Re: [Biomodels-net-support] SBML Support for APMonitor Modeling Language

[Nicolas R. <rod...@eb...>]

On 10/12/2011 05:54 AM, John Hedengren wrote:
> Dear Developers,
>
> I'm interested in an SBML to APMonitor Modeling Language conversion.  It appears that XPP or Octave format is most closely aligned with APMonitor.

Yes, it seems quite similar. You could start from the SBML to XPP 
converter and adapt it to produce the APMonitor Modeling Language.

You have already there some facilities to check which mathML element is 
supported by your language and it can abort the conversion if there
is some. There is also already some facilities to distinguish parameters 
and variables.

So to go forward, you would have to have a look at the SBFC (System 
Biology Format Converter) project where the code of the SBML to XPP is :
http://sbfc.sourceforge.net/

May be you can contribute your converter, later on, back to the project.

To checkout the sources :
svn co https://sbfc.svn.sourceforge.net/svnroot/sbfc/trunk sbfc

The code for XPP is located in src/org/sbfc/converter/sbml2xpp/

I would advice to read the SBML specifications anyway before going 
further with the converter as it will help you to understand the code.

Regards,
Nico


>
> http://en.wikipedia.org/wiki/APMonitor
>
> I'm somewhat new to the SBML format.  I just joined the faculty at Brigham Young University in the Chemical Engineering department.  Previously, I was at ExxonMobil Chemical deploying large-scale models of chemical processes.  It looks like a great source of models and collaboration.
>
> I've made the APMonitor Modeling Language freely accessible through a MATLAB or Python interface to solve the Differential and Algebraic systems.  There are thousands of on-line users that solve simulation and optimization problems from a variety of disciplines.
>
> http://apmonitor.com/wiki/index.php/Main/PythonApp
>
> The Python and MATLAB interfaces drive the simulation, however, the actual model has to be in the APMonitor format.  It looks like I can benefit from your work to convert the programs.  Instead of writing an interface to interpret SBML models directly, I need to translate the models into the APMonitor Language.
>
> I'd appreciate your thoughts on whether it would be possible to create the conversion program.  We are considering a research project in this area so your guidance will be greatly appreciated before we start.
>
> Best regards,
>
> John Hedengren
> joh...@by...
> +001  801-477-7341
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