Re: [SOSlib-discuss] Python binding for odesolver

[Christoph F. <xt...@tb...>]

hi colin,

yes, it is possible, it is done during the generation of the Perl
binding. also our compilation-on-the-fly feature required, that we compile
the library with the -fPIC option.

=;) xtof

-- 
Christoph Flamm
Institut fuer Theoretische Chemie | email: xt...@tb...
Universitaet Wien                 | phone: ++43-1-4277-527-39
Waehringerstrasse 17/3/308        | fax:   ++43-1-4277-527-93
A-1090 Wien, Austria              | www: http://www.tbi.univie.ac.at/~xtof


Colin Gillespie writes:
 > Hi Michele,
 > 
 > An easier way to interface with python is to use the ctypes library (I 
 > think it's part of the standard python installation). It would also make 
 > your code much more portable.
 > 
 > To use ctypes is quite straighforward see
 > 
 > www.jjj.sun.ac.za/~bgoli/codelib/libsbml3_ctypes-0.1.py
 > 
 > for an example of using it with libsbml (of course you should just use 
 > the libsbml binding for python that is provided.)
 > 
 > To access a C library, you have to be able to build a dynamic version of 
 > the library.
 > 
 > Christoph, is it possible to create a dynamic version of ODEsolver?
 > 
 > HTH,
 > 
 > Colin
 > 
 > 
 > 
 > Michele Mattioni wrote:
 > > Can you tell me how to do that in C/C++?
 > > 
 > > In the worst case scenario I can try to see how to integrate a C code
 > > part directly in my application.
 > > I need to see if I can achieve the results that I need for my
 > > simulation, then I can try to play with swig.
 > > 
 > > If you can send me the swig command you used for perl we can start
 > > with really ugly but working python
 > > bindings and refine them on the way :)
 > > 
 > > Cheers,
 > > Michele.
 > > 
 > > 
 > > On Wed, Feb 11, 2009 at 3:37 PM, Christoph Flamm <xt...@tb...> wrote:
 > >> hi michele,
 > >>
 > >> things like are in principle possible. Unfortunately the only bindings we
 > >> currently have are Perl (experimental) and R bindings. To semi-automate the
 > >> generation of the Perl bindings we use SWIG (http://www.swig.org/).
 > >>
 > >> Since we wanted to avoid to "pollute" the SOSlib Perl namespace with
 > >> additional bindings to libSBML types like SBMLDocument_t (they have their
 > >> own bindings), the SWIG interface file and typemaps contain a lot of Perl
 > >> specific things and I currently don't know how to translate them to their
 > >> Python equivalentes.
 > >>
 > >> I hope to get help with this problem during the SBML hackathon end of
 > >> march.
 > >>
 > >> =;) xtof
 > >>
 > >> --
 > >> Christoph Flamm
 > >> Institut fuer Theoretische Chemie | email: xt...@tb...
 > >> Universitaet Wien                 | phone: ++43-1-4277-527-39
 > >> Waehringerstrasse 17/3/308        | fax:   ++43-1-4277-527-93
 > >> A-1090 Wien, Austria              | www: http://www.tbi.univie.ac.at/~xtof
 > >>
 > >> Michele Mattioni writes:
 > >>  > Hello list,
 > >>  >
 > >>  > I would like to know if it's possible to have a python binding for
 > >>  > OdeSolver and an example code how to run a timecourse of a model.
 > >>  >
 > >>  > In particular what I would like to do is:
 > >>  >
 > >>  > run a model for x time
 > >>  > get the species value
 > >>  > change one specie value
 > >>  > carry on the simulation with the new value for that specie and the
 > >>  > last calculated value for all the others.
 > >>  >
 > >>  > Is possible to do something like that with odeSolver using some python
 > >>  > binding?
 > >>  >
 > >>  > Thanks,
 > >>  > Michele.
 > >>
 > > 
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 > > 
 > 
 > -- 
 > Dr Colin Gillespie
 > http://www.mas.ncl.ac.uk/~ncsg3/