[SOSlib-devel] Re: Parameter Scan functions in SOSlib

[Witold E. W. <W.E...@nc...>]

Hi Rainer and all,


Yes, parameter scans are important and must be supported by Soslib at 
this stage. However, there are so many strategies to construct designs 
(parameter scans) that I am not sure if they should be part of soslib at 
any stage.

A sufficient support for parameter scans would be if there are functions 
which enable to change a value of one or more variables and afterwards 
to evaluate (integrate) the model. I understand this can be accomplished 
by one or several calls to "IntegratorInstance_setVariableValue"?

I have suggested a few months ago and submitted code which takes new 
values for one or more variables ( a so called design point), sets them 
and returns a SBMLResult.

Furthermore I suggested to include and submitted code for a function 
which given a set of design points returns an array of SBMLResults. 
Given this function it is trivial to generate a 2D Cartesian design 
requested by Norhiko.

However I can not find this functions which would enable me to interface 
easily with soslib.

Instead, I find a lot of very specialized function which generate a 
concrete experimental design. In my opinion such functions  should not 
be included into soslib at least at this stage for the following reasons:

First, given the functions suggested above it would be easily possible 
for a library user, the application developer, to implement any concrete 
design he needs. Norihiro, why do you think that the parameter scan 
should be implemented in Soslib and not in CellDesigner?

Secondly, adding functions to generate a concrete designs to soslib 
makes the library unecessarily more complex. Lets take a look at 
Model_odeSolverBatch. Rainer, what kind of design this function 
generates? I don't understand. What are the references? Why a 2D matrix 
representation of the results is generated? The same questions I have to 
ask regarding your question 1 and 2 below.


Frohe Ostern

Happy Eastern.



Rainer Machne wrote:
> Hi Akira, Eryk and Norihiro,
> 
> (CCed also to the SOSlib development list)
> 
> you are all using/interested in the high-level SOSlib interface 
> SBML_odeSolverBatch for efficient parameter/initial condition scans.
> 
> Currently, it is implemented with a serious and stupid malfunction - 
> i.e. n parameters can be varied over m arbitrary points (design points), 
> but there are no combinations of parameter values.
> 
> CellDesigner needs results for each combination of parameter values, and 
> this is the general requirement for such a batch function.
> I want to correct this now.
> 
> There are two questions:
> 
> 1) Do you see a need for n parameters to be varied, and to get a result 
> structures for each combination? This would result in a n*n*m*m matrix 
> of SBMLResults. Or is it generally sufficient to provide this scan only 
> for 2 parameters?
> 
> 2) As we now want to vary over m arbitrary design points, m (the number 
> of parameter values to be scanned for one parameter) could be different 
> for each parameter. I.e. one parameter might be varied over 3 values, 
> while the other parameter might be varied over 16 values.
> 
> Implementing 2, i.e. a different m for each parameter would be much 
> easier if we restrict the batch function to 2 parameters!
> 
> What do you think? Or better asked: what are your requirements?
> 
> If you want you can add things to the respective section at
> http://www.tbi.univie.ac.at/wiki/index.php/SOSlibDevel#Batch_Mode_for_Parameter_Scan 
> 
> (email ha...@tb... to get an account, mention that you want to 
> contribute to SOSlibDevel Wiki).
> 
> Rainer
> 
> 

-- 
Witold Eryk Wolski
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