David Nickerson wrote:
What is your xml:base URL on the importing model (this is set
automatically to the absolute URI being loaded by the API if you do a
synchronous load, and it isn't already set)? Obviously the process of
resolving a relative URL by an absolute URI is getting the wrong
Original Message
Subject:AUTH48 [SG]: RFC 4708 NOW AVAILABLE
Date: Mon, 9 Oct 2006 16:38:51 -0700
From: rfc-editor@rfc-editor.org
To: [EMAIL PROTECTED]
CC: rfc-editor@rfc-editor.org
IMPORTANT*
Updated 2006/10/09
RFC AUTHOR(S):
--
) :
Area Director(s) :
Best regards,
Andrew Miller
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David Nickerson wrote:
Hi Andrew,
Using the linux snapshot given below I try to load my model (CellML 1.1)
and I get some messages flash up in the status bar about loading the
files and looking for further imports - the only URI I see is that of
the units model which is imported by all
Jonathan Cooper wrote:
Many thanks for your swift and thorough response.
* Andrew Miller [EMAIL PROTECTED] [2006-10-24 22:51]:
Jonathan Cooper wrote:
Hi Andrew,
You may be aware that a group of people are writing a review article
on CellML and associated tools, for a special
David Nickerson wrote:
Hi all,
I have just been looking through the graphing metadata specification
(http://www.cellml.org/specifications/metadata/graphs) and have a couple
of questions (pretty much due to my continuing RDF ignorance). This
specification seems to have dropped behind the
Hi all,
The RFC defining the correct media type for CellML documents to be
application/cellml+xml has now been published, as RFC4708.
It can now be viewed at ftp://ftp.rfc-editor.org/in-notes/rfc4708.txt.
Best regards,
Andrew Miller
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David Nickerson wrote:
Therefore, you have to be aware of the relationship between RDF/XML and
the RDF data model, and make sure you put your rdf:ID in the right place
(as with any other attribute in RDF).
ok - I think something just dropped into place. So in this case what I
would
with the
release candidate are identified, the API will be released. Please
report any bugs you find at http://www.cellml.org/tools/api/api_tracker,
or to this list, or directly to [EMAIL PROTECTED]
Best regards,
Andrew Miller
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David Nickerson wrote:
Andrew Miller wrote:
David Nickerson wrote:
I just grabbed the CellML API 1.0rc1 and found that it does not have a
configure file. The README that comes with the distribution says to
follow the instructions in the INSTALL which talk about the standard
enhancements to the CellML, DOM. MathML
and CCGS implementations, to fix the performance problems seen in the
CCGS with 1.0rc1.
Best regards,
Andrew Miller
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Matt wrote:
Sure. I replied to that earlier thread last night.
I haven't seen your post on the list, so I guess it got lost somewhere
(the mailman has been delaying my messages for rather random periods of
time recently, so I am guessing there is some bottleneck that could also
be timing
Hi all,
I have put some more work into getting cctools to compile on OS X (the
Mac port needs this, in order to be able to run the generated code). We
can't use the official binaries for licensing reasons (and also, for
portability reasons, see below).
There are numerous known problems
being lost when using CORBA
(due to CORBA message size limits being exceeded) was fixed.
You can download the source code for the CellML API 1.0rc3 from
http://www.cellml.org/tools/api/downloads/cellml-dom-api-core-implementation/releases/1.0rc3
Best regards,
Andrew Miller
Bob Gustafson wrote:
Are the models/metadata/simulation-results in any sort of Version
Control System (Subversion comes to mind)?
Models are assigned a 'version' and a 'variant', and the model curation
workflow means that models are never changed or deleted, instead a copy
of the model
David Nickerson wrote:
I have attached two implementations of the same equation, y = sin(x).
In the case where the equation is given in a component within the same
model as its parent in the encapsulation hierarchy (import_bug-ok.xml)
everything works fine and CellML2C gives me the expected
David Nickerson wrote:
Hi all,
Just wanted to see what people think about using the BioModels
qualifiers (http://biomodels.net/index.php?s=Qualifiers) in CellML
models? i.e., following the SBML annotation specification (see section 6
of the SBML level 2 version 2 specification).
The
difference as to how this case is handled.
Best regards,
Andrew Miller
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protect the utility of CellML as a model interchange format?
5) Does the proposed approach fit well with the design of CellML?
Thanks and Best regards,
Andrew Miller
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) CellML with external (non-standardised) code.
Best regards,
Andrew Miller
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David Nickerson wrote:
ECMAScript is not practical for use in modelling, because it is an
interpreted, non-typed language, which necessarily means that it cannot
be compiled and will be slower than compiled code.
But CellML is an language for the description and exchange of
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 validation. With procedural code this amounts to
passing
Hi,
As discussed at the last CellML meeting, there are some models which
reference both the paper about the model, and a reference about the
biology. Since there is no way to determine between them, this creates
problems for CellML metadata processing tools which want to identify the
paper
David Nickerson wrote:
Hi Andrew,
Are you thinking that you'd have metadata like when variable IStim is
non-zero reduce maxDt to x or more like when variable IStim is
non-zero system becomes stiff and let the software decide the best way
to handle that?
I was actually thinking more along
David Nickerson wrote:
I am working on developing a CellML model (using external code) of
transcriptional control in yeast which is 23 MB in size. I hope to
eventually do a similar thing for organisms which have much more
complicated sets of interactions, in which case this size may grow
Hi,
I have been wanting to use some functionality present in the CellML Code
Generation Service, for a quite different type of problem (not a system
of ODEs). The problem is, the functionality isn't exposed. I think there
is actually quite a lot of useful functionality in the CCGS which could
Randall Owen wrote:
In message [EMAIL PROTECTED] CellML Discussion List
cellml-discussion@cellml.org writes:
Hi,
I am working on developing a CellML model (using external code) of
transcriptional control in yeast which is 23 MB in size. I hope to
eventually do a similar thing for
Hi,
I am looking at refactoring the CCGS into several components, as
discussed in an earlier e-mail. As part of this, I am looking at how I
can separate out the language specific parts of code generation. At this
stage, I am focusing on how expressions get generated, rather than
entire
at the level of the format specification.
Best regards,
Andrew
Andre.
Andrew Miller wrote:
Hi,
I am looking at refactoring the CCGS into several components, as
discussed in an earlier e-mail. As part of this, I am looking at how I
can separate out the language specific parts of code
with CellML, and any suggested improvements (or patches :) ).
Best regards,
Andrew Miller
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Jonathan Cooper wrote:
* Andrew Miller [EMAIL PROTECTED] [2007-04-29 23:51]:
I have defined a file format specification, called MAL (or
MathML-language mapping) designed to contain all the information needed
to generate expressions for a specific programming language. I would
welcome
be edited in something
other than a text editor. However, they do not give the same flexibility
as the other options would.
I welcome any opinions on what approach would be best.
Best regards,
Andrew Miller
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Best regards,
Andrew Miller
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are encouraged to upgrade.
Should you find a bug in PCEnv, please report it at
http://www.cellml.org/tools/pcenv/bugs .
Best regards,
Andrew Miller
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regards,
Andrew Miller
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Tommy Yu wrote:
Hi,
I have written down some of my thoughts on how the model repository could be
put together.
http://www.cellml.org/Members/tommy/repository_redesign.html
It is still a pretty rough document. The usage example section gives a rough
outline on what I see people might be
rules for the list.
5) Transitional measures for the Auckland group:
a) A list [EMAIL PROTECTED] will be created.
b) All members of the list [EMAIL PROTECTED] will
be subscribed to [EMAIL PROTECTED]
c) Andrew Miller will be the initial designated administrator of
[EMAIL PROTECTED]
d
David Nickerson wrote:
Hi Randall,
Two quick points. PCEnv is an Auckland tool and as discussed previously
it should be kept quite distinct from the community sections of
cellml.org - i.e., there shouldn't be a common tracker for PCEnv and the
specifications and cellml.org etc.
I
, and the people who make the final decision
can do so on the basis of discussions (which may include them) on the
list. I don't see any need for a second mailing list for this.
Andre.
Andrew Miller wrote:
Hi,
There has been some discussion recently about how best to handle local
CellML
David Nickerson wrote:
Andrew Miller wrote:
Hi,
At the Auckland CellML meeting today, we discussed the possibility of
changing to a better tracker and moving some of the mailing list
discussions onto that tracker. Everyone at the meeting agreed with this
idea, so I am now looking
David Nickerson wrote:
Andrew Miller wrote:
David Nickerson wrote:
Hi Andrew,
I think this is an excessive response to a very minor problem. I very
easily see this evolving into many separate and distinct local
communities with little interaction.
The intention
David Nickerson wrote:
Andrew Miller wrote:
David Nickerson wrote:
From what I gather, publicity. We need some way to direct people's
attention to our intention to deprecate reaction elements.
sure - but its still not clear to me if 1.1.1 is making clear our
David Nickerson wrote:
Correct me if I am wrong, but I believe that nothing in the text of the
CellML 1.1 specification says that reactions will or will not be
deprecated in any future version of CellML, and therefore there is no
need for an erratum to CellML 1.1 (and indeed, such an
David Nickerson wrote:
I think that we disagree about how the specification process should work
and what it aims to address. I see a given version of a CellML
specification as being a 'protocol' which both tools and model authors
speak, therefore allowing them to interwork.
All I'm
/ security issue options), and you also have
the option when commenting on an issue to send your comment to the list.
Best regards,
Andrew Miller
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to change this - I am just not
sure how to make it less confusing - perhaps once we have at least one
duplicate in statistics for the database it won't be as confusing?
Best regards,
Andrew
Thanks,
David.
Andrew Miller wrote:
Hi all,
Following discussions with the IT group yesterday
David Nickerson wrote:
What does this mean?
I guess that CellML_1.1.1 is a bad name for the flag. Flags are a
generic facility in Bugzilla which are requested and then granted or
denied. I intended for this to be used for proposals to be requested for
CellML 1.1.1 (i.e. suggested for a
for your feedback on PCEnv.
Best regards,
Andrew
Thanks again.
From: Andrew Miller [EMAIL PROTECTED]
To: CellML Discussion List cellml-discussion@cellml.org
CC: [EMAIL PROTECTED]
Subject: Re: [cellml-discussion] CellML technical question.
Date: Wed, 01 Aug 2007 09:30:26 +1200
Alan Garny wrote:
Again, this is a feature that it would be useful to be able to turn on
and off. However I think in most cases the software will not be smart
enough to figure out what the units should be.
Wrong, it can easily be done. I was about to work on that in COR when Peter
got
David Nickerson wrote:
Hi all,
I know Andrew and I have discussed this in the past but just thought I'd
raise the issue here and see if anyone has any ideas.
I have just begun trying to build the C++ API implementation using the
latest svn trunk code. I'm using a freshly installed Fedora
Alan Garny wrote:
David Nickerson wrote:
Andrew Miller wrote:
David Nickerson wrote:
Thanks Andrew. So just to make sure I'm getting it right, in the trunk
code CCGS is now a service sitting on top of CaVAS, MaLaES, etc.,
right?
Thats right, so you need
9.4.1.2:
* An import element may not contain any pair of components which are
related by encapsulation.
Please send any comments you have about this proposed changed to
[EMAIL PROTECTED]
Best regards,
Andrew Miller
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Hi,
A few review comments for this commit are inline.
CellML Automated Notifications wrote:
Author: agarny
Date: 2007-09-19 05:47:09 +1200 (Wed, 19 Sep 2007)
New Revision: 1755
Modified:
pce/trunk/chrome/content/controls/graph.xml
pce/trunk/chrome/content/controls/model.xml
Hi all,
The CellML Specification does not define the format in which real
numbers will be represented at all (it just says, for initial_value:
The value of the |initial_value| attribute may be a real number or a
variable). The MathML specification defines
A real number is presented in decimal
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 version CellML, including whether we would put all elements
for the next version of CellML in a completely different namespace, or
David Nickerson wrote:
Therefore, I think that we need to restrict it down to something like
(in regular expression syntax):
(\-|)[0-9]+(\.[0-9]+|)(E(-|)[0-9]+|e(-|)[0-9]+|)
In other words:
An optional - , followed by 1 or more digits from 0 to 9, followed by
an optional decimal
Randall Britten wrote:
Don't you think we should put a test in somewhere for this? (Perhaps a
manual test for it is already in Litmus?).
It is already in Litmus, although we could probably do automated testing
of PCEnv too (it requires running Javascript as part of the tests, but
Mozilla
Matt Halstead wrote:
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 model as say 1.1 even if it contains
David Nickerson wrote:
Thanks Matt. Would be nice to get a permanent solution soon...
Hi Andre,
This is one of a list of services that I also would like to have. I have
discussed this with Randall recently and I believe he intends to follow
them up one-by-one with IT:
1) Bug tracker
of the markup (although perhaps easier than
XML, depending on taste and familiarity with each markup language).
Best regards,
Andrew
On 7/11/2007, at 2:16 PM, Andrew Miller wrote:
Hi,
One issue which came up at today's meeting for people at Auckland
involved with CellML is how we will represent
Matt wrote:
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.
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).
Hi Randall,
Pros:
-Widely used, lots of user familiarity.
Although MediaWiki mark-up is similar to MoinMoin and other wiki
software
Alan Garny wrote:
git is also a distributed version control system - the two tools have a
fairly similar conceptual model in terms of how they work, with a lot of
flow of ideas between the too tools. I have found git slightly faster
and a bit more extensible (and with a larger set of commands
Alan Garny wrote:
Andrew Miller wrote:
Alan Garny wrote:
There are viewable web interfaces for git - see the gitweb at e.g.
http://repo.or.cz/w/cellml-draft-
miller.git?a=tree;h=normative;hb=normative
How does it work?
Using Opera, if I click on blob for abstract.xml, I
David Nickerson wrote:
Hi Andrew,
I have just starting looking at using git and checking your current
draft of the specification. I have made a few changes and attach the
patch (generated with git diff -p andre.patch). Not really sure the
best way to do things in order to share changes - I
David Nickerson wrote:
Hi Andrew,
I have just starting looking at using git and checking your current
draft of the specification. I have made a few changes and attach the
patch (generated with git diff -p andre.patch). Not really sure the
best way to do things in order to share changes -
Hi all,
The CellML 1.1 specification says:
6.5.3 Groups must not imply metadata information
Modellers must not use CellML groups to associate properties or
classification information with sets of components. The metadata
functionality is the proper method for making such associations. This
Hi all,
There have recently been some discussions of changes which would
drastically break forwards or backwards compatibility of CellML (for
example, changing the way that connections work).
I think that it is important that we come to some consensus on what the
policy for inter-version
wishes
Poul
On 2008 Jan 09, at 11:58, Andrew Miller wrote:
Hi all,
There have recently been some discussions of changes which would
drastically break forwards or backwards compatibility of CellML (for
example, changing the way that connections work).
I think that it is important
Randall Britten wrote:
I don’t think we would need attribute values like “public_private” or
“both”, since I think “public” access should imply “private” access,
similar to say c++ or Java’s use of those terms.
The usage of the words public and private in CellML is conceptually
different
-
[EMAIL PROTECTED] On Behalf Of Andrew Miller
Sent: Thursday, 10 January 2008 1:39 p.m.
...
For example, the total sodium current in the Beeler-Reuter model is
meaningless to the parts which contribute to the sodium current, and
isolating them properly from each other helps prevent
Hi all,
I have had a look through the proposals at
http://sbml.org/wiki/SBML_Level_3_Efforts . I don't know if there is a
draft for the 'core' of SBML level three yet, although it seems the plan
is that it will not change much from level 2.
I think that under the current approach of splitting
Hi all,
I have recently been working on developing an unofficial 'base'
normative CellML specification to provide something off which proposed
changes can be based and merged into.
The aim of this unofficial draft specification is to provide a
minimalistic, and normative, specification of all
-discussion-
[EMAIL PROTECTED] On Behalf Of Andrew Miller
Sent: 16 January 2008 23:30
To: For those interested in contributing to the development of CellML.
Subject: [cellml-discussion] Base normative CellML Specification for
further work
Hi all,
I have recently been working on developing
Hi all,
I filed a tracker item on where RDF/XML should be allowed in CellML
Infosets.
https://tracker.physiomeproject.org/show_bug.cgi?id=331
Please feel free to comment on the tracker item.
Best regards,
Andrew
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Hi all,
To aid in working out what features we should include in CellML 1.2, I
have been looking into one of the major difficulties with creating
re-usable metabolic models at the moment: that to compute a derivative,
you need to know all the fluxes, but when a model is extended, new
fluxes
if connections
don't have directionality, then it makes no sense in the language to say
that a connection is from A to B, as opposed to from B to A, and we
wouldn't want to force users to duplicate information and provide both
directions.
Best regards,
Andrew
Cheers,
Quoting Andrew Miller [EMAIL
Michael Cooling wrote:
because if connections don't have directionality, then it makes no
sense in the language to say
that a connection is from A to B, as opposed to from B to A, and we
wouldn't want to force users to duplicate information and provide both
Oops I didn't mean to
Michael Cooling wrote:
if both state variables have the same initial values and
rates (which they would...
why should they have the same initial values? I agree if they did then
it makes
no difference to the correctness of the model but it seems very possible to
create a model of
David Nickerson wrote:
Hi Andrew,
This looks quite intriguing. As you mention later in this thread I
currently take the approach of adding an extra real scalar term and
exposing that as a way to hook future (in my case) currents into ion
concentration rate equations. Such and approach
Hi all,
I am proposing that in CellML 1.2, we make connections between variables
undirected (that is, we don't have an in or out on public or private
interfaces for variables).
I am also proposing that we remove the map_components element and move
the component_1 and component_2 attributes
Hi all,
I have now defined a mapping between CellML 1.1 and one draft of CellML
1.2. I have put this up at:
http://www.cellml.org/Members/miller/mapping-1-1-to-draft-1.2/mapping
It currently has all the mappings from 1.1 to a particular 1.2 draft,
although it may be missing some of the reverse
Alan Garny wrote:
Hi Andrew,
I have now defined a mapping between CellML 1.1 and one draft of CellML
1.2. I have put this up at:
http://www.cellml.org/Members/miller/mapping-1-1-to-draft-1.2/mapping
It currently has all the mappings from 1.1 to a particular 1.2 draft,
although it may
Hi all,
As has been previously discussed on this mailing list, grouping in the
general sense can be used to represent information such as containment
which would more appropriately be treated as metadata and represented in
RDF/XML. The overall process of moving this information out into
Hi all,
There are a number of items in the CellML tracker regarding decisions
about the next version of the CellML specification, which have been
discussed in the past and around which consensus seems to have been
reached, but on which we have yet to declare a final decision. By making
a
Dear all,
Based off the UML diagram at
http://miase.cvs.sourceforge.net/*checkout*/miase/miaseOM/miaseOM/miaseOM.pdf?revision=1.5
, I notice that the UniformTimeCourse UML class makes the assumption
that the model is being evaluated across a time variable (in other
words, that time is
Hi all,
One issue which has recently been discussed amongst those of us working
on CellML tools is the best way to handle models which require systems
of equations to be solved efficiently. For example, if a model has
equations like:
f1(a, b, c) = 0
f2(a, b, c) = 0
f3(a, c) = 0
f4(b, c, d, e)
Randall Britten wrote:
However, in general, I haven't been able to find an efficient
(polynomial time) algorithm to compute this break-down (but I also
haven't yet proved that the problem is NP-complete, so there may be a
polynomial time solution even if P != NP).
Hi Andrew
If possible,
Hi all,
I have spent some time looking into how we might be able to represent
stochastic models in CellML. This is something that would be useful to
ensure we have properly contemplated for CellML 1.2. I have pasted in
the notes I wrote on this below.
Please let me know if you have any
James Lawson wrote:
Hi Andrew,
I have to confess I really didn't understand Erik Butterworth's email.
However this is a forward of a reply I just got from Frank Sachse, the
original model author.
I think he has a point - it seems that Jsim does do the dimensional
conversion but PCEnv
' setting for the integrator in Jsim will not run the model -
the CVode integrator must be selected manually.
Kind regards,
James Lawson
Erik Butterworth wrote:
On Thu, 29 May 2008, Andrew Miller wrote:
I think James had something more along the lines of:
I_inter_fibro = 10^6
Randall Britten wrote:
Hi
While I think that the approach you are taking to use the CellML api via
CORBA is probably your best option at the moment, there is one other option
to consider. There is a CellML-API that was developed in Java some years
ago. Sarala uses this for her work. While
Hi all,
I have been looking into how we could define a typed lambda calculus
system in CellML, and have written up a document to collect ideas on this:
http://www.cellml.org/Members/miller/outline-of-a-typed-lambda-calculus-system
This document does not yet aim to be a formal specification, but
Randall Owen wrote:
Andrew:
This seems like a very good idea. How much work has actually been done in
this area?
Hi Randy,
I presume you are only asking about work in relation to CellML? The
document I linked is pretty much it in terms of actual written up
documents... once we allow
Alan Garny wrote:
Hi Andrew,
I have been looking into how we could define a typed lambda calculus
system in CellML, and have written up a document to collect ideas on this:
http://www.cellml.org/Members/miller/outline-of-a-typed-lambda-calculus-
system
This is a good starting
song zhen wrote:
Hi Alan,
I have read those documentations, but I am not familiar with this kind
stuff, and the problem is that I don't really know what kind of the
Linux systems I am using. Here is the information for my iMac: Mac OS
X Version 10.4.11 (Tiger), Fink installed. Could you tell
Hi all,
I have recently coded up a prototype designed to demonstrate how a
program to convert from SBML to CellML might work. This prototype is
written in Ruby using the REXML XPath parser, which was rapid to develop
but makes it very slow to run - the intention is that once the
algorithms
Hi all,
In response to a request by Poul Nielsen, I have produced a model
demonstrating how this functionality might be used.
type_library.cellml is the beginnings of a type library, which provides
a complex number type and some other types needed to support it. The
complex number type is
Hi all,
I have created a tracker item to discuss the possibility of using a
functional programming language to express models. Please see my
description of how it could be done, add any comments you have on the
idea there.
Best wishes,
Andrew
___
Andrew Miller wrote:
Hi all,
I have created a tracker item to discuss the possibility of using a
functional programming language to express models. Please see my
description of how it could be done, add any comments you have on the
idea there.
My apologies, I missed out the tracker item
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