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David Nickerson wrote:

>> We release the models publicly twice a year.
>
> just wondering what you mean by this? is it that the public database is
> only gets updated twice a year, while the model curators are working on
> the (private) next release of the models?

Yes. This is exactly that. That allow some flexibility in the curation
schedule, and also we want a certain level of annotation before release.
Finally, some models are not released for public consumption because of
problems discovered late (did-you notice there was no BIOMD0000000019?)

> Also, do you have any sense of curation (over and above the libSBML
> consistency checks) for a model not based on a particular peer-reviewed
> publication?

All the models distributed by BioModels Database are described in the
peer-reviewed literature. We do not want to be involved in any discussion
about the biological relevance of the models.


> For example, models that are designed simply as test-cases
> for particular expected software behaviour - where the structure and
> expected behaviour of the model are well known but not described in any
> specific published article. From what I remember, MIRIAM uses published
> articles as the reference description of a model in regard to MIRIAM
> compliance, but could another source reference description be used in
> model curation, albeit not in conjunction with MIRIAM compliance?

This is actually incorrect. MIRIAM does not require publication in an
article. It requires a unique reference description, that can be an
article, a technical report, a web-page etc.

>> finally that one can reproduce published results *using different
>> software than the one used by the authors*.
>
> I think this is very important requirement for model curation, but one
> that is quite daunting for CellML models, especially CellML 1.1 based
> models. One question I have is how different different tools need to be
> to satisfy such curation? What I'm getting at is that there could
> potentially be many "different" tools based on a common library (the
> CellML API and code generation service, or libSBML for example), but to
> me these wouldn't be different enough as the actual interpretation of
> the model is essentially done by the common layer underneath whatever
> extra bits the specific tool is adding in. Or is throwing the model
> through a different numerical integrator, for example, enough to satisfy
> this requirement?

:-)

We did not formalise that far. You are entirely right of course. Let's say
it very much depends on the model. Some can be simulated in many software
and it is easy to get the results using different solvers. Some tricky
models can only be simulated by a couple of software ...

--
Nicolas LE NOVERE, Computational Neurobiology,
EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
Tel: +44(0)1223494521, Fax: 468, Mob: +44(0)7833147074 Skype:n.lenovere
http://www.ebi.ac.uk/~lenov, AIM: nlenovere, MSN: nlenovere at hotmail.com

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• [cellml-discussion] curation of BioModels Database, Nicolas Le Novere, 07/18/2007
  • [cellml-discussion] curation of BioModels Database, David Nickerson, 07/18/2007
    • [cellml-discussion] curation of BioModels Database, Nicolas Le Novere, 07/19/2007
      • [cellml-discussion] curation of BioModels Database, David Nickerson, 07/19/2007
  • [cellml-discussion] curation of BioModels Database, Matt , 07/19/2007
    • [cellml-discussion] curation of BioModels Database, Nicolas Le Novere, 07/20/2007

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