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 labelled as a
variant is a variation of the one it is a variant of. However, this
isn't really a very
Procedural code relies on the CCGS server provided by the CellML API, and if
the server is down or being restarted that happens.
As for the model metadata and curation, they don't always have data populated
properly due to various issues. I've been aware of this issue for quite a
while now
As for the model metadata and curation, they don't always have data
populated properly due to various issues. I've been aware of this issue for
quite a while now (since last year, actually) but was not able to fix it
reliably without a proper CellML metadata library. Now that library is
David Nickerson wrote:
Hi Tommy,
Thought I'd just jot down some initial thoughts after following your
invitation to have a play with the new metadata tools on the model
repository :-) These are generally cosmetic suggestions more for your
consideration than any urgent requirement you
Just had a discussion with Peter, Randall and James about this.
The keywords are in the metadata for the models, and there is no limit to what
can go in there. The concern about that is the list could get too big (for
minor categories), or variations in the name (electrophysiology vs
David Nickerson wrote:
I really don't like the idea of giving a model a keyword of other.
Hopefully the repository will be smart enough to automatically add
models to the other listing if they don't have any of the other
predefined key words.
I agree, and I don't think I will put an
Matt wrote:
I'm not sure what the physiome ontology is. Currently the anatomy
ontology is the one I've been working on and this has no physiological
processes in it yet.
I was hoping I had been clear in my previous emails that I want the
current and future author supplied keywords to help
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 metadata at all.
Actually they are. Keywords are defined in the CellML metadata specifications
and
David Nickerson wrote:
I'd suggest that since you are deciding how keywords are extracted,
edited, and put back into the models that you are the best person to
answer that. Otherwise there should have been some discussion on this
mailing list as to how to handle this issue.
Okay, I've
Ugh, looks like Thunderbird clobbered my last message when I told it to
converted html to plain text. This is my reply.
Okay, I've re-read the metadata specification, specifically the RDF
schema draft section at the bottom of the document, and the RDF schema
for Dublin Core (which was
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.
My assumption was that the category field selections are not persisted
in the model metadata at all.
Actually
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 doing with the
Hi Andrew,
A couple notes:
I don't think it is a bad thing to have a one-way cache of metadata
somewhere for technical / performance reasons (perhaps in a relational
database), but I think that we should replicate data for each model
(perhaps using a deep copy-on-write approach if this is
of the model does annotate
components properly (e.g. giving some comment to cmeta:id of some component of
some file) it will be searchable (provided that the creator publishes that
model).
Thanks for your inputs,
Tommy.
Thanks,
David.
Tommy Yu wrote:
Hi,
I have written down some of my
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 but am having
some problems.
Firstly, it didn't pick up some of the model metadata during the upload
process. At least there were
/variant that
would be _2 for Mary in my example? I had been assuming the 2007_1 meant
January 2007.
It could conceivably mean the first paper John Doe published in 2007, or
January, as that haven't been decided yet.
Thanks,
Tommy.
Thanks,
Andre.
Tommy Yu wrote:
Hi,
I thought Andrew's
Greetings,
The minutes of the Auckland CellML group meeting on 2007-09-26 is published at
this URI:
http://www.cellml.org/meeting_minutes/meeting-minutes-26-september-2007
Cheers,
Tommy.
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cellml-discussion@cellml.org
Greetings,
The minutes of the Auckland CellML group meeting on 2007-10-03 is published at
this URI:
http://www.cellml.org/meeting_minutes/meeting-minutes-03-october-2007
Cheers,
Tommy.
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cellml-discussion@cellml.org
Greetings,
The minutes of the Auckland CellML group meeting on 2007-10-17 is published at
this URI:
http://www.cellml.org/meeting_minutes/meeting-minutes-17-october-2007
Starting from today, the minutes of the latest weekly meeting of this group
will be posted on Friday, between the hours of
Greetings,
The minutes of the Auckland CellML group meeting of 2007-11-21 can now be found
at:
http://www.cellml.org/meeting_minutes/latest
Kind Regards,
Tommy.
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Greetings,
The minutes to the Auckland CellML group meeting of 2008-01-09 can now be found
at:
http://www.cellml.org/meeting_minutes/latest
Kind Regards,
Tommy.
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Greetings,
The minutes of the Auckland CellML group meeting of 2008-02-07 can now be found
at:
http://www.cellml.org/meeting_minutes/latest
Kind Regards,
Tommy.
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Greetings,
The minutes of the Auckland CellML group meeting of 2008-02-13 can now be found
at:
http://www.cellml.org/meeting_minutes/latest
Kind Regards,
Tommy.
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Greetings,
The minutes of the Auckland CellML group meeting of 2008-04-30 can now be found
at:
http://www.cellml.org/meeting_minutes/abi-meeting-minutes-2008-04-30
Kind Regards,
Tommy.
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Greetings,
The minutes of the Auckland CellML group meeting of 2008-05-07 can now be found
at:
http://www.cellml.org/meeting_minutes/abi-meeting-minutes-2008-05-07
Kind Regards,
Tommy.
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Apologies to Hamid, the message somehow got dropped due to non-membership
status. This was his message.
Original Message
Subject: Re: [cellml-discussion] little b - shared models built from reusable
parts
Date: Fri, 25 Jul 2008 12:03:24 -0700
From: Hamid Bolouri [EMAIL
Nicolas Le Novere wrote:
The SBML community has know little b for a while since they first came to
us, a long time ago, saying roughly we're much better than you, and we do
everything in a simpler way, understandable by users.
I think (and this is a personal opinion, that does NOT reflect
on the usage please feel free to ask me.
Information to log on to the prototype PMR2 is quoted below.
Cheers,
Tommy.
Tommy Yu wrote:
Greetings,
The PMR2 prototype has been staged to:
http://67.223.228.57:8282/cellml/
Please register an account there to try it out, and please post any feedback
need my sleep.
Bob G
On Tue, 2008-07-29 at 16:14 +1200, Tommy Yu wrote:
Greetings,
Just a friendly reminder, the lease for the server space for the PMR2
(Physiome Model Repository v2) Prototype will expire in approximately two
weeks. There were only a limited number of people who signed
Greetings everyone,
Following up on the discussions made regarding the PMR2 prototype exercise,
found at:
https://tracker.physiomeproject.org/show_bug.cgi?id=248
I have summarized all the major issues and points to be addressed as we develop
the final PMR2. The document can be found at:
"006792";
google_color_url = "006792";
google_color_text = "000000";
//-->
[cellml-discussion] Adding an information page for each model category
Tommy Yu
Reply via email to
Greetings,
Team CellML is pleased to announce the release of v0.2 of the Physiome Model
Repository 2 software. The CellML model repository (http://models.cellml.org/)
has been upgraded to this version.
Major changes include:
- Rewriting of the exposure mechanism. Each file now have views
Greetings,
The first release candidate of PMR2 v0.3 can be accessed at
http://184.73.44.8:8380/pmr/. If you have any questions, comments, or have
encountered issues, please file comments or block tracker item at
https://tracker.physiomeproject.org/show_bug.cgi?id=2557.
Kind Regards,
Tommy.
Greetings,
The CellML Model Repository (http://models.cellml.org/) has upgraded to the
latest release of PMR2, v0.3. Please file any issues you may find with this
instance at https://tracker.physiomeproject.org/show_bug.cgi?id=2613.
This instance of the repository will be used for storage of
Dear all,
The machines that host CellML website and its model repository will undergo
maintenance on 30th May between 09:00 and 11:00 NZST (2011-05-29 21:00-23:00
UTC), as the original scheduled maintenance on 9th May did not proceed as
planned.
Regards,
Tommy.
Tommy Yu wrote:
Tommy Yu wrote:
Dear all,
The machines that host CellML website and its model repository will
undergo maintenance on 30th May between 09:00 and 11:00 NZST
(2011-05-29 21:00-23:00 UTC), as the original scheduled maintenance on
9th May did not proceed as planned.
Update
] On Behalf Of Tommy Yu
Sent: 24 June 2011 06:49
To: CellML Discussion Group
Subject: [cellml-discussion] ABI CellML Meeting Minutes, 22nd June 2011
Greetings,
The minutes of the Auckland Bioengineering Institute CellML meeting of
22nd
June 2011 can now be found at:
http://www.cellml.org/community
Greetings,
As the ABI ITS team are continuing the improvements of their infrastructure,
they have scheduled the installation of puppet - a centralize management tool
for servers. This will occur between 11th Oct 2011 10am - 12am Auckland
Daylight Time (or 2011-10-10 21:00-23:00 UTC). As
Hi,
There is a minor correction needed to my previous announcement. The CellML API
version I used was a specific snapshot of the CellML API some time after 1.10
was released and not the 1.11, and that one fixed one of the MATLAB code
generation issue.
Regards,
Tommy.
Tommy Yu wrote:
Hi
Hi,
There will be a brief outage following a software upgrade for the CellML
website (www.cellml.org) and the model repository (models.cellml.org). The
outage is to be occur on 2012-03-25 between the hours of 18:30-20:00 UTC (or
Monday morning 7:30am to 9:00am for the people in Auckland).
Hi,
The server maintenance had been delayed to 2012-04-01 between the hours of
19:30-21:00 UTC (or 2012-04-02 07:00-09:00 NZST). The same set of services
will be affected as stated.
Regards,
Tommy.
Tommy Yu wrote:
Hi,
There will be a brief outage following a software upgrade
Hi,
There will be a brief outage following a software upgrade for the CellML
website (www.cellml.org) and the model repository (models.cellml.org). The
outage is to be occur on 2012-04-29 between the hours of 18:30-20:00 UTC (or
Monday morning 7:30am to 9:00am for the people in Auckland).
Hi,
PMR2 v0.6 is ready for release, but the final deployment is pending on final
preparation and testing. A snapshot of the data residing on
models.physiomeproject.org (along with models.cellml.org) is taken and is
staged with the production buildout profile at this location:
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