Hi again,
The migration is scheduled to go ahead this weekend. Any messages sent
to the mailing lists during the migration will be queued for delivery
once the migration is complete.
Cheers,
David.
On Tue, May 28, 2013 at 3:20 PM, David Nickerson
david.nicker...@gmail.com wrote:
Hi all
ahead this coming weekend.
Thanks,
David.
On Tue, May 28, 2013 at 3:20 PM, David Nickerson
david.nicker...@gmail.com wrote:
Hi all,
The CellML mailing lists are scheduled to be migrated to a new
infrastructure from 10am - 5pm on Saturday, 8 June 2013 (NZST). During
this time the mailing
Hi all,
The CellML mailing lists are scheduled to be migrated to a new
infrastructure from 10am - 5pm on Saturday, 8 June 2013 (NZST). During
this time the mailing lists will not be available, although any
messages sent to the lists will be queued for delivery once the
migration is complete.
Hi all,
See the message below for some initial details on the programme for
the COMBINE meeting to be held in Paris this September. The website
for the meeting is: http://co.mbine.org/events/COMBINE_2013
Cheers,
Andre.
-- Forwarded message --
From: Nicolas Le Novere
Hi all,
HARMONY 2013 is coming up in a couple of weeks
(http://www.co.mbine.org/events/HARMONY_2013). Two of the CellML
editors will be present (Jonathan Cooper and myself) at the meeting,
so if any of you are planning on attending and have any CellML-related
topics you would like to discuss,
-- Forwarded message --
From: Golebiewski, Martin martin.golebiew...@h-its.org
Date: Apr 29, 2013 8:22 AM
Subject: [Combine-discuss] ICSB Tutorial: Modelling and Simulation of
Quantitative Biological Models on September 4th, 2013
To: combine-disc...@mbine.org
-- Forwarded message --
From: Moraru,Ion mor...@panda.uchc.edu
Date: Mon, Apr 22, 2013 at 9:17 AM
Subject: [Combine-announce] HARMONY travel funds
To: combine-annou...@mbine.org combine-annou...@mbine.org
Dear Colleagues,
This is a reminder that HARMONY 2013 is just one month
Hi all,
OpenCOR (http://opencor.ws) is an open source cross-platform modeling
environment which can be used to organise, edit, simulate and analyse
CellML files on Windows, Linux and OS X
(http://opencor.ws/user/supportedPlatforms.html). OpenCOR version 0.1
is now available from
Hi all,
The 7th International CellML Workshop will be running Monday and
Tuesday next week in Auckland, New Zealand. Details for the workshop
are available at:
http://www.cellml.org/community/events/workshop/2013/, including the
workshop programme. We will be using Google Hangouts On Air to
Hi all,
Lucian Smith will be delivering web-presentation next week on the topic:
Modular Modeling: Standards and Tools. Lucian Smith, Caltech
Friday March 8, 2013 2pm EST (8am Saturday 9th, NZDT)
Model exchange and re-use has been greatly enhanced over the last
decade by the emergence of
Hi all,
I have just updated the workshop webpage with some information on
local accommodation options available at discounted University of
Auckland hotel rates. More information and the booking form is up at:
http://www.cellml.org/community/events/workshop/2013
Also, don't forget to register
Hi all,
The results from the recent editor election have been counted and
validated. The results are as follows:
Mike T. Cooling: 8
Andrew Miller: 8
Randy Thomas:7
To resolve the tie, we will be having a run-off election between Mike
and Andrew to determine the new editor. The
Hi all,
Registration for the 7th International CellML Workshop is now open.
The workshop will be held on the 25 26 March 2013 at the Goldie Room
on Waiheke Island, New Zealand. Please see the workshop page for all
the details:
just a reminder: a week left to vote for a new CellML Editor!
http://goo.gl/XY3ww
On Tue, Jan 8, 2013 at 9:52 AM, David Nickerson
david.nicker...@gmail.com wrote:
Hi all,
The recent call for nominees for CellML Editor resulted in three
eligible nominees, all of whom have accepted
Hi all,
The recent call for nominees for CellML Editor resulted in three
eligible nominees, all of whom have accepted their nomination. The
vote to select a new CellML editor to serve for the period Jan 2013 -
Dec 2015 is now open and available at: http://goo.gl/XY3ww
Voting will close on
Hi all,
Just a reminder that the below call for nominations for CellML editor
closes in a couple of days, so be sure to get your nominations in
before the end of the year!
Cheers,
Andre.
On Wed, Dec 12, 2012 at 7:55 AM, David Nickerson
david.nicker...@gmail.com wrote:
Hi all,
Just
not eligible for re-election. Needless to say, he will
remain involved in the final push to complete the CellML 1.2
specification process.
Cheers,
Andre.
On Tue, Dec 11, 2012 at 9:43 AM, David Nickerson
david.nicker...@gmail.com wrote:
Hi all,
As per the inaugural election for the CellML Editorial
Hi all,
As per the inaugural election for the CellML Editorial Board, Edmund
Crampin's term as editor finishes at the end of this year
(http://www.cellml.org/community/editorial_board). In preparation for
the election of a new member of the CellML Editorial Board we are
soliciting nominations of
2013 Workshop on Interoperability in Scientific Computing
==
In conjunction with ICCS 2013 June 5-7 2013, Barcelona, Spain.
http://www.cs.ox.ac.uk/david.johnson/wisc13/
The 13th annual International Conference on Computational Science (ICCS
2013)
Hi all,
We are pleased to announce that the 7th International CellML Workshop
will be held on the 25th and 26th of March 2013 in Auckland, New
Zealand. More details will be posted to this list and on the website
(http://www.cellml.org/community/events/workshop/2013) as plans
develop.
Cheers,
Please sign up to SED-ML-discuss if you'd like to contribute to this
important decision in the evolution of SED-ML.
(https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss)
Cheers,
David.
-- Forwarded message --
From: Dagmar Waltemath dagmar.waltem...@uni-rostock.de
Date:
*Dear all,
At the 5th International CellML
Workshophttp://www.cellml.org/community/events/workshop/2011/,
we discussed the main list of features that were desirable to have in
CellML 1.2. The CellML Editorial Board has been discussing the
implementation of these features in regard to the next
Hi Michel,
Thanks for the enquiry. Just because this is a completely new type of
application, to me at least, could you please provide a couple of
pointers to some more information. A quick google shows
http://openrave.org/ - is that the simulation tool that you are
referring to? But I can't find
-- Forwarded message --
From: Michael Hucka mhu...@caltech.edu
Date: Tue, Jul 10, 2012 at 6:53 AM
Subject: [sysbio] Reminder: please register for COMBINE 2012
To: sys...@caltech.edu
Greetings, all you systems-oriented, biologically-inclined people:
With COMBINE 2012 only a month
Hi Andrew,
Thanks for your input. I have a couple of comments that are relevant here.
Firstly, as noted on tracker item 55 for CellML 1.2, the editorial
board is just starting on the process of establishing what changes and
additions will go into CellML 1.2. Please don't view the current state
-- Forwarded message --
From: Michael Hucka mhu...@caltech.edu
Date: Mon, Apr 16, 2012 at 12:26 PM
Subject: [sysbio] Reminder: Please register for HARMONY 2012
To: sys...@caltech.edu
For all who are planning on attending HARMONY 2012, please register
soon. Please don't wait
*Doctoral candidate position (PhD student) in Systems Biology/Database and
Information Systems*
Closing date: 1st of May, 2012
Junior research group „Simulation Experiment Management System“ (SEMS) at
the University of Rostock (Germany), Systems Biology and Bioinformatics
group of Prof. Olaf
-- Forwarded message --
From: Nicolas Le Novère le...@ebi.ac.uk
Date: Thu, Mar 8, 2012 at 11:27 PM
Subject: [Combine-announce] HARMONY 2012 registration is open
To: combine-annou...@mbine.org
***
Hi all,
Registration for the 2012 CellML Workshop is now open. Please see
http://www.cellml.org/community/events/workshop/2012 for information
on how to register. Registration for the workshop is free and remote
attendance at the workshop will be possible.
Cheers,
David.
Possibly of interest to some...
-- Forwarded message --
From: Stuart Moodie moo...@ebi.ac.uk
Date: Sat, Jan 7, 2012 at 12:47 AM
Subject: [sbml-discuss] Draft Distrib Package Proposal
To: SBML Discussion List sbml-disc...@caltech.edu
Dear All,
I have been pulling together the
Hi all,
On behalf of the Auckland Bioengineering Institute and the CellML
Editorial Board, I am pleased to announce that the 2012 CellML
Workshop (http://www.cellml.org/community/events/workshop/2012/) will
be held March 12 13 2012 at Goldwater Estate, the University of
Auckland vineyard on
Thanks Lucian.
For CelML model developers and curators, I wrote a new section on using
JSim to help curate the model:
http://physiome.org/jsim/docs/MML_CellML.html#curation
that looks particularly helpful!
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*The CellML Editorial Board (consisting of Jonathan Cooper, Edmund Crampin,
Alan Garny, David “Andre” Nickerson and Poul Nielsen) had their inaugural
meeting on the 8th of December 2011. All members of the board were present.*
David Nickerson was unanimously elected chairman of the editorial
Hi Lucian,
On Sat, Dec 17, 2011 at 7:53 AM, Lucian Smith lpsm...@spod-central.org wrote:
A couple questions. One: is there a defined way in CellML to find the
independent variables? The spec says (about 'initial_value'):
This attribute provides a convenient means for specifying the value
Would it be helpful to encode this information into the model itself, or
semantically, do you want to keep them distinct? I suppose it's edging
into the SEDML territory of 'what you do with a model' instead of 'what
the model is'--I can imagine models where you vary the components of the
(University of Oxford, UK)
Programme Committee
---
David Nickerson (University of Auckland, New Zealand)
Herbert Sauro (University of Washington, USA)
Steve Harris (University of Oxford, UK)
Jonathan Cooper (University of Oxford, UK)
Rutger Vos (University of Reading, UK)
Dagmar
You can reach the person managing the list at
cellml-discussion-ow...@cellml.org
When replying, please edit your Subject line so it is more specific
than Re: Contents of cellml-discussion digest...
Today's Topics:
1. Re: nested components in CellML (David Nickerson
On Sat, Oct 22, 2011 at 10:10 AM, Lucian Smith lpsm...@spod-central.org wrote:
* Maxwell Neal mn...@u.washington.edu [2011-10-21 22:03] writes:
Hi all,
I was wondering - can CellML models have nested components? That is, are
there instances where some model component is a component in
Regarding the link to SED-ML web-tools: Both do work for me right now, maybe
one was temporarily down...
yep - apparently a bit of a problem with the server/DNS that Frank has
now sorted out.
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COMMITTEE
David Nickerson (University of Auckland, New Zealand)
Herbert Sauro (University of Washington, USA)
Steve Harris (University of Oxford, UK)
Jonathan Cooper (University of Oxford, UK)
Rutger Vos (University of Reading, UK)
Dagmar Waltemath (University of Rostock, Germany)
Daniele Gianni
This is maybe something we want to work through and adopt in regard to
the secondary specifications to be included in CellML 1.2.
-- Forwarded message --
From: Mike Hucka mhu...@caltech.edu
Date: Fri, May 20, 2011 at 10:58 AM
Subject: [sbml-discuss] About the upcoming votes on L3
Hi all,
The initial programme for the 2011 CellML workshop is now available:
http://www.cellml.org/community/events/workshop/2011/workshop-programme
You can also find the details required to attend the workshop remotely
using the EVO software:
will be available at:
http://www.cellml.org/community/events/workshop/2011
We look forward to welcoming you to Auckland, New Zealand.
Cheers,
David Nickerson, on behalf of the organisers.
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http
This is the first announcement for the 2011 CellML Workshop
(http://www.cellml.org/community/events/workshop/2011). We plan to
hold a two day meeting at The University of Auckland from 11th-12th
April. If you are interested in attending this event please mark these
dates in your calendar. More
and Astronautics, China
and California State University, USA
* Axel Lehmann, Universitaet der Bundeswehr Muenchen, Germany
* Cristiano Leorato, Rhea, The Netherlands
* Brian Lewis, Vanguard Software Corporation, USA
* Steve McKeever, University of Oxford, UK
* David Nickerson, Auckland
Hi Felix,
The diagrams in the repository are all drawn by hand - using Adobe
Illustrator, I think. The source format is SVG and I think there is a
collection of template objects that are used to create the diagrams
which should be available. Perhaps Dougal might be able to help if
that might be
I think what Alan might be getting at, and something that I am also
concerned with, is that rather than letting the solver do its job,
we are going down the route of replacing the well tested and supported
IDA initial condition solver with something that is perhaps better
suited to the types of
Hi Justin,
Does this also serve notice that there is a version 1.7 release
candidate of the API available for testing as well?
Thanks,
Andre.
On Fri, Mar 12, 2010 at 6:34 PM, Justin Marsh j.ma...@auckland.ac.nz wrote:
Hi all,
The third release candidate for OpenCell version 0.7 has been
I cc:ed Ion as I must confess I didn't follow developments on VCell neither.
Maybe he could state on how things evolved.
Additionally, Richard Adams at Edinburgh University did some work on Java
library development for SED-ML.
It is all at:
Hi Dagmar,
Thanks for your comments! I'll just make a couple of notes inline below...
* Andre said that SED-ML does not yet support everything that we
need to do for simulation and graphing.
I agree that SED-ML still is at quite an early stage and might not cover
everything needed.
I'm considering HDF5 for my storage needs in simulating a CellML model under
multiple parameter scenarios. HDF5 is designed for efficient storage,
retrieval, navigation and subsetting of huge data sets [1], with annotation
[2].
[2]
On Thu, Aug 21, 2008 at 7:02 AM, James Lawson [EMAIL PROTECTED] wrote:
Dear CellML community,
We have had an IRC channel in the past, but I believe that it fell into
disuse. I have been pretty interested in getting it going again for
sometime, so I thought I'd canvass interest. Who thinks
-discussion
--
David Nickerson, PhD
Research Fellow
Division of Bioengineering
Faculty of Engineering
National University of Singapore
Email: [EMAIL PROTECTED]
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Hi all,
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
Hi Justin,
As I mentioned on the tracker item, it would be really good if you could
put together a proposal (perhaps as a document under your cellml.org
member page) which describes exactly what it is you are proposing here.
Something along the lines of what Andrew presented when putting
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--
David Nickerson, PhD
Research Fellow
Division of Bioengineering
Faculty of Engineering
National University of Singapore
Email: [EMAIL PROTECTED
I think this creates a bit of a 'catch-22' situation because we need a
decision process to decide on a decision process. I think that until we
have such a process, we need to stick to the status quo, which has
generally been that we discuss things with the community, and if there
is
just a couple of points arising from these meeting minutes...
Any outcomes from the breakaway session discussing the if and how of
creating an annotated or informative version of the normative 1.2
specification draft?
Under the SBML to CellML conversion, I'm just wondering what
://www.cellml.org/mailman/listinfo/cellml-discussion
--
David Nickerson, PhD
Research Fellow
Division of Bioengineering
Faculty of Engineering
National University of Singapore
Email: [EMAIL PROTECTED]
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://www.cellml.org/mailman/listinfo/cellml-discussion
___
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cellml-discussion@cellml.org
http://www.cellml.org/mailman/listinfo/cellml-discussion
--
David Nickerson, PhD
Research Fellow
Division of Bioengineering
Faculty
Andrew Miller wrote:
David Nickerson wrote:
I think option 1 would be much better than 2.
An alternative might be the RDF and RDF/XML approach? Not too sure what
that implies, but personally I see it as an RDF graph and then the XML
serialisation of that graph. Could we use something like
] On Behalf Of Andrew Miller
Sent: Wednesday, 28 November 2007 9:14 a.m.
To: For those interested in contributing to the development of CellML.
Subject: Re: [cellml-discussion] specification draft and docbook
David Nickerson wrote:
Hi Andrew,
I have just starting looking at using git and checking
http://www.cellml.org/mailman/listinfo/cellml-discussion
--
David Nickerson, PhD
Research Fellow
Division of Bioengineering
Faculty of Engineering
National University of Singapore
Email: [EMAIL PROTECTED]
___
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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 guess if there are
That way is
define the specific inputs and post processing you
wish to define. Generally I find it convenient to define different
levels of models for importing with more and more specifics set at each
level in order to make each model as reusable as possible.
David.
--
David Nickerson, PhD
Research Fellow
For the purpose of presentation math, LaTex substrings get my vote.
the problem with LaTeX math is that it is quite unfamiliar to a lot of
people, whereas most people involved in CellML probably have a
reasonable grasp of at least content MathML if not presentation MathML
also. The
1) can represent MathML in either content or presentation format and
can render MathML in the HTML output using image replacements instead
of expecting that the browser can render MathML (content or
presentation)
is the use of image based equations still required? if people are using
a
mailing list
cellml-discussion@cellml.org
http://www.cellml.org/mailman/listinfo/cellml-discussion
--
David Nickerson, PhD
Research Fellow
Division of Bioengineering
Faculty of Engineering
National University of Singapore
Email: [EMAIL PROTECTED
Hi all,
Not sure if anyone checks the existing API tracker on cellml.org, but I
just filed an issue
(http://www.cellml.org/tools/api/api_tracker/7/pcng_issue_view) on the
configure option requirements when building the API DOM implementation
from source.
Andre.
Hi all,
I was just wondering if there is any possibility at providing a ViewVC
or similar interface to the subversion repository housing the API
implementation
(https://svn.physiomeproject.org/svn/physiome/CellML_DOM_API/trunk/)?
This would make (my) life much easier for browsing around the
/physiomesynctrac/browser/CellML_DOM_API/trunk
While this was put up for demonstration purposes, I 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
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.
My bad,
- At the moment, CellML doesn't explicitly support the rem element
(remainder function in MathML), even though CellML does allow its use (at
the risk of ending in a situation where a model may work fine in a given
CellML tool -- that supports the rem element --, but not in a nother -- that
1) Lower case 'c' in 'cellML': The usual spelling is CellML.
The logo uses 'cellML' - I guess the person to ask is Poul, but I'll use
'CellML' for now.
the logo is a graphic that also has extra writing beneath the word
cellML and three arrows above the 'c', hence the lower case, as well as
Hi Jonna,
Jonna Terkildsen wrote:
Dear Andre,
I appreciate that a change such as this would not be useful for you in
terms of the way you set up your models. But I believe you have to
consider the fact that every person who creates models has their own way
of debugging or checking for
Hi Taishin,
Firstly, I think most people on the team list are also on the
cellml-discussion list so I'm dropping off the CC to the team list. Rest
on my comments inline below...
Taishin Nomura wrote:
Dear all,
We had a discussion on CellML format in response to the comment
made by
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?
Andre.
Andrew Miller wrote:
David Nickerson wrote:
Hi all,
I have just done an update on my working copy of the CellML API C++
implementation
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
to enable CCGS.
ok
/
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--
David Nickerson, PhD
Research Fellow
Division of Bioengineering
Faculty of Engineering
National University of Singapore
Email: [EMAIL PROTECTED
on an issue to send your comment to the list.
Best regards,
Andrew Miller
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--
David Nickerson, PhD
Research Fellow
Division
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
Tracker
AssignedTo: [EMAIL PROTECTED]
ReportedBy: [EMAIL PROTECTED]
on the page
http://bowmore.elyt.com/bugzilla/enter_bug.cgi?product=Using%20CellMLformat=generalhelp
there is a missing space in the second sentence of the Keep Private help
text.
--
David Nickerson
sorry, I was more meaning what it means that you have asked for
something and what we're supposed to do about it?
But, yes - inclusion_CellML_1.1.1 might be better, or maybe
target_CellML_version_1.1.1? for_inclusion_in_CellML_1.1.1 ?
Andrew Miller wrote:
David Nickerson wrote:
What does
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 as the
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
intention to deprecate reaction elements
I think the current use of an embedded stimulus current is due to the
repository being limited to CellML 1.0 models. The correct way to
approach this problem is this: (1) define the mathematical model
independent of parameter values and boundary/initial conditions; (2)
(this is an optional
with it for now.
Your feedback would be appreciated. Thanks.
Regards,
Randall
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--
David Nickerson, PhD
Research Fellow
Division
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 for some input from the wider
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 is that these lists only be used for messages like
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. Thinking about this more we should probably try:
1
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 this more we should probably try:
1) cellml-discussion@cellml.org
2) [EMAIL PROTECTED] - for specific
element of model in the CellML 1.0
namespace and give the user an error and not accept the model?
Andre.
James
Tommy Yu wrote:
David Nickerson wrote:
Hi,
I just tried to load the attached model into the model repository to use
as an example with the graphing metadata specification
In terms of the policy for allocating addresses, we don't want to become
a free e-mail redirection host for anyone on the Internet, but I think
as long as someone at least has some connection with CellML, they should
be allowed an alias (subject to review of what that alias is to ensure
Do we really want to proxy remote repositories? Can we start smaller for now
but keep that in mind?
I think this will be an essential feature of the model repository as we
move forward. We are trying to present model authors with a common
platform for the distribution and archiving of their
and/or build on top of it.
Cheers,
Tommy.
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Faculty
since I can run simulations of the model
fine using my tool based on the CCGS and API and the code generation tab
works fine and gives me the expected C code.
Anyone have any suggestions?
Thanks,
Andre.
--
David Nickerson, PhD
Research Fellow
Division of Bioengineering
Faculty
and the expected outputs.
David.
--
David Nickerson, PhD
Research Fellow
Division of Bioengineering
Faculty of Engineering
National University of Singapore
Email: [EMAIL PROTECTED]
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Jonathan Cooper wrote:
On Thu, Jun 21, 2007 at 02:12:38PM +0800, David Nickerson wrote:
Wilfred Li wrote:
Maybe instead of the star system, which may be open to interpretation at
first sight, an abbreviation or a specific word may be used to represent
its status?
I guess that if you use
http://www.cellml.org/mailman/listinfo/cellml-discussion
--
David Nickerson, PhD
Research Fellow
Division of Bioengineering
Faculty of Engineering
National University of Singapore
Email: [EMAIL PROTECTED]
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No, there are no stars, anywhere, that are on by default. They are all
off by default until someone, probably me, certifies that the model
meets the requirements to get itself a star, or two. Or maybe three.
ok - good to know.
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