Dear all,
This is to let you know that OpenCOR 0.1.1
http://www.opencor.ws/download.php has just been released.
A few useful links:
- What is new? http://www.opencor.ws/user/whatIsNew.html
- Supported platforms
http://www.opencor.ws/user/supportedPlatforms.html
-
Hi Andrew,
I don't know for the others, but in my case it would certainly help me
understand your document better and, hopefully, provide you with more useful
feedback, if you were to give us some concrete examples of the type of
models that your specification document targets.
I appreciate that
in Auckland; instead, Alan Garny (based
at
Inria) is working on a complete rewrite which he is calling OpenCOR
(Website: http://opencor.ws).
...
I think Alan will be able to give you more information about OpenCOR and
its
status, such as whether it is suitable as a replacement for particular
Having just downloaded both the debug and release MSVC version of the CellML
API (the ZIP version), it would be nice when extracting the files if those
were to be extracted in a different directory. Right now, both sets of files
are being extracted to cellml-sdk-1.11-Win32-MSVC10. Maybe we could
Hi,
Having just read the minutes, I was wondering whether you guys could clarify
the situation with regards to web service support for PMR2? Tommy said that
REST support is iffy and that's also what I understood from the email he
sent around earlier this week. However, the minutes read that the
Having just read the minutes, I was wondering whether you guys could
clarify the situation with regards to web service support for PMR2?
Tommy said that REST support is iffy and that's also what I
understood from the email he sent around earlier this week. However,
the minutes read that
Hi Andrew,
- Do we really want to go with csymbol? From your document, I
understand that it might be to keep compatibility with CellML 1.0 and
1.1? If so, then I really don't see why you would want that, since
most (all?) of the existing CellML-capable software are unable to deal
with
TeLICeMS is the Text Language for the Input of CellML Models Service
component, a new component/service that Andrew recently added to the API
to parse a text language (i.e. COR like text language, dubbed TeLICeM)
into
CellML, and back. It is based on the COR like text language parsing that
Hi,
Reading through the minutes:
- 1) OpenCell development - enabling the COR-like view (Alan)
It would have been nice to have been told of those bugs in the
COR-like view earlier, but nevermind. At the end of the day, though it would
be nice to have a version of OpenCell that supports
case some assistance from the software in recalculating new consistent
IC's is
invaluable.
Regards,
Randall
-Original Message-
From: cellml-discussion-boun...@cellml.org [mailto:cellml-discussion-
boun...@cellml.org] On Behalf Of Alan Garny
Sent: Friday, 23 April 2010 11:43 p.m
Regarding 5) OpenCell development - update and Justin's Scale work in
particular:
- How much time has been spent on this so far?
- Where can one get a binary version of the demo for Windows, Linux and Mac
OS X?
- What are internal DSLs?
- Where can one get the source code? (Incidentally, I really
Thanks Justin, it does work fine now indeed. One tiny thing regarding the
OpenCell website: you give the link to the complete list of closed tracker
items, but the link is not clickable. Not a big deal, but it would be nice
to change that (I tried by logging in, but I am not allowed to edit the
James Lawson wrote:
We (Catherine, Poul and I) were thinking that there are basically
three places where you'd want to display / store this information
within PMR2: in the metadata itself (thereby allowing it to be
rendered by software, indexed and searched etc.), on the exposure
somewhere
Andrew Miller wrote:
alan.ga...@dpag.ox.ac.uk wrote:
We should be open and therefore allow people to go for whatever license
they want. However, they should be made aware that by doing so, they
take
the risk of their model not being used, etc. This being said, some
authors
might still
From: cellml-discussion-boun...@cellml.org [mailto:cellml-discussion-
boun...@cellml.org] On Behalf Of Dougal Cowan
Sent: 17 December 2009 01:55
To: cellml-discussion@cellml.org
Subject: [cellml-discussion] ABI CellML meeting minutes 2009-12-16
I have put the minutes from this week's
Hi guys,
Just a couple of things regarding the minutes:
- It might be useful, whenever referring to a particular tracker item (as is
the case in the Last week's action items section) to have a link to the
tracker item itself. Not only would it make it more convenient for those of
us who use the
Hi,
A comment about item #1 of this week's agenda (terms of use for CellML
models and associated content hosted on models.cellml.org).
I don't know enough about licensing to suggest one over another. The only
thing I do know, however, is that it is important to ensure that the license
that
Dear all,
First, thanks to the Auckland team for sending the minutes within 24 hours.
I, personally, certainly very much appreciate it!
Second, a couple of comments regarding the minutes:
- Point 3.5 (It was noted that the syntax is slightly different from the
COR language): it's true that the
For what it is worth:
- 7.2: it is CellML to COR-like code that is working, not the other way
around;
- 7.3: regarding the metadata, it should be easy to keep track of them, so
that when we go from COR-like code to CellML they get 'reinserted'. This is
the way COR works for instance. Also, even
anyone.
Dr Alan Garny
University of Oxford, Department of Physiology, Anatomy Genetics
Sherrington Building, Parks Road, Oxford, OX1 3PT, England
http://noble.physiol.ox.ac.uk/people/agarny/
http://cor.physiol.ox.ac.uk/
Note: I am currently in New Zealand and will be back in Oxford on 27
I know that I have already requested that before and that everybody is busy
and everything, but is it really not possible to circulate the minutes of
the last meeting earlier than one day before the next meeting? You guys in
Auckland are obviously up-to-date with what's going on, so it doesn't
Hi Justin,
The first release candidate for PCEnv version 0.6 has been released.
This is the first version of PCEnv since 0.1 that can run on OS X;
there
are also a number of other improvements since PCEnv 0.5.
More information, and the released files themselves, are available at
Hi,
I was wondering whether the minutes could be announced sooner? I understand
that they need to be approved, but still I would expect them to be announced
within 24 hours. If we look at last week's meeting, I received notice of the
minutes on Monday evening (i.e. Tuesday morning NZ time), i.e.
From: [EMAIL PROTECTED] [mailto:cellml-discussion-
[EMAIL PROTECTED] On Behalf Of David Nickerson
On Wed, Nov 12, 2008 at 9:38 PM, Jon Olav Vik [EMAIL PROTECTED] wrote:
David Nickerson [EMAIL PROTECTED] writes:
As for generic generation of HDF5 data structures from CellML models,
I think
A few from the top of my head:
- What is CellML? (i.e. CellML for dummies)
- Why should I use CellML?
- What is the difference between CellML 1.0 and 1.1?
- Are there any CellML tools? (simple link to the CellML tools page?)
- How can I use CellML in my modelling environment? (i.e. CellML API;
Hi Randy,
I hope Justin won't mind me stepping in, though I am sure he will in case I
have got something wrong!
What about us Mac users? :) Any plans for a binary Mac (Intel)
build? I tried downloading the source and 'configure' gave me:
A Mac version is in the work, but it is not quite
Dear Song,
Did you have a look at the installation documentation?
https://svn.physiomeproject.org/svn/physiome/CellML_DOM_API/trunk/docs/
Hopefully, you use one of the Linux systems for which we have some
documentation.
Regards, Alan
From: [EMAIL PROTECTED]
[mailto:[EMAIL
In our case, we would also need to know the units associated with
those
variables. So, again using a C/C++ syntax, we could have something
like:
~~~
int_metre A;
double_millivolt V;
bool_dimensionless T;
~~~
Variables as types:
---
- Do we really want to allow generic types? I am concerned that this
could
lead to models that are not bullet-proof.
The core of CellML can be very generic, and then secondary
specifications can narrow down CellML to a subset of CellML which can
I have recently needed to revive an early CellML 1.0 model of mine which
I need to use within some more recent modelling work. The model is very
complicated it was going to take a long time to separate out the deeply
embedded parameter values and initial conditions in order to make the
model
I believe I know who that is from. I have BCCed that person in case s/he
isn't subscribed to this mailing list. I have talked to that person a few
days ago and this is certainly the kind of things that I, personally, would
like to see in the merging of PCEnv (http://www.cellml.org/tools/pcenv/)
Hi Andrew,
- Section 2.6.1: you may want to be consistent in the way you refer
to
attributes in general. Compare this section with Section 4.2.1 for
example.
- Section 3.3: are we missing 3.3.b and 3.3.c (in
http://www.cellml.org/Members/miller/mapping-1-1-to-draft-
1.2/mapping/toplev
Dear Andrew,
I quite like the structure of your document. Just one thing though: I would
like, at this stage, to suggest references to the official CellML
specification. Indeed, you are no doubt very familiar with the official
CellML specification, but in my case it has been years since I have
CellML Automated Notifications wrote:
Author: agarny
Date: 2008-01-04 00:50:37 +1300 (Fri, 04 Jan 2008)
New Revision: 2054
Modified:
CellML_DOM_API/trunk/CIS/sources/CISImplementation.cxx
CellML_DOM_API/trunk/configure.ac
Log:
64-bit related issues:
- Updated
I don't know much (if anything!) about the solutions offered here, but:
- the current HTML version is nice for viewing from a web browser, but if
you have ever tried to print things out you will no doubt have noticed that
it doesn't look great anymore. I remember that there used to be a 'proper'
Andrew Miller wrote:
Alan Garny 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
So something like (assuming my use of the syntax is correct):
(\+|\-|)[0-9]+(\.[0-9]+|)((E|e)(\+|\-|)[0-9]+)
Note that I have also 'simplified' the exponent part.
I don't think the exponent should be mandatory, however, as this would
break the majority of models in use.
agreed.
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 point (not a comma
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
only
Agreed, but we should then also delete (?) the second point of rule 3.4.5.4
(Proper use of the component_1 and component_2 attributes for the
map_components element).
Alan.
-Original Message-
From: [EMAIL PROTECTED] [mailto:cellml-discussion-
[EMAIL PROTECTED] On Behalf Of
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 to enable those services in configure in order
-Original Message-
From: [EMAIL PROTECTED] [mailto:cellml-discussion-
[EMAIL PROTECTED] On Behalf Of James Lawson
Sent: 06 August 2007 00:40
To: For those interested in contributing to the development of CellML.
Subject: [cellml-discussion] how to units make a difference to
As you know we (Catherine, you and I) spent a bit of time this morning
trying to understand some models. One of the models that Catherine has
been
working on had problems with units. My understanding is that PCEnv
didn't
pick those problems up, while COR did. Correcting the problems,
As you know we (Catherine, you and I) spent a bit of time this
morning
trying to understand some models. One of the models that Catherine
has
been
working on had problems with units. My understanding is that PCEnv
didn't
pick those problems up, while COR did. Correcting the problems,
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
Hi Ely,
I have the feeling that this might a locale issue. In Brazil, the decimal
separator is ,, while it is . in New Zealand (where PCEnv 0.2 is being
developed). So, while 0.3 will be a valid floating point number in, at
least, English speaking country, it won't be in Brazil (and a few other
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 current
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 and provide several examples
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 all - it is
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of
David Nickerson
Sent: 10 November 2006 03:18
To: For those interested in contributing to the development of CellML.
Subject: Re: [cellml-discussion] Quick questions about units...
CellML
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of
Andrew Miller
Sent: 19 October 2006 21:32
To: For those interested in contributing to the development of CellML.
Subject: Re: [cellml-discussion] Binary and source snapshots
for PCEnv on Win32 and
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