Re: [Biomodels-net-support] SBML L3V1 to L2 conversion issue

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

On 12/09/12 14:32, Nicolas Le Novère wrote:
> Both :-)
>

Will do.

I think we should be ready to start answering questions about the 
species present without any transitions.
Probably a path2models or kegg2sbml FAQ would be good.

Nico


>
> On 12/09/12 14:31, Nicolas Rodriguez wrote:
>> On 12/09/12 14:15, Nicolas Rodriguez wrote:
>>> On 12/09/12 13:51, Nicolas Rodriguez wrote:
>>>> On 12/09/12 11:11, Nicolas Rodriguez wrote:
>>>>> On 12/09/12 11:05, Katie Viljoen wrote:
>>>>>> Hi Nico,
>>>>>>
>>>>>> Thanks for your prompt response! IPA does support Biopax files
>>>>>> (although I'm not sure up to which level, I will ask them) as 
>>>>>> well as
>>>>>> SIF files.
>>>>>>
>>>>>
>>>>> You should pressure them to support SBML L3 as well as the qual
>>>>> proposal (which is almost final).
>>>>>
>>>>> I will keep you aware if and when we manage to convert the SBML qual
>>>>> model to SIF or biopax.
>>>>
>>>> Should we advised to use CySBML that seems to support SBML qual ?
>>>> http://www.charite.de/sysbio/people/koenig/software/cysbml/
>>>>
>>>> We should probably test how much and how it support it first.
>>>
>>> Ok, after testing it, CySBML can load the file into Cytoscape but it 
>>> does
>>> not do anything with the qual specific elements so
>>> it does not support qual !!
>>>
>>
>> Sorry, I have to correct myself here !!
>>
>> Downloaded Cytoscape-2.8.3 and CySBML-1.25 (latest versions for both) 
>> and
>> it does read the qual information properly now :-)
>>
>> Although, the network does not look too impressive, that's a start.
>>
>> Do I send Katie the files directly or advice to use the latest Cytoscape
>> and CySBML or both ?
>>
>> Nico
>>
>>>
>>>>>
>>>>>> On Wed, Sep 12, 2012 at 11:59 AM, Nicolas Rodriguez
>>>>>> <rod...@eb... <mailto:rod...@eb...>> wrote:
>>>>>>
>>>>>>     Hi Katie,
>>>>>>
>>>>>>
>>>>>>     On 12/09/12 10:32, Katie Viljoen wrote:
>>>>>>>
>>>>>>>         Hi.
>>>>>>>
>>>>>>>         I'm trying to convert an SBML Level 3 Version 1 file to an
>>>>>>>         SBML Level 2 fie for use in Ingenuity Pathway Analysis, 
>>>>>>> since
>>>>>>>         they only support up to SMBL L2V4 files.  I've tried the
>>>>>>>         online conversion tool, but I still can't load the file 
>>>>>>> into
>>>>>>>         IPA (they say its a KGML file).  Sorry, I'm new to these 
>>>>>>> file
>>>>>>>         formats, so not sure what I might be doing wrong?  The file
>>>>>>>         I'm trying to convert is at:
>>>>>>>         http://biomodels.caltech.edu/BMID000000026230
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>     The problem is that the file you are trying to convert is not a
>>>>>>     simple L3V1 core model. It contain also some qualitative
>>>>>>     information through the SBML qual package proposal.
>>>>>>
>>>>>>     Until more software support this package (and SBML L3 in 
>>>>>> general)
>>>>>>     it would be nice if we could provide some converters so that
>>>>>>     people can use this model more easily.
>>>>>>     We might be able to extend our biopax converter to support 
>>>>>> that or
>>>>>>     provide SIF files. Does IPA support biopax L3 or SIF files ?
>>>>>>
>>>>>>     Thanks,
>>>>>>     Nico
>>>>>>
>>>>>>
>>>>
>>>
>>
>>
>>
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>
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