated and measured results)
• Return this sum as the output of the function

-Arthur

[protein]

Hi Arthur,

Thanks a lot. I use the same outline as you have given. Now I only want to use the 'solvers of tomlab'.

In Simbiology normally I use:

                     configsetObj = getconfigset(model);
                     set(configsetObj, 'StopTime', 86400, 'SolverType', 'ode15s');   % for 'ode15s'solver

now is it possible to follow same procedure:??

                 set(configsetObj, 'StopTime', 86400, 'SolverType', *'SNOPT'*);  %  a TOMLAb solver

or, what will be the actual code for 'SNOPT' , 'NPSOL' etc.

Regards,

Emran

[Arthur Goldsipe]

Hi Emran

Let me reiterate... SNOPT and NPSOL cannot replace ode15s or sundials. These functions have different purposes. ode15s and sundials solve a set of ordinary differential equations. SNOPT and NPSOL are used to minimize an objective function. Just like you can't use sqrt in place of sin, you can't use SNOPT in place of ode15s.

-Arthur

[protein]

Hi Arthur,

Thanks again. I've understood that now. Just please tell me, I have to apply 'any' tomlab solver to the following code instead of 'ode15s' :

             set(configsetObj, 'StopTime', 86400, 'SolverType', 'ode15s');

How can it be possible?

Regards,

Emran

[Arthur Goldsipe]

Hi Emran,

SimBiology currently only allows you to set the SolverType to one of the built-in solvers (as of R2012b, that includes 'ode15s', 'ode23t', 'ode45', 'sundials', 'ssa', 'expltau', and 'impltau'):

http://www.mathworks.com/help/simbio/ref/solvertype.html

-Arthur