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[cellml-discussion] tools that use and / or work with CellML


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  • From: j.lawson at auckland.ac.nz (James Lawson)
  • Subject: [cellml-discussion] tools that use and / or work with CellML
  • Date: Fri, 08 May 2009 13:01:49 +1200
Thanks Nico, I'll put that info up.

Kind regards,
James

Nicolas Rodriguez wrote:
> James Lawson wrote:
>> James Lawson wrote:
>>> Hi all,
>>>
>>> We're currently doing some work on the Tools page of the website at
>>> http://www.cellml.org/tools and I'd just like people to have a look
>>> through the listing there and check that your tools are all there.
>>> The listing is fairly old so I know we're missing a few. Apologies
>>> in advance if your tool is missing, but please let us know and we'll
>>> rectify that ASAP.
>>>
>>> Kind regards,
>>> James Lawson
>>> _______________________________________________
>>> cellml-discussion mailing list
>>> cellml-discussion at cellml.org
>>> http://www.cellml.org/mailman/listinfo/cellml-discussion
>>>
>> In particular, we don't have the CellML <-> SBML translators up
>> there. So if anyone could link me to them and maybe give me a short
>> paragraph description about them, that would be great.
>>
> The page general page about SBML converters developed at EBI is :
> http://www.ebi.ac.uk/compneur-srv/sbml/converters/SBMLConverters.html
>
> Specific CellML pages:
> http://www.ebi.ac.uk/compneur-srv/sbml/converters/SBMLtoCellML.html
> http://www.ebi.ac.uk/compneur-srv/sbml/converters/CellMLtoSBML.html
>
> Note : The stylesheets on these pages are not entirely up-to-date with
> the ones used to create the export formats of Biomodels DB, I still
> have to work on some issues before updating the web site.
>
> As for a really short description, they are translation tools, written
> using XSLT.
>
> The SBML to CellML converter is creating a CellML file using reactions
> and we need to update it. Andrew is currently working on writing a new
> version of it, the prototype is done but we need to correct some
> issues before to use replace the XSLT version. This new version is
> written in Ruby and is focusing mainly on getting the units as right
> as possible and using the latest CellML specs without using reactions,
> not doing anything about metadata yet. We are also planning to update
> the CellML to SBML converter, probably written in Java when the new
> specifications are out.
>
> Cheers,
> Nico
>
>
> _______________________________________________
> cellml-discussion mailing list
> cellml-discussion at cellml.org
> http://www.cellml.org/mailman/listinfo/cellml-discussion

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