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,
>
My guess is to keep it simple:
1) don't prescribe how simulation software is to calculate this -
i.e. don't prescribe a particular mathematical formulation for
representing time delays
2) calculate the variable(s) representing the output of delayed
function separately - e.g. in a separate co
>
>> 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
___
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
Without making a choice at the moment, I want to highlight that the
following are probably the most important aspects to consider in any
of these:
1) can represent MathML in either content or presentation format and
can render MathML in the HTML output using image replacements instead
of e
pache
deathmatch that exists there at the moment.
cheers
Matt
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don't see any
reason to remove it until we have a permanent solution.
cheers
Matt
On 10/1/07, David Nickerson <[EMAIL PROTECTED]> wrote:
> Hi all,
>
> I was just wondering if there is any possibility at providing a ViewVC
> or similar interface to the subversion rep
> Otherwise, Matt wrote:
>
> > ... You might want to scan a document to see what
> > "versions" the model conforms up to, but one of the nice things about
> > pushing these new elements/attributes into new namespaces is that you
> > can still treat a
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:"
> >
> &g
xisting elements and attributes then? So
that when 1.2 comes along 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 (
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 comp
On 8/15/07, David Nickerson <[EMAIL PROTECTED]> wrote:
> Hi Matt,
>
> This makes quite a bit of sense to me.
>
> > So, more concretely, I am proposing that:
> > - we start the notion of a versioned workspace or package.
>
> yep. It would also be good to decide o
ost purposes in our discussions we will be talking about
this abstract version and what it would mean to increase its major or
minor numbers, alpha, beta, or release status etc.
cheers
Matt
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The names of variables should not be pushed into being useful in such
a way. Metadata would be more appropriate to identify variables that
are related.
On 8/8/07, James Lawson <[EMAIL PROTECTED]> wrote:
> Hi all,
>
> I was sitting in bed last night, and this idea came to me:
>
> It would be really
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 misund
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
___
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
> > "model is the same
m people
about it - it might turn out to be a silly proposal.
cheers
Matt
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that goes with
whatever it is that governs new version numbers and the notices we
provide with those.
cheers
Matt
On 7/19/07, David Nickerson <[EMAIL PROTECTED]> wrote:
> > I think that we disagree about how the specification process should work
> > and what it aims to address.
On 7/18/07, David Nickerson <[EMAIL PROTECTED]> wrote:
> Hi Matt,
>
> > I think there does need to be some description of what the parts of a
> > cellml specification version number is and how it relates to the
> > cellml namespace(s).
> >
> > My understa
>
> Furthermore, I don't exactly agree that we need to give 'notice' of
> things by way of formal specifications. Submitting a proposal for the
> CellML community to review is sufficient 'notice'.
>
> In the case of mature standards which require a high level of
> interoperability, a +-1 compatibil
On 7/18/07, David Nickerson <[EMAIL PROTECTED]> wrote:
> Hi Andrew,
>
> To simply delete reaction elements from a version 1.1.1 specification
> seems the wrong approach to me. This means that while a 1.0 model is a
> valid 1.1 model it could be an invalid 1.1.1 model. So the most minor
> version ch
> >>
> > I don't know of any per-issue subscription feature in PCNG, and a web
> > search didn't seem to find anything about this.
> >
> > Perhaps you have details about this?
>
> hI guess I was getting a bit confused about the subscription
> ability with plone on, for example, wiki pages.
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
On 6/26/07, Tommy Yu <[EMAIL PROTECTED]> wrote:
> Matt wrote:
> > I don't understand the purpose of this.
> >
> > It looks like you are inventing a versioning system to implement from
> > scratch.
> >
>
> That's what it looks like, but if y
ttp://www.cellml.org/Members/tommy/BaseRepository
>
> Cheers,
> Tommy.
>
>
>
> Andrew Miller wrote:
> > Matt wrote:
> >>> - Version/Variant
> >>> It already clogged up the system. There is no proper revision control
> >>> mechanism, w
> >
> >> events like the CellML Workshop. There is also the members directory for
> >> everyone who has an account on cellml.org.
> >>
> >
> > But is that available to visitors and other members?
> >
> You can view:
> http://www.cellml.org/Members/member_search_results
> without being logged in (of
> I still don't like the idea of a 'core project team' simply because that
> would require defining what the core project is, and it would appear to
> then give exclusive domain over such aspects to a limited set of people.
> In some sense, my objection is that the CellML 'project' is not strictly
On 6/26/07, James Lawson <[EMAIL PROTECTED]> wrote:
> David Nickerson 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
&g
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
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. Thinking about t
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 do
On 6/25/07, James Lawson <[EMAIL PROTECTED]> wrote:
> What is 'agnositic' and what does it mean here?
It's one of those english terms that is being hijacked in some IT
circles. E.g. platform agnostic :
http://www.e-consultancy.com/knowledge/glossary/20312/platform-agnostic.html
I quite like it be
I think BioModels had every intention of harbouring CellML models too
if we were interested. I'm sure they are listening :-)
On 6/22/07, David Nickerson <[EMAIL PROTECTED]> wrote:
> It might also be worth looking into what the folks over at
> http://www.biomodels.net/ are up to. Given they seem
On 6/22/07, Andrew Miller <[EMAIL PROTECTED]> wrote:
> Matt wrote:
> >> - Version/Variant
> >> It already clogged up the system. There is no proper revision control
> >> mechanism, what we have now is an ad-hoc emulated system.
> >>
> >
> >
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
tem. So this is another reason to just focus on these
levels for now and the rules for making transitions.
cheers
Matt
On 6/22/07, James Lawson <[EMAIL PROTECTED]> wrote:
> David Nickerson wrote:
> >> I have been thinking about this and I think it's worth proposing
> >
TED]> 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 desc
y use-cases. We 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,
>
>
On 6/12/07, Tommy Yu <[EMAIL PROTECTED]> wrote:
> Matt wrote:
> > On 6/11/07, Tommy Yu <[EMAIL PROTECTED]> wrote:
> >> Matt wrote:
> >>> I have concluded that they are now talking about the web site and not
> >>> keywords in general.
> >&
On 6/11/07, Tommy Yu <[EMAIL PROTECTED]> wrote:
> Matt wrote:
> > I have concluded that they are now talking about the web site and not
> > keywords in general.
> >
> > My assumption was that the category field selections are not persisted
> > in the model
. The 2nd sort facility will present several options such as keyword
> > search, species, cell type, etc, and access to more extensive boolean
> > searches (author, year, etc).
> >
> > Cheers,
> > Peter
> >
> > Matt wrote:
> >> On 6/8/07, James L
On 6/8/07, James Lawson <[EMAIL PROTECTED]> wrote:
> So for example someone's trying to build a large model but the only
> components (or data to build components) available are from non-matching
> species?
Yes.
> So the LFID (I looked it up but it went over my head) provides
> a way we can do th
where imports should be helping us to put
circles around species specific submodels.
cheers
Matt
On 6/8/07, James Lawson <[EMAIL PROTECTED]> wrote:
> Actually, I'd venture to say that the majority of them aren't models of
> human biological systems. A lot of them are ani
e
ontology, 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 tha
ned keywords since 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
uld act as a "blessed" list of keywords
> that will serve as a guide 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)
&g
On 6/6/07, David Nickerson <[EMAIL PROTECTED]> wrote:
> James Lawson wrote:
> > David Nickerson 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 fro
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 woul
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 current
b rdf 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
above?). I see this as being more
critical than anything since we don't particularly want people
downloading and trying to update essentially corrupt data.
cheers
Matt
On 5/15/07, Tommy Yu <[EMAIL PROTECTED]> wrote:
> David Nickerson wrote:
> > What I'd like to see is t
pointers to terabytes?
A database backend would make a nice addition to the implementation of
the API as an optional storage backend.
Addressing write-locks would become a more general problem to resolve.
cheers
Matt
On 4/26/07, Andrew Miller <[EMAIL PROTECTED]> wrote:
> Randall Owen wrot
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 inter
ed to simplify them out into dimensionless
yourself?
Also. What does it matter that some software simplifies them out
before multiplicating them? So long as it checks units consistency
prior to simplifying them (if it really needs to do that anyway) then
the result should be the same.
cheers
On 4/21/07, David Nickerson <[EMAIL PROTECTED]> wrote:
> > going back to the following equation Andrew supplied:
> >
> > amount_Na [nmol] = 10^-6 [dimensionless] * conc_Na [nmol / L] *
> > vol[microL]
> >
> > How do you make this more 'valid'? (it is already valid dimensionally
> > and numerical
ensionally
and numerically).
Also, I'm not sure what 'converting units at connections' has to do
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.
dels where practices haven't exposed a
useful structure - e.g. need to bubble up some variables from
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 'prac
decomposing models where practices haven't exposed a
useful structure - e.g. need to bubble up some variables from
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
on listed should also
include the name of the person who made the changes in a
element and the date the document was modified in the
Dublin Core date qualifier element, . The definition
of modification history metadata is demonstrated in Figure 16
see
http://www.cellml.org/speci
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 labe
capture the
mental logical grouping that the author is placing on them ...
e.g.
model-1/generic/1.xml
model-1/parameterisations/1.xml
model-1/parameterisations/2.xml
Anyway, yes. Needs a working group, but also needs a starting document
that at least lists the objectives of this before we all throw
These models should 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:
> Ad
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 t
ble to produce valid metadata for the wider
community. It is in fact where I expect most pressure to add new
properties and datatypes to the global schemas to come from.
> Who will do-it?
> The SBML-team is actually providing XML-schemas for SBML, and this
ary tied to the
> > life cycle or necessary for the intended use of the resource. This
> > relationship might be used to link an article critical of a resource
> > to that resource, a satire of a speech to the original speech, etc."
> >
> > Surely that provides s
Hi Nicolas,
On 3/30/07, Nicolas Le Novere <[EMAIL PROTECTED]> wrote:
On Fri, 30 Mar 2007, Matt wrote:
>>> In those cases, for example bqs, where the object of the reference is
>>> indeterminate or not of interest, it would be helpful to be able to
>>> filte
On 3/30/07, Nicolas Le Novere <[EMAIL PROTECTED]> wrote:
> On Fri, 30 Mar 2007, Matt wrote:
>
> > In those cases, for example bqs, where the object of the reference is
> > indeterminate or not of interest, it would be helpful to be able to
> > filter metadata witho
a need to iterate
over all isDescribedBy predicates and evaluate the objects of these
and reverse engineer these back into some knowledge of what kind of
description this is?
cheers
Matt
>
>
>
> --
> Nicolas LE NOVERE, Computational Neurobiology,
> EMBL-EBI, Wellcome-Trust G
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-sr
On 3/29/07, Nicolas Le Novere <[EMAIL PROTECTED]> wrote:
> On Thu, 29 Mar 2007, Matt wrote:
>
> > We have been working on
> > trying to integrate explicitly with biopax (http://www.biopax.org/
> > states and generics proposal - level 2 was too limiting) in the hope
ple choose their own ontology and just reference
> > it.
> > An example of this practice is in the MIAME project:
> > http://www.mged.org/Workgroups/MIAME/miame_1.1.html
> >
> > About the citations- my memory of this is fuzzy, but I
> > think the original intent
ng 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 inf
ifferent models, 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 abou
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 a
a URL? I think this problem is related to 5. For
example, if the source code for an external component is submitted 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
metadata of a simulation needs to force a version
change (or variant) in a similar way to models so that a mismatch
between graphs or result sets can be detected.
This part of the discussion thread seems to belong on CellML discussion now.
cheers
Matt
In no particular order
1. Review the long term roadmap document and the current development
document (especially those items that sit down the bottom and aren't
being bumped up yet).
2. Identify the exact people resources we need for various jobs.
3. A model reuse group with specific goals and a
ls so that a mismatch
between graphs 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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The outline for what is to be done over the next week is at:
http://www.cellml.org/current-development
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where there seems
to be lack of information about a particular development in progress
or slated for the near future.
cheers
Matt
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Hello all.
Due to the less than enthusiastic use of campfire cellml channels,
I've decided to stop paying for them and go back to good old IRC.
I'll hang out in #bioeng on irc.shlick.net - hopefully others will too.
This will be logged. I'll make the logs searchable/readable so
>From the meeting minutes <<
http://www.cellml.org/meeting_minutes/13.11.2006/>> we have:
"There was discussion about what should be on the CellML roadmap.
Peter noted that Matt was also keen on seeing a roadmap get created.
Alan thought that curation information should be a
t of agendas we come 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
ggles that people would like to bring up off
the cuff.
cheers
Matt
On 10/27/06, Andrew Miller <[EMAIL PROTECTED]> wrote:
> Matt wrote:
> > Hi,
> >
> > I think it will now be beneficial to move CellML meetings to a
> > conference call forum to include contributors o
Reply to those bits I missed last time.
On 11/09/2006, at 4:02 PM, Andrew Miller wrote:
> David Nickerson wrote:
>> If I understand the discussion so far, I agree with Matt and we
>> should
>> be looking at a higher level API than providing methods to manipulate
>> t
On 11/09/2006, at 4:02 PM, Andrew Miller wrote:
> David Nickerson wrote:
>> If I understand the discussion so far, I agree with Matt and we
>> should
>> be looking at a higher level API than providing methods to manipulate
>> the RDF directly.
>>
> Wou
On 6/09/2006, at 4:53 PM, Andrew Miller wrote:
> Matt wrote:
>> The fact there is no standardized API does not mean we invent our
>> own. There are plenty of RDF implementations around and a huge amount
>> of overlap between them. I suggest we find that subset tha
want.
Specifying and implementing our own RDF API does not make sense to me
at all.
cheers
Matt
On 6/09/2006, at 1:44 PM, Andrew Miller wrote:
> Hi all,
>
> The CellML API currently provides two ways to access RDF for the
> model:
> 1) As a single serialised chunk, or
> 2
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