[cellml-discussion] PMR2 v0.6 staging

2012-10-08 Thread Tommy Yu
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:

[cellml-discussion] Server maintenance

2012-04-26 Thread Tommy Yu
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).

Re: [cellml-discussion] Upcoming server maintenance on www.cellml.org and models.cellml.org.

2012-03-27 Thread Tommy Yu
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

[cellml-discussion] Upcoming server maintenance on www.cellml.org and models.cellml.org.

2012-03-22 Thread Tommy Yu
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).

Re: [cellml-discussion] CellML Model Repository upgraded to PMR2 v0.5

2012-02-15 Thread Tommy Yu
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

[cellml-discussion] CellML Model Repository upgraded to PMR2 v0.5

2012-02-14 Thread Tommy Yu
Hi, The CellML model repository underwent a software upgrade and is now running PMR2 v0.5. If you encountered any issues with this update please file a tracker item that blocks the following tracker item: https://tracker.physiomeproject.org/show_bug.cgi?id=3211 New features that were added

[cellml-discussion] Scheduled CellML webservers upgrade on 2011-10-10 21:00-23:00 UTC

2011-10-06 Thread Tommy Yu
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

[cellml-discussion] CellML Model Repository now on PMR2 v0.4

2011-10-04 Thread Tommy Yu
Greetings, The CellML Model Repository (http://models.cellml.org/) is now upgraded to the latest release of PMR2, v0.4. Please file any issues you may find with this release at https://tracker.physiomeproject.org/show_bug.cgi?id=3071. Notable features supported now includes: General: -

Re: [cellml-discussion] cellml-discussion Digest, Vol 84, Issue 10

2011-08-01 Thread Tommy Yu
Maxwell Neal wrote: Hi all - I was wondering - is there a webservice that would allow me to programmatically download all the cellml models in the cellml repository? Many thank, Hi Maxwell, Thank you for your interest in the CellML Model Repository. While we currently don't have a

Re: [cellml-discussion] ABI CellML Meeting Minutes, 22nd June 2011

2011-06-24 Thread Tommy Yu
] 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

[cellml-discussion] ABI CellML Meeting Minutes, 22nd June 2011

2011-06-23 Thread Tommy Yu
Greetings, The minutes of the Auckland Bioengineering Institute CellML meeting of 22nd June 2011 can now be found at: http://www.cellml.org/community/meeting/minutes/2011/06.22 Kind Regards, Tommy. ___ cellml-discussion mailing list

Re: [cellml-discussion] CellML Website/Repository Maintenance

2011-05-29 Thread Tommy Yu
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

[cellml-discussion] CellML Website/Repository Maintenance

2011-05-25 Thread Tommy Yu
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.

[cellml-discussion] CellML Model Repository now running on PMR2 v0.3

2010-06-22 Thread Tommy Yu
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

[cellml-discussion] Staging of PMR2 v0.3 rc1

2010-05-20 Thread Tommy Yu
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.

[cellml-discussion] Upcoming Maintenance Downtime for CellML websites.

2010-04-22 Thread Tommy Yu
Greetings, The UoA ITS group will be performing an OS upgrade on the servers that host the CellML websites on Tuesday 27th April 2010, 10:30am to 12:30pm (UTC: 2010-04-26 22:30 to 2010-04-27 00:30). Both the CellML website (http://www.cellml.org/) and the CellML Model Repository

[cellml-discussion] PMR2 v0.2 has been released

2010-01-07 Thread Tommy Yu
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

Re: [cellml-discussion] Announcement of the new CellML Model Repository (and release of PMR2 v0.1)

2009-06-22 Thread Tommy Yu
. Alan -Original Message- From: cellml-discussion-boun...@cellml.org [mailto:cellml-discussion- boun...@cellml.org] On Behalf Of Tommy Yu Sent: 22 June 2009 02:28 To: CellML Discussion Group Subject: [cellml-discussion] Announcement of the new CellML Model Repository (and release of PMR2

[cellml-discussion] Announcement of the new CellML Model Repository (and release of PMR2 v0.1)

2009-06-21 Thread Tommy Yu
Greetings, Team CellML is pleased to announce the immediate availability of the new CellML Model Repository running on PMR2 v0.1 at http://models.cellml.org/. All CellML models which were hosted within PMR1 (which was at http://www.cellml.org/models) have been migrated into PMR2. In

[cellml-discussion] Summary of PMR2 Prototype Discussions

2008-09-02 Thread Tommy Yu
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:

Re: [cellml-discussion] little b - shared models built from reusable parts

2008-07-28 Thread Tommy Yu
Michael Hucka wrote: My own $0.02, as another software developer and an old Lisp hacker myself (and of course, everything I say here is purely personal opinion). TY I think this can be done with a programming language. Yup, you can exchange programs as your model description, and

Re: [cellml-discussion] PMR2 Prototype Public Demo Server

2008-07-28 Thread Tommy Yu
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

Re: [cellml-discussion] PMR2 Prototype Public Demo Server

2008-07-28 Thread Tommy Yu
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

[cellml-discussion] [Fwd: Re: little b - shared models built from reusable parts]

2008-07-25 Thread Tommy Yu
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

Re: [cellml-discussion] little b - shared models built from reusable parts

2008-07-25 Thread Tommy Yu
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

[cellml-discussion] PMR2 Prototype Public Demo Server

2008-07-16 Thread Tommy Yu
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 to: https://tracker.physiomeproject.org/show_bug.cgi?id=248 Kind Regards, Tommy. ___

[cellml-discussion] CellML Metadata Specification - citation tracker item

2008-06-03 Thread Tommy Yu
Greetings, CellML Metadata Specification has provisions for logging citations using terms and classes under the cellml bqs namespace, which was derived from OMG's Bibliographic Query Service Draft Specification. This was done early this decade before there was a RDF schema for creating

[cellml-discussion] Auckland CellML Group Meeting Minutes (2008-05-07)

2008-05-08 Thread Tommy Yu
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. ___ cellml-discussion mailing list

[cellml-discussion] Auckland CellML Group Meeting Minutes (2008-04-30)

2008-05-04 Thread Tommy Yu
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. ___ cellml-discussion mailing list

[cellml-discussion] Auckland CellML Group Meeting Minutes (2008-02-13)

2008-02-14 Thread Tommy Yu
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. ___ cellml-discussion mailing list cellml-discussion@cellml.org

[cellml-discussion] Auckland CellML Group Meeting Minutes (2008-02-07)

2008-02-07 Thread Tommy Yu
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. ___ cellml-discussion mailing list cellml-discussion@cellml.org

[cellml-discussion] Auckland CellML Group Meeting Minutes (2008-01-30)

2008-01-31 Thread Tommy Yu
Greetings, The minutes of the Auckland CellML group meeting of 2008-01-30 can now be found at: http://www.cellml.org/meeting_minutes/latest Kind Regards, Tommy. ___ cellml-discussion mailing list cellml-discussion@cellml.org

[cellml-discussion] Auckland CellML Group Meeting Minutes (2008-01-23)

2008-01-24 Thread Tommy Yu
Greetings, The minutes of the Auckland CellML group meeting of 2008-01-23 can now be found at: http://www.cellml.org/meeting_minutes/latest Kind Regards, Tommy. ___ cellml-discussion mailing list cellml-discussion@cellml.org

[cellml-discussion] Auckland CellML Group Meeting Minutes (2008-01-16)

2008-01-17 Thread Tommy Yu
Greetings, The minutes of the Auckland CellML group meeting of 2008-01-16 can now be found at: http://www.cellml.org/meeting_minutes/latest Kind Regards, Tommy. ___ cellml-discussion mailing list cellml-discussion@cellml.org

[cellml-discussion] Auckland CellML Group Meeting Minutes (2008-01-09)

2008-01-10 Thread Tommy Yu
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. ___ cellml-discussion mailing list cellml-discussion@cellml.org

[cellml-discussion] Auckland CellML Group Meeting Minutes (20071121)

2007-11-22 Thread Tommy Yu
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. ___ cellml-discussion mailing list cellml-discussion@cellml.org

[cellml-discussion] Auckland CellML group meeting

2007-10-18 Thread Tommy Yu
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

[cellml-discussion] Auckland CellML group meeting minutes (2007-10-03)

2007-10-04 Thread Tommy Yu
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. ___ cellml-discussion mailing list cellml-discussion@cellml.org

[cellml-discussion] Auckland CellML group meeting minutes (2007-09-26)

2007-09-27 Thread Tommy Yu
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. ___ cellml-discussion mailing list cellml-discussion@cellml.org

Re: [cellml-discussion] Concerning the CellML Model Repository

2007-06-26 Thread Tommy Yu
/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

Re: [cellml-discussion] Concerning the CellML Model Repository

2007-06-26 Thread Tommy Yu
are the kinds of relationships between permissions and roles. I know you have some ideas here, but it's not very replete and perhaps needs to be put in a table. They will be put on the table. I think aliases in for web URIs are the least of the problems at the moment. On 6/26/07, Tommy Yu [EMAIL

Re: [cellml-discussion] Concerning the CellML Model Repository

2007-06-25 Thread Tommy Yu
Hi, I thought Andrew's ideas here is worth expanding, and I wrote a page based on that. http://www.cellml.org/Members/tommy/BaseRepository Cheers, Tommy. Andrew Miller wrote: Matt wrote: - Version/Variant It already clogged up the system. There is no proper revision control mechanism,

Re: [cellml-discussion] model upload problems

2007-06-25 Thread Tommy Yu
David Nickerson wrote: Hi Tommy, Thanks for picking that up, I didn't even think to check the CellML namespace! Hi Andre, I have updated the XSLT used by the model repository to accept both 1.0 and 1.1 models, but the repository itself still does not distinguish between the two

Re: [cellml-discussion] model upload problems

2007-06-22 Thread Tommy Yu
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

[cellml-discussion] Concerning the CellML Model Repository

2007-06-21 Thread Tommy Yu
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

Re: [cellml-discussion] Concerning the CellML Model Repository

2007-06-21 Thread Tommy Yu
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

Re: [cellml-discussion] Concerning the CellML Model Repository

2007-06-21 Thread Tommy Yu
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

Re: [cellml-discussion] Concerning the CellML Model Repository

2007-06-21 Thread Tommy Yu
all my thoughts about the threads here, along with the other thoughts I already have but not written down there. More comments below. Likewise. On 6/22/07, Tommy Yu [EMAIL PROTECTED] wrote: Matt wrote: Hi Tommy, I found the document seemed to be too far ahead of itself. I also didn't

Re: [cellml-discussion] PMR categories

2007-06-11 Thread Tommy Yu
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

Re: [cellml-discussion] PMR categories

2007-06-11 Thread Tommy Yu
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

Re: [cellml-discussion] PMR categories

2007-06-11 Thread Tommy Yu
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

Re: [cellml-discussion] PMR categories

2007-06-10 Thread Tommy Yu
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

Re: [cellml-discussion] PMR categories

2007-06-07 Thread Tommy Yu
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

Re: [cellml-discussion] PMR categories

2007-06-07 Thread Tommy Yu
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

Re: [cellml-discussion] PMR categories

2007-06-05 Thread Tommy Yu
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

Re: [cellml-discussion] initial feedback on new repository metadata tools

2007-05-16 Thread Tommy Yu
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

Re: [cellml-discussion] broken tabs on the repository pages

2007-05-15 Thread Tommy Yu
David Nickerson wrote: What I'd like to see is that for models which don't have any metadata and/or curation information that rather than a complicated plone site error users are presented with a simple message that the model doesn't contain any data of the type required for that

Re: [cellml-discussion] broken tabs on the repository pages

2007-05-14 Thread Tommy Yu
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

Re: [cellml-discussion] broken tabs on the repository pages

2007-05-14 Thread Tommy Yu
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

Re: [cellml-discussion] model variants(?): e.g. where multiple cell types are described by the same model in different files

2007-04-11 Thread Tommy Yu
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

[cellml-discussion] Adding an information page for each model category

-- Thread Tommy Yu
"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