[SOSlib-devel] Re: Parameters with undefined values in odeSolver

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

sorry, this is the test program that also does the consistency check.
r

On Mon, 29 May 2006, Rainer Machne wrote:

> Hi Michael and Ben
>
> Michael had reported a mis-behaviour of SOSlib in the email below.
>
> The non-constant parameters a and b in the example file have no initial 
> value, but are interpreted as 0 by SOSlib.
>
> I have attached a simple example program, which I compiled with libsbml 
> 2.3.4, probably from a version that was updated from CVS on Feb 14 this year.
>
> It shows that Parameter_getValue returns 0 for both parameters even though 
> Parameter_isSetValue correctly returns "no" for both parameters.
> No errors are reported by the consistency check.
>
>
> It is quite some bug in SOSlib.
> Unfortunately, we didn't think earlier of this problem.
>
> So I'd have some questions to start repairing SOSlib:
>
> Does this happen on purpose, i.e. is 0 the default value to return, if no 
> value is set?
>
> For which other values (species, compartments) does this happen?
>
> and:
>
> Should there be a test in the consistency check?
>
> Thanks
> Rainer
>
>
>
>
>
> On Wed, 24 May 2006, Michael Hucka wrote:
>
>> Hi guys,
>> 
>> Harish has been using odeSolver to test models during
>> curation and has bumped into the following behavior.  If you
>> have a model that has a parameter with an undefined value,
>> odeSolver doesn't complain, and seems to assume a value of 0
>> for the parameter.  The attached model demonstrates this
>> behavior for parameter 'b'.
>> 
>> Unless I'm misunderstanding something, I think this is an
>> error.  Missing values in an SBML model should be considered
>> as unknown and a software tool should acquire the value from
>> an external source (such as asking the user).  I checked the
>> online documentation but couldn't find mention of whether
>> there is a way to tell odeSolver to behave differently in
>> this situation.
>> 
>> Please don't take this as criticism!  I think odeSolver is
>> outstanding and the online facilities are terrific :-).  We
>> merely wanted to point out this issue, and ask if our
>> understanding is in fact correct about what's going on.
>> 
>> Best regards,
>> MH
>