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

[Nicolas Rodriguez]

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
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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


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[cellml-discussion] ABI Meeting minutes 2009-05-06

[Dougal Cowan]

I have put the minutes from Wednesday's meeting up at:

http://www.cellml.org/meeting_minutes/abi-meeting-minutes-2009-05-06/

Dougal


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Re: [cellml-discussion] ABI Meeting minutes 2009-05-06

[Andrew Miller]

Dougal Cowan wrote:

I have put the minutes from Wednesday's meeting up at:

http://www.cellml.org/meeting_minutes/abi-meeting-minutes-2009-05-06/
It is worth noting that the changes I sent earlier today weren't 
included in the minutes:



Hi all,

A few extra things:
4) Andrew will add a tracker item about [alternative graphical platforms]
Andrew has done this, and there has been some discussion on the tracker 
about the issue, including from David Nickerson, Alan Garny, and Carey 
Stevens.


and futher down add two bullet points to:

5) OpenCell development - update

Andrew mentioned that he had been looking into some of the options for 
the graphical platform.
He has also continued with the work on refactoring the model tree view 
so that the metadata support can be implemented more easily.


Best wishes,
Andrew


I also think we need to consider giving people a bit longer to reply to 
draft minutes (especially if there is not enough time to ensure that 
suggested changes get included).


It is important that if we are claiming that people have said things, 
they have a proper chance to review what we claim they said beforehand.


Best wishes,
Andrew



Dougal


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