Matt wrote:
>> It seems there is some misunderstanding as to whether we are discussing
>> a proposal to remove the reaction element from CellML or a proposed new
>> specification. I thought it was the latter but you seem to be talking
>> about the former...
>
>
> Both. I think.
>
> So I will try
>> 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
> > If we had our specification in a version control system and tagged
> out
> > releases and release candidates etc, and if we followed a protocol of
> > releasing at least one stable minor release that marks depreciation
> > only, then the following would be the result (in my mind)
> >
> > - The
> >>> Depending on the end-user, it could be a, b and/or c, as well as
> the
> >> fact
> >>> that apart from PCEnv, no other CellML-capable software that I am
> >> aware of
> >>> can deal with CellML 1.1 models. This emphasises my view that we
> have
> >> to
> >>> make the CellML API easy to use an
> > It would definitely be cool to get some basic documentation for these
> > tools. If you have a go at installing CellML2Dot in Linux Alan, let
> me
> > know. I'd like to see Andre's simulator too. How does it differ from
> > PCEnv or COR Andre?
>
> its quite different in that it has no GUI at a
> > > It would definitely be cool to get some basic documentation for
> these
> > > tools. If you have a go at installing CellML2Dot in Linux Alan, let
> > me
> > > know. I'd like to see Andre's simulator too. How does it differ
> from
> > > PCEnv or COR Andre?
> >
> > its quite different in that i
Hi Nicolas,
> Users can currently submit models in CellML and SBML (VCML is coming).
> All the models are then converted to SBML, which is our internal format.
Can you point me to the transforms/code/alogorithm for this?
cheers
Matt
___
cellml-discussi
You can find our converters at:
http://www.ebi.ac.uk/compneur-srv/biomodels/download.html
Matt wrote:
> Hi Nicolas,
>
>> Users can currently submit models in CellML and SBML (VCML is coming).
>> All the models are then converted to SBML, which is our internal format.
>
> Can you point me to the
David Nickerson wrote:
> Matt wrote:
>>> It seems there is some misunderstanding as to whether we are discussing
>>> a proposal to remove the reaction element from CellML or a proposed new
>>> specification. I thought it was the latter but you seem to be talking
>>> about the former...
>>
>> Both.
Matt wrote:
> On 7/19/07, David Nickerson <[EMAIL PROTECTED]> wrote:
>>> Of course. And in the same sense you could simply delete the stimulus
>>> protocol component if you didn't want it. I think the issue is in fact a
>>> curation issue - we are specifying one of our curation 'levels' as
>>> "mod
More generally I think this issue is tapping on the bigger issue of a
core modelling language and specification, and then special use cases,
of which biological modelling would be a particular case of.
Without reactions, we pretty much have that core language.
My inclination is that biological mo
I think what Matt was getting at is that until more people are
publishing models in tandem with CellML or other encodings of their
model, a model curated to level 1 standard will generally not be useful.
It has always been seen that these models are a valuable "historical"
reference to have in
Hi all,
Following discussions with the IT group yesterday, we have arranged to
set up the Bugzilla based CellML tracker for testing on an externally
hosted site. The URL is http://bowmore.elyt.com/bugzilla/
This will not be the final tracker URL (and may not be the final tracker
technology), a
Hi Andrew,
Just to point out that you might want to update the front page to
indicate that this tracker is not in fact maintained at the University
of Auckland.
David.
Andrew Miller wrote:
> Hi all,
>
> Following discussions with the IT group yesterday, we have arranged to
> set up the Bug
>> Still, I have managed to recompile it.
>
> Oops, this got sent too early and I have yet to get CellML2Dot to compile...
> In fact, I have given up and I think it does illustrate the point I made in
> a previous message of mine: documentation, documentation, documentation...
> :)
I was a bit su
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