up with.
cheers
Matt
On 10/30/06, Nigel Lovell [EMAIL PROTECTED] wrote:
Dear All,
Thanks for also CCing us in Sydney. We would certainly be happy to
contribute to a conference call once every two months. We have been
continuing to develop tools for parameter optmisation of CellML models
or result sets can be detected.
This part of the discussion thread seems to belong on CellML discussion now.
cheers
Matt
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to
a repository and becomes licensed according to that, then the URL
should probably be related to that. So I think ultimately the domain
that wants to guarantee that the source is perpetually available
should be the domain that forms the base of the URL.
cheers
Matt
On 3/18/07, Andrew Miller [EMAIL
On 3/19/07, Andrew Miller [EMAIL PROTECTED] wrote:
Matt wrote:
I have often thought referencing external code through a clearly
defined interface would be useful, and mostly because procedural code
is another natural way to solve problems. But I have always banged my
head up against
, and whether we should be complimenting bibliographic
data with pubmed Ids and the like.
cheers
Matt
On 3/29/07, Andrew Miller [EMAIL PROTECTED] wrote:
Hi,
As discussed at the last CellML meeting, there are some models which
reference both the paper about the model, and a reference about
in your picture :-)
thanks again
cheers
Matt
On 3/29/07, Melanie Nelson [EMAIL PROTECTED] wrote:
Wow, I haven't posted to this list in a long time...
But I feel compelled to give a little advice as
someone who's spent a lot of time integrating
biological information and therefore has made a lot
, there is
a CellML paper published in one that is not), so the
model needs to handle full citation info, too. The BQS
model handles both, and then some, which is why we
chose it.
Hope this is helpful,
Melanie
--- Andrew Miller [EMAIL PROTECTED] wrote:
Matt wrote:
I don't think
On 3/29/07, Nicolas Le Novere [EMAIL PROTECTED] wrote:
On Thu, 29 Mar 2007, Matt wrote:
Can you explain in more detail or point to explanations of
bqmodel:isDescribedBy?
You can find some explanations at:
http://www.ebi.ac.uk/compneur-srv/miriam-main/mdb?section=qualifiers
So
) didn't
interest you so much.
cheers
Matt
--
Nicolas LE NOVERE, Computational Neurobiology,
EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
Tel: +44(0)1223494521, Fax: +44(0)1223494468, Mob: +44(0)7833147074
http://www.ebi.ac.uk/~lenov, AIM:nlenovere, MSN:[EMAIL
)1223494468, Mob: +44(0)7833147074
http://www.ebi.ac.uk/~lenov, AIM:nlenovere, MSN:[EMAIL PROTECTED]
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Matt
On 4/3/07, Nicolas Le Novere [EMAIL PROTECTED] wrote:
You will always need to pull apart the 'URI' (table2 MIRIAM document)
to retrieve the datatype and identifier.
Well, yes you have to recognise what belongs to the data-type and what
belong to the identifier. But you do that all the time
use imports so that we can at least point to
the generic model and then the specialised parameterised ones. But
that won't work right now because the repository can't handle 1.1
models.
cheers
Matt
On 4/12/07, James Lawson [EMAIL PROTECTED] wrote:
Addendum:
The model in the repository
On 4/12/07, James Lawson [EMAIL PROTECTED] wrote:
Matt wrote:
This scratches a couple of important pending issues:
1) I feel the term 'variant' is odd (even though I originally
suggested it). It was intended to mean that the model labelled as a
variant is a variation of the one
encapsulated variables.
- methods to automatically compose simple reuse such as hooking up a
different set of parameter values to a generic model.
I guess I am pointing towards the 'practical application' of reuse here.
cheers
Matt
Each of the above have very specific meanings within
encapsulated variables.
- methods to automatically compose simple reuse such as hooking up a
different set of parameter values to a generic model.
I guess I am pointing towards the 'practical application' of reuse here.
cheers
Matt
Each of the above have very specific meanings within the software
with this discussion - that only ensures value consistency in the
assigning of values to inputs and outputs of components and has
nothing to do with ensuring units consistency inside the math.
cheers
Matt
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So one way out to avoid having to hope that software does the right
thing is to make it compulsory that there is units consistency for
each dimension across all variables (defined in variable elements) in
a CellML component so that the only units conversions that need to
take place are at the
description elements for
each of them.
If you send me a component that has been decomposed from a reaction
element using Andrew's script, then I'll add in the rdf metadata in
the way I was thinking and post it back here.
cheers
Matt
On 5/17/07, James Lawson [EMAIL PROTECTED] wrote:
Dear All
Some of those are subsets of others. You might want to generalise a
bit more and then fit some of the useful specifics into that. I would
be interested to see what you come up with.
cheers
Matt
On 6/6/07, James Lawson [EMAIL PROTECTED] wrote:
Hi folks,
Tommy is currently working on a sorting
On 6/6/07, David Nickerson [EMAIL PROTECTED] wrote:
Would I be correct in assuming that these terms will be key words added
to the model metadata and that the division into categories on the main
repository page will be assembled from queries on each of these
predefined key words?
I would
to what should be added to the model, and as a
broad category filter for the main repository listing. Users would still be
able to add or search by other keywords (from the advance search interface)
if they wish.
Tommy.
Matt wrote:
On 6/6/07, David Nickerson [EMAIL PROTECTED] wrote
this
is the best input for trying to organise an ontology of keywords
(including synonyms etc that come up).
cheers
Matt
On 6/7/07, Peter Hunter [EMAIL PROTECTED] wrote:
Dear All,
The intention of this discussion was to decide on a list of items for a
drop-down list of predefined terms that would
, not the other way around.
On 6/8/07, James Lawson [EMAIL PROTECTED] wrote:
Peter Hunter wrote:
It may be that the additional key words
should adhere to terms from an ontology as Matt suggests and should
use the
predictive completion facility that Andre suggests.
Will we use the Physiome
discussed a few weeks ago that if this
environment is going to provide the security layer, then there needs
to be a relationship between this and the subversion repository at
quite a detailed level.
cheers
Matt
On 6/21/07, Tommy Yu [EMAIL PROTECTED] wrote:
Hi,
I have written down some of my
] wrote:
Matt wrote:
Hi Tommy,
I found the document seemed to be too far ahead of itself. I also
didn't find any of the pros and cons very compelling because they
don't address specific problems and those problems are not described.
1) What are you actually trying to achieve? It would
On 6/22/07, Tommy Yu [EMAIL PROTECTED] wrote:
Matt wrote:
Hi Tommy,
Can you continue to update/fill out your document as well as begin
associated proposals with information contained in the replies people
are submitting. The goal of this process is a scoping document with
associated
This seems like it's going in circles. I'm not really sure why anyone
would want to contact us personally with something they didn't want to
send to the list. Thinking about this more we should probably try:
1) cellml-discussion@cellml.org
2) [EMAIL PROTECTED] - for specific enquiries that you
On 6/25/07, David Nickerson [EMAIL PROTECTED] wrote:
Matt wrote:
On 6/25/07, David Nickerson [EMAIL PROTECTED] wrote:
Matt wrote:
This seems like it's going in circles. I'm not really sure why anyone
would want to contact us personally with something they didn't want to
send to the list
This is my view of where things should be heading:
The main impetus for this thread is moving the cellml.org site
forward. In this sense I would like to see a description of what it
currently does and what features have been informally slated.
Then I'd like to see a document that re-writes these
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
modelling is a specification of
minimum required annotation of mathematical models using the 'core'
language.
Poul's turn.
On 7/20/07, James Lawson [EMAIL PROTECTED] wrote:
David Nickerson wrote:
Matt wrote:
It seems there is some misunderstanding as to whether we are discussing
a proposal
Semantically I think this is fine and theoretically does not change
the meaning of connections.
It's important to highlight that software developers will need to:
1) relax the validation constraint for the existing rule (i.e. only
one connection between any two components)
2) understand that
On 8/11/2007, at 10:27 AM, Randall Britten wrote:
Hi all
Another option to add to the mix: using a Wiki. In this case, I would
specifically suggest MediaWiki (a la Wikipedia).
Pros:
-Widely used, lots of user familiarity.
-Easy collaboration: edits done via web interface.
-Built in
More generally, I think XML source formats should be avoided if
possible.
Just wondering if you can explain your reasoning for this?
reading plain text in a text editor is more pleasant
reading diffs of plain text is more pleasant
___
specific types of metadata; the most obvious implication
of that is you would also need to write an RDF Schema library also.
So the public API considered here may be very small - consume or
produce triples.
cheers
Matt
On 1/05/2008, at 9:49 PM, David Nickerson wrote:
Hi Justin,
As I mentioned
and its interpretation we only really have
1.2 and 1.1 to deal with.
cheers
Matt
On 9/19/07, Andrew Miller [EMAIL PROTECTED] wrote:
Hi all,
At the break-away session on the versioning strategy for CellML (which
followed the Auckland CellML meeting today) we discussed the future of
how we would
On 9/19/07, Andrew Miller [EMAIL PROTECTED] wrote:
Matt Halstead wrote:
Andrew was opposed to the idea of changing all the namespaces, and
suggested changing the namespace of a particular element in only some
circumstances:
I agree very strongly with this. It would make writing out
deathmatch that exists there at the moment.
cheers
Matt
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