Re: [Ecell-users] implementing new processes

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

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