Re: [SED-ML-discuss] How to resolve models

[Dagmar W. <dag...@un...>]

Hej,

I think there are two things here: One is what we demand in the SED-ML 
spec. Another thing is how we would like to advise people to use SED-ML.

My personal opinion is that we should not /force/ users (spec-wise) to 
create a sed-ml.archive whenever they want to exchange a simulation 
experiment. But that we rather should let SED-ML be independent, offer 
different ways of building a simulation description. We could well 
/advise/ users to use the proposed archive format, if multiple files are 
needed for the experiment.

We do not know what the future will look like, and what kind of 
standardised data sources we will have, do we? So, why not keep it 
flexible?

And I agree completely with what Nicolas said: The missing 
versioning/change track for existing models is not the problem of 
SED-ML. So for me "changing files" is no argument that would completely 
forbid to have SED-ML files with links to standardised model URNs.

Dagmar


Richard Adams wrote:
> OK, but the existence of   large datasets   doesn't negate the utility  
> of the possibility of including small, processed datasets in a SED-ML  
> archive.
>
>
>   
>> Richard Adams wrote:
>>
>>     
>>>   If the idea is to access datasets as well in future, then that would
>>> be even more of a reason to be able to bundle files together, as there
>>> are ( afaik )no nice, official, communal dataset repositories as there
>>> are for SBML and CellML models.
>>>       
>> There are, albeit often unprocessed. Think about gene expression
>> timeseries. And you do not want to attach the result of an Illumina run to
>> a SED-ML file.
>>
>>
>> --
>> Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, Wellcome-Trust
>> Genome Campus, Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521
>> Fax:468,Skype:n.lenovere,AIM:nlenovere,MSN:nle...@ho...(NOT email)
>> http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/, @lenovere
>>
>>
>>
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