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

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

Hej Frank,

OK, then it was probably just me to misunderstand the discussion,
among several options to also advocate for a standardised archive,
that is fine with me as well (I thought from the discussions that was not what was argued about,
sorry),

Dagmar


________________________________________
From: Frank Bergmann [fbergman@u.washington.edu]
Sent: 08 March 2010 18:20
To: sed...@li...
Subject: Re: [SED-ML-discuss] How to resolve models

Hello ...

> 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 we are not forcing users at all. The users are free to choose the format
that they want. They can go for the plain SED-ML description ... and
manually manage all their models and other references ... or they can go for
the archive and be ready to exchange their information. All we ensure by
describing the archive format in the specification is that those archives
will be interoperable.

> 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.
>

Don't you think in order to make such an advise, you would have to refer to
the specification of the archive format. So in order to do that it needs to
be described in the spec, which is all I was arguing for.

> 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?
>

Please let me know how the archive format is not flexible? I don't see any
limitations imposed with an archive format.

> 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.
>

What about wanting to open a simulation experiment description, while
without internet connection? What about being able open it instantly, rather
than resolving the model first and downloading it later? Even if you argue
for big models, that are referred to by URN, I at least much rather have
that 20+MB model included in an archive format, rather than having to
download it *each time* I execute the SED-ML experiment from the web.

Cheers
Frank

> 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...(NO
> T
> >> email) http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/,
> >> @lenovere
> >>
> >>
> >>
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> >
> >
> >
> >
>
>
>
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