Re: [Ecell-users] implementing new processes

[Moriyoshi K. <mo...@sf...>]

It seems I sent you a wrong version of the model file. Try this one instead.

-- moriyoshi



On Fri, Feb 6, 2009 at 7:07 PM, Moriyoshi Koizumi <mo...@sf...> wrote:
> On Fri, Feb 6, 2009 at 12:51 AM, giuseppe aprea
> <apr...@gm...> wrote:
>
>> I guess ecell will associate ODE2Process' velocity to X2 Variable (PHA).
>> Is that right?
>
> Right, X2 is accumulated according to the value of the ODE2Process's activity.
>
>> Now I have 2 problems:
>>
>> - during compilation I get los of warnings of the kind:
>> "/usr/include/ecell-3.1/libecs/Entity.hpp:73: warning: comparison with
>> string literal results in unspecified behaviour"
>> I don't really understand if I am doing some fatal error in the code,
>> anyway I successfully get my .so objacts. Can I ignore this warning?
>
> Those warnings are basically harmless, but it was addressed in the
> newer releases. Give 3.1.107rc2 a try.
>
>> - if I compare the results with matlab ones they are quite different
>> both quantitatively (~20%) and qualitatively after "only" 60 sec.
>
> You apparently specified an wrong coeffient (-1). Each process denotes
> a flux, so variables given with negative coefficients have negative
> deltas.
>
>> By the way, does anybody know if there is some documentation about
>> Stepper settings (timestep, tolerance) or about how to make your own Stepper?
>
> Assuming you took a look at the E-Cell manual, there has been no
> comprehensive document known that elaborates on Stepper
> specifications. Sorry.
>
> By the way, you can write such simple equations with
> ExpressionFluxProcess'es. Attached is a version rewritten with them.
>
> Regards,
> Moriyoshi
>