If you go to their actual site (http://cave.ucalgary.ca/), the emphasis
seems to be on the auditorium used for 3D viewing.
I ran the 3D viewer from their site. The demo's are not anywhere near
as impressive as the article makes out: just viewing a 3D heart. The
viewer on the site is not
A separate phylogeny attribute is probably also needed.
It is not clear whether all the models are meant to pertain to human
physiology. One example certainly does not: # Baylor, Hollingworth,
Chandler, 2002, 'Comparison of Simulated and Measured Calcium Sparks
in Intact Skeletal Muscle
Andrew Miller wrote:
Hi,
...
I would recommend Bugzilla (Randall also mentioned JIRA, but it seems to
be a commercial product, and price aside, if we can't review the tracker
source code I'm not sure we should trust it with our data).
Jira provide their source code (surprising as that
Regarding the example at:
http://www.cellml.org/news_items/draft-graphing-metadata-specification-updated
I'm quite new to RDF. I haven't had success producing the RDF-graph for
this example, but I would be interested in seeing it. Perhaps posting a
snapshot of the RDF-graph would be helpful,
for
feedback on this.
Regards,
Randall Britten
___
Software Development Leader
Bioengineering Institute
Auckland University
Phone: +64 9 373 7599 ext 83402
___
cellml-discussion mailing list
cellml-discussion@cellml.org
http
My vote goes to your current version.
-Original Message-
From: [EMAIL PROTECTED] [mailto:cellml-discussion-
[EMAIL PROTECTED] On Behalf Of Andrew Miller
Sent: Thursday, 22 November 2007 9:24 a.m.
To: For those interested in contributing to the development of CellML.
Subject:
Is there a way we could use some kind of variable substitution for the term
CellML file/CellML document?
-Original Message-
From: [EMAIL PROTECTED] [mailto:cellml-discussion-
[EMAIL PROTECTED] On Behalf Of Andrew Miller
Sent: Wednesday, 28 November 2007 9:14 a.m.
To: For those
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.
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Poul Nielsen
Sent: Sunday, 23 December 2007
Hi all
Another case that illustrates that perhaps the concept of uni-directional
connections may be flawed in a declarative language:
Component A has variables x and y that are both public, but only one
algebraic equation, hence insufficient maths to find values for x and y
(e.g. x+y=5).
] On Behalf Of Andrew Miller
Sent: Thursday, 10 January 2008 12:17 p.m.
To: CellML Discussion List
Subject: Re: [cellml-discussion] A list of proposed changes to
semantics to makein CellML 1.2
Randall Britten wrote:
I don't think we would need attribute values like public_private or
both
-Original Message-
From: [EMAIL PROTECTED] [mailto:cellml-discussion-
[EMAIL PROTECTED] On Behalf Of Andrew Miller
Sent: Thursday, 10 January 2008 4:10 p.m.
I think that this discussion has now forked into two different aspects,
although they are somewhat intermingled.
1)
Hi all
I think the policy depends on the answer to these two questions:
1) In terms of how widely CellML has been adopted worldwide, how does the
current status compare to what we expect in say 6 months, and say a year
from now?
2) How successful have we been in terms of achieving the vision
I think this is really neat, well done on an elegant idea.
One thing is bugging me: I'll illustrate by means of an example:
We would be inferring that the set fluxes consists of only the elements
{f1,f2,f3} from the three statements: f1 in fluxes, f2 in fluxes, f3 in
fluxes.
But if
-Original Message-
From: David Nickerson
Sent: Monday, 11 February 2008 4:43 p.m.
To: CellML Discussion List
Subject: Re: [cellml-discussion] Auckland CellML Group Meeting
Minutes(2008-02-07)
just a couple of points arising from these meeting minutes...
Any outcomes from the
Hi
David Nickerson has recently revived the discussion on how we handle
proposals, for example proposals relating to specifications such as the
CellML 1.2 specification that is currently in progress.
If you are interested in contributing to this discussion, please add your
comments to
Hi
I have summarised the decision as a comment on the Proposal handling tracker
item (https://tracker.physiomeproject.org/show_bug.cgi?id=347)
This currently only applies for the CellML specification work.
Regards,
Randall
-Original Message-
From: [EMAIL PROTECTED]
Hi
-Original Message-
From: [EMAIL PROTECTED] [mailto:cellml-discussion-
[EMAIL PROTECTED] On Behalf Of David Nickerson
...
Currently I am getting the impression that any discussion of tracker
items is superfluous and decisions will always be made by the Auckland
meeting.
We had a
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, please outline the
Hi
CellML has been using the Physiome tracker for some months now. For various
technical reasons, we would like to remove the old PCNG tracker from
www.cellml.org. If have any comments or objections, please note them at:
https://tracker.physiomeproject.org/show_bug.cgi?id=397
This is
Hi
Minutes of the recent meeting of PCEnv developers are available at
http://www.cellml.org/meeting_minutes/cellml-developers-meetings/pcenv-devel
opers-meeting-20080509/
Regards,
Randall
___
cellml-discussion mailing list
Hi
I'd prefer Skype at that time.
I've found the Skype conference calls work fairly well, easiest if one
person initiates the call, and all others make sure that the initiator knows
their skype-name, and that they want to be called to join in. Also, Skype
from within the ABI works well too,
Hi
We now have a simpler URL for the Physiome CellML Environment software
(PCEnv): www.pcenv.org
That should hopefully make it easier to remember.
Regards,
Randall
___
cellml-discussion mailing list
cellml-discussion@cellml.org
Hi
There is likely to be a short tracker outage this afternoon as we import
data from the CMGUI tracker into the physiometracker
(http://tracker.physiomeproject.org).
We apologise for any inconvenience this may cause.
Regards,
Randall
Tracker is back up now.
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Randall Britten
Sent: Tuesday, 10 June 2008 12:37 p.m.
To: 'CellML Discussion List'
Subject: [cellml-discussion] Tracker outage this afternoon (NZ timezone)
Hi
There is likely to be a short tracker
Hi
There will be a tracker outage early tomorrow morning (NZ time) as we apply
some minor changes to the Physiome tracker
(http://tracker.physiomeproject.org).
We apologise for any inconvenience this may cause.
Regards,
Randall
___
Hi all
I have added a news item regarding the release candidates.
Regards,
Randall
-Original Message-
From: [EMAIL PROTECTED] [mailto:cellml-discussion-
[EMAIL PROTECTED] On Behalf Of Alan Garny
Sent: Wednesday, 11 June 2008 7:13 p.m.
To: 'CellML Discussion List'
Subject: Re:
Hi all
Tommy recently made a minor improvement to the CellML-repository RSS feed,
so you can now see the login name of the user who submitted the new model or
new version of a model.
Try it out at http://www.cellml.org/models/pmr_rss
Regards,
Randall
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 it is not actively
Hi
Auckland ABI-IT have notified us that there are expected outages during the
night of Tuesday 1 July, 18:00 - 2100 (NZ time).
This will mean that all the following services relevant to CellML will be
unavailable for 3 hours.
* websites - www.cellml.org
- www.physiome.org.nz
Hi
Following the recent release of PCEnv 0.4, the primary developers of the
PCEnv application met to plan the next version.
Note: Please don't see this plan as limiting what can be included in the
next version, but rather as what our team plans to contribute. On an open
source project,
Hi
I have added tracker item 1163
(https://tracker.physiomeproject.org/show_bug.cgi?id=1163) for discussion of
the which VCS the PMR2 (Physiome model repository 2) should be based on.
Please submit any comments you have there, or CC yourself to it if you want
to follow the discussion.
Dougal has written a document explaining the prototype. While it is
possible to navigate to it, for convenience, here is a link to the current
draft: http://67.223.228.57:8282/cellml/models/documentation
-Original Message-
From: [EMAIL PROTECTED] [mailto:cellml-discussion-
[EMAIL
Hi
Although this was discussed some months ago
(http://www.cellml.org/meeting_minutes/meeting-minutes-2008-01-30/), plans
for progress on this are underway (see
https://tracker.physiomeproject.org/show_bug.cgi?id=1226 and
https://tracker.physiomeproject.org/show_bug.cgi?id=1238, which are part
Hi
Please note that we will be shutting down this prototype on 17 August, so
there are only a few more days to try it out.
Also, I'd suggest corresponding with Tommy when you try it out, as we have
found that just trying to explore it without a guide is not as productive.
Regards,
Randall
Hi all
The tracker (tracker.physiomeproject.org) will be down for a few minutes for
an update to be applied.
Regards,
Randall
___
cellml-discussion mailing list
cellml-discussion@cellml.org
Hi
I'd prefer to be able to have at least some community input by the time we
discuss these types of things at the meeting.
Regards,
Randall
-Original Message-
From: [EMAIL PROTECTED] [mailto:cellml-discussion-
[EMAIL PROTECTED] On Behalf Of Catherine Lloyd
Sent: Tuesday, 19 August
-Original Message-
Hi all,
...
All IT servers will be unavailable from about 0730 to 1230.
This will mean that all the following services will be unavailable for 5
hours.
...
* websites - www.cellml.org
- www.physiome.org.nz
-
Hi
We are considering making an alteration to the page view used per tracker
item. The tracker item for this is
https://tracker.physiomeproject.org/show_bug.cgi?id=1343.
Please CC yourself to it and make comments there.
Regards,
Randall
Hi
Some Auckland University network switches are getting a software upgrade.
FROM: 11 December 2008 00:00
TO: 11 December 2008 01:00
The Subversion server used by CellML will be affected by this outage.
Regards,
Randall
___
on Monday 15 June.
Old URL's for CellML models will be preserved, and the plan is that most
users will find the transition seamless.
We will send a follow up e-mail once this is done.
Regards,
Randall Britten
___
Leader of the Bioengineering Software Development
Hi
Please continue the discussion of this COR text sequencing issue on the
tracker. I've put references to other mailings on the relevant tracker
item:
https://tracker.physiomeproject.org/show_bug.cgi?id=152
Regards,
Randall
-Original Message-
From:
Due to some issues with model listings, we will defer this to Wednesday at
the soonest.
From: cellml-discussion-boun...@cellml.org
[mailto:cellml-discussion-boun...@cellml.org] On Behalf Of Randall Britten
Sent: Friday, 12 June 2009 12:33 p.m.
To: cellml-discussion@cellml.org
Subject
Recent work on addressing issues with the CellML specification have focussed
on reset rules (see
https://tracker.physiomeproject.org/show_bug.cgi?id=1543). Some of the
discussion on reset rules has touched on how delays may need to be
expressed, though this is still unresolved. I have added a
inconvenience this may cause.
Regards,
Randall Britten
___
Leader of the Bioengineering Software Development Group
Auckland Bioengineering Institute
Auckland University
Auckland, New Zealand
___
cellml-discussion mailing list
DAEs are a little more complex, it isn't always obvious which unknowns
require initial conditions, or how to ensure ICs are consistent.
Regards,
Randall
On 23/04/2010, at 8:50 PM, Alan Garny alan.ga...@dpag.ox.ac.uk
wrote:
Sorry, one more (non-OpenCell) comment:
- ... the biggest problem
-discussion-boun...@cellml.org [mailto:cellml-discussion-
boun...@cellml.org] On Behalf Of Randall Britten
Sent: 25 April 2010 22:54
To: 'CellML Discussion List'
Subject: Re: [cellml-discussion] ABI CellML Meeting Minutes, 21st
April
2010
Andrew pointed out some time ago that even if consistent IC's
,
Andre.
On Tue, Apr 27, 2010 at 8:16 AM, Randall Britten
r.brit...@auckland.ac.nz wrote:
From what I understand, this is exactly what Andrew is setting up.
Regards,
Randall
On 26/04/2010, at 8:17 PM, Alan Garny alan.ga...@dpag.ox.ac.uk
wrote:
Then, the approach that I would
://tracker.physiomeproject.org/show_bug.cgi?id=2588). The tracker
item has further details.
Regards,
Randall Britten
___
Leader of the Bioengineering Software Development Group
Auckland Bioengineering Institute
Auckland University
Auckland, New Zealand
Hi Alan
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
will send a follow-up e-mail.
Regards,
Randall Britten
___
Leader of the Bioengineering Software Development Group
Auckland Bioengineering Institute
Auckland University
Auckland, New Zealand
___
cellml-discussion mailing list
Hi
The site has been restored and the previous vulnerabilities addressed.
A very special thanks to Tommy Yu and Andrew Cantell for heroic efforts and
sleepless hours to rectify this!
Regards,
Randall
On 14/04/2011, at 12:47 PM, Randall Britten r.brit...@auckland.ac.nz wrote:
Hi
We
Hi
This is relevant to the discussion at last week's CellML meeting:
http://sbml.org/Events/Other_Events/statistical_models_workshop_2011
It will also be possible to join using EVO.
Regards,
Randall
___
cellml-discussion mailing list
Hi all
My apologies, I forgot to review the minutes on time before our deadline to
make them public. I will suggest some minor wording changes to those who
attended the meeting, and if they agree, we will modify the posted version,
and send a mail to this list.
Regards,
Randall
-Original
Thanks Dagmar
I've fixed the SED-ML issues, and updated the exposure, fixed version now
available at http://models.cellml.org/e/80/Lorenz_1963.cellml/view
By the way, the URL for the SED-ML web-tools didn't work (i.e.
http://sysbioapps.dyndns.org/SED-ML%20Web%20Tools), but this one did work
Hi
I have been informed by the ABI IT department that the CellML website will be
unavailable for a short time period tomorrow for infrastructure maintenance.
This will also affect the CellML mailing lists. Apologies for any
inconvenience this may cause.
Regards,
Randall
Hi
Probably the easiest way to get MATLAB code for CellML models that are in the
CellML model repository if via the generated code link available for each
exposed cellml model. However, models.cellml.org uses a buggy version of the
API, but this has already been fixed by Tommy, and is staged
Hi all
The weekly above meeting for 14 December and 21 December will be cancelled, due
to conflicts with other ABI events.
Regards,
Randall
___
cellml-discussion mailing list
cellml-discussion@cellml.org
Hi Mark
If you send a bit more detail about the model structure change, perhaps we
can solve it.
Regards,
Randall
On 27/02/13 9:32 PM, Mark Cannell mark.cann...@bristol.ac.uk wrote:
On 26/02/2013, at 9:43 PM, Andrew Miller ak.mil...@auckland.ac.nz wrote:
On 27/02/13 10:09, Mark Cannell
Hi Michel
Mechanical constitutive laws perhaps? Many are likely to be able to be
simulated fast enough for interactivity, I'm guessing. (I'm sure there
will be some other good suggestions.)
Regards,
Randall
On 23/03/13 3:08 AM, Audette, Michel A. maude...@odu.edu wrote:
Dear members of the
59 matches
Mail list logo
