Re: [SOSlib-discuss] [SOSlib-devel] [ sbmlsolver-Support Requests-1597040 ] Altering the parameters of an ODE object.

[Rainer M. <ra...@tb...>]

Dear Dr. Fernando,

yes you can change any parameter or variable (in SBML: global 
parameters, species, compartments) between iterative integration runs 
and even during an integration (e.g. to handle external events).

First, you need to get a pointer to structure variableIndex_t for your 
parameter from the odeModel structure:

odeModel = ODEModel_createFromFile("model.xml");
vi = ODEModel_getVariableIndex(odeModel, "paramX");
   /* where paramX is the SBML ID of the parameter you want to set */

Then you can use this variableIndex to get or set the value of this 
parameter or variable via the integratorInstance:

IntegratorInstance_setVariableValue(ii, vi, 55);

There is one caveat with this function:

If you run multiple integrations wiht one integratorInstance, you need 
to do an
IntegratorInstance_reset(ii);
before the next integration run, and this will reset your initial 
conditions and parameters to the original values in the input SBML file!
And thus, currently the setVariableValue function MUST be called AFTER 
the reset function! (We hope to provide additional reset functions with 
the next release, which keep current or manually reset values.)

See
http://www.tbi.univie.ac.at/~raim/odeSolver/doc/api/group__variableIndex.html
for functions to get the variableIndex from the odeModel, and
http://www.tbi.univie.ac.at/~raim/odeSolver/doc/api/group__integrator.html#ga25
for setting variable/parameter values in the integrator.

See
examples/ChangingIntegratorInstance.c
for an example program which changes variables during an integration.

Please, keep asking if anything is unclear.

Thanks,
Rainer



SourceForge.net wrote:
> Support Requests item #1597040, was opened at 2006-11-15 07:00
> Message generated for change (Tracker Item Submitted) made by Item Submitter
> You can respond by visiting: 
> https://sourceforge.net/tracker/?func=detail&atid=744812&aid=1597040&group_id=139893
> 
> Please note that this message will contain a full copy of the comment thread,
> including the initial issue submission, for this request,
> not just the latest update.
> Category: None
> Group: None
> Status: Open
> Priority: 5
> Private: No
> Submitted By: Nobody/Anonymous (nobody)
> Assigned to: Nobody/Anonymous (nobody)
> Summary: Altering the parameters of an ODE object. 
> 
> Initial Comment:
> Is there any way of altering the rate constants once an SBML file has been read in? This is quite important for using evolutionary algorithms, because a significant amount of time is wasted reading the new SBML file into the ODEsolver. 
> 
> Yours, 
> Dr. C. Fernando 
> Birmingham University 
> UK. 
> 
> 
> ----------------------------------------------------------------------
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> You can respond by visiting: 
> https://sourceforge.net/tracker/?func=detail&atid=744812&aid=1597040&group_id=139893
> 
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