Re: [Biomodels-net-support] SBML to XPP converter

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

Hello Omar,

On 11/09/2011 10:48 PM, Omar Guiterrez Arenas wrote:
>
> Dear Colleague,
>
> My name is Omar Gutierrez Arenas and I'm a post-doc at KTH in 
> Stockholm. I'm interested in using the SBML to XPP capability of the 
> SBML converter but my machine runs Windows 7.
>
> The instructions I found at 
> http://www.ebi.ac.uk/compneur-srv/sbml/converters/SBMLtoXPP-Aut.html are 
> for people running Linux and the like. How can I do to run this 
> converters in Windows? My experience with Java is very limited.
>

We are at the moment designing a new converter library that would make 
it easier to use, so you can give it a try.

Here are the short instructions on how to do it.

First you need to things, you need to install apache ant, which is a 
tool that we will use to build the library.
You can download it from there : http://ant.apache.org/bindownload.cgi
The ant bin directory need to be in the windows PATH.

Then, you need to have a tool to use subversion (svn), you can download 
some windows client from 
http://subversion.apache.org/packages.html#windows or there 
http://tortoisesvn.tigris.org/

Then you need to checkout the SBFC project.

For the command line :  svn co 
https://sbfc.svn.sourceforge.net/svnroot/sbfc/branches/osgi/ sbfc/

Then you need to compile the library. Open a msdos prompt, go to the 
folder were you checkout sbfc, then type :

ant osgi

Now, you are ready to use the converters there and sbml2xpp in 
particular. If you have any problems doing all of that, I could create a 
zip file quickly and send it over to you, so that you have only to unzip 
it and start using the converters as explain below.


 From the command line, in the sbfc folder :

java -jar sbfc-launcher.jar help

java -jar sbfc-launcher.jar -converter sbml2xpp -inputfile 
c:\path\to\sbml\file

The generated xpp file will be saved in the same folder as the sbml 
file, with the same name and the extension .xpp

> It seems that XLS is another option but I'm lost here as well.
>

The XSL version is quite old and limited so I would advice you not to 
use it, even if it can work fine on some models.


Do not hesitate to contact us again if you have any problems.

Thanks,
Nico