Re: [cellml-discussion] Mailing list migration

2013-06-13 Thread David Nickerson
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

Re: [cellml-discussion] Mailing list migration

2013-06-09 Thread David Nickerson
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

[cellml-discussion] Mailing list migration

2013-05-27 Thread David Nickerson
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.

[cellml-discussion] Fwd: [Combine-announce] Update on COMBINE 2013

2013-05-26 Thread David Nickerson
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

[cellml-discussion] Harmony 2013

2013-05-07 Thread David Nickerson
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,

[cellml-discussion] Fwd: [Combine-discuss] ICSB Tutorial: Modelling and Simulation of Quantitative Biological Models on September 4th, 2013

2013-04-29 Thread David Nickerson
-- 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

[cellml-discussion] Fwd: [Combine-announce] HARMONY travel funds

2013-04-25 Thread David Nickerson
-- 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

[cellml-discussion] OpenCOR 0.1 Released

2013-04-03 Thread David Nickerson
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

[cellml-discussion] CellML Workshop coming up next week

2013-03-21 Thread David Nickerson
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

[cellml-discussion] Modular Modeling: Standards and Tools. Lucian Smith, Caltech

2013-03-01 Thread David Nickerson
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

Re: [cellml-discussion] Editor election results and call for vote in run-off election

2013-02-10 Thread David Nickerson
focus on getting the 1.2 specification moved forward... Cheers, Andre. On Thu, Jan 31, 2013 at 9:41 AM, David Nickerson david.nicker...@gmail.com wrote: Hi all, The results from the recent editor election have been counted and validated. The results are as follows: Mike T. Cooling: 8

[cellml-discussion] 7th International CellML Workshop - accommodation options

2013-02-06 Thread David Nickerson
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

[cellml-discussion] Editor election results and call for vote in run-off election

2013-01-30 Thread David Nickerson
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

[cellml-discussion] 7th International CellML Workshop - registration now open.

2013-01-21 Thread David Nickerson
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:

Re: [cellml-discussion] Call for votes: one new CellML Editor for 2013-2015

2013-01-17 Thread David Nickerson
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

[cellml-discussion] Call for votes: one new CellML Editor for 2013-2015

2013-01-07 Thread David Nickerson
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

Re: [cellml-discussion] Call for CellML editor nominations for 2013

2012-12-28 Thread David Nickerson
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

Re: [cellml-discussion] Call for CellML editor nominations for 2013

2012-12-11 Thread David Nickerson
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

[cellml-discussion] Call for CellML editor nominations for 2013

2012-12-10 Thread David Nickerson
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

[cellml-discussion] 2nd call for papers - Workshop on Interoperability in Scientific Computing

2012-12-05 Thread David Nickerson
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)

[cellml-discussion] 7th International CellML Workshop - 25 26 March 2013

2012-12-02 Thread David Nickerson
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,

[cellml-discussion] Fwd: [SED-ML-discuss] SED-ML proposal vote: Nested

2012-11-09 Thread David Nickerson
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:

[cellml-discussion] Solicitation of feedback on CellML 1.2

2012-10-29 Thread David Nickerson
*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

Re: [cellml-discussion] naive questions about modeling blood-brain barrier and its disruption

2012-08-15 Thread David Nickerson
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

[cellml-discussion] Fwd: [sysbio] Reminder: please register for COMBINE 2012

2012-07-09 Thread David Nickerson
-- 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

Re: [cellml-discussion] CellML 1.2 and MathML 3

2012-06-12 Thread David Nickerson
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

[cellml-discussion] Fwd: [sysbio] Reminder: Please register for HARMONY 2012

2012-04-15 Thread David Nickerson
-- 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

[cellml-discussion] Open PhD student position in Rostock, Germany

2012-03-29 Thread David Nickerson
*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

[cellml-discussion] Fwd: [Combine-announce] HARMONY 2012 registration is open

2012-03-08 Thread David Nickerson
-- 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 ***              

[cellml-discussion] Registration for the 2012 CellML Workshop is now open

2012-01-17 Thread David Nickerson
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.

[cellml-discussion] Fwd: [sbml-discuss] Draft Distrib Package Proposal

2012-01-06 Thread David Nickerson
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

[cellml-discussion] Announcing the 2012 CellML Workshop

2011-12-19 Thread David Nickerson
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

Re: [cellml-discussion] Improved CellML support in latest version of JSim

2011-12-19 Thread David Nickerson
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! ___ cellml-discussion mailing list

[cellml-discussion] Summary of the inaugural CellML Editorial Board meeting

2011-12-19 Thread David Nickerson
*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

Re: [cellml-discussion] Independent variables, and delay

2011-12-16 Thread David Nickerson
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

Re: [cellml-discussion] Independent variables, and delay

2011-12-16 Thread David Nickerson
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

[cellml-discussion] IEEE e-Science 2011 WISC Call for Participation

2011-11-15 Thread David Nickerson
(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

Re: [cellml-discussion] cellml-discussion Digest, Vol 87, Issue 10

2011-10-24 Thread David Nickerson
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

Re: [cellml-discussion] nested components in CellML

2011-10-21 Thread 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

Re: [cellml-discussion] ABI CellML Meeting Minutes, 14th September 2011

2011-09-20 Thread David Nickerson
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. ___ cellml-discussion mailing list

Re: [cellml-discussion] ABI CellML Meeting Minutes, 14th September 2011

2011-09-18 Thread David Nickerson
I saw that you are providing a SED-ML file together with your Lorenz attractor model http://models.cellml.org/e/7f. I tried to run the example, and it does work perfectly on SED-ML web tools on http://sysbioapps.dyndns.org/SED-ML%20Web%20Tools. I tried also the validators on SED-ML web

[cellml-discussion] Fwd: [Combine-announce] COMBINE mailing lists

2011-09-17 Thread David Nickerson
-- Forwarded message -- From: Nicolas Le Novère le...@ebi.ac.uk Date: Sun, Sep 18, 2011 at 5:36 AM Subject: [Combine-announce] COMBINE mailing lists To: combine-annou...@mbine.org Dear Colleagues, Some of you may not have attended the last day of COMBINE2011, and may not be

[cellml-discussion] Workshop on Interoperability in Scientific Computing

2011-05-24 Thread David Nickerson
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

[cellml-discussion] Fwd: [sbml-discuss] About the upcoming votes on L3 package proposals

2011-05-19 Thread David Nickerson
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

[cellml-discussion] CellML Workshop 2011 programme now available

2011-04-06 Thread David Nickerson
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:

[cellml-discussion] Registration for the 2011 CellML workshop is now open

2011-02-13 Thread David Nickerson
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. ___ cellml-discussion mailing list cellml-discussion@cellml.org http

[cellml-discussion] Announcing the 2011 CellML workshop

2011-02-03 Thread David Nickerson
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

[cellml-discussion] COMETS 2011 - 2nd International Track on Collaborative Modeling and Simulation - CfP

2011-01-16 Thread David Nickerson
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

Re: [cellml-discussion] Schematic diagram

2010-10-13 Thread David Nickerson
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

Re: [cellml-discussion] ABI CellML Meeting Minutes, 21st April 2010

2010-04-26 Thread David Nickerson
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

Re: [cellml-discussion] Announcement of OpenCell 0.7rc3

2010-03-14 Thread David Nickerson
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

Re: [cellml-discussion] ABI CellML meeting minutes 2009-09-30

2009-10-26 Thread David Nickerson
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:

Re: [cellml-discussion] ABI CellML meeting minutes 2009-09-30

2009-10-12 Thread David Nickerson
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.

Re: [cellml-discussion] Auto-generate HDF5 from CellML?

2008-11-19 Thread David Nickerson
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]

Re: [cellml-discussion] Auto-generate HDF5 from CellML?

2008-11-13 Thread 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 this would need some thinking :) Is there a generic way to define a useful HDF5 data structure for any

Re: [cellml-discussion] Auto-generate HDF5 from CellML?

2008-11-10 Thread David Nickerson
detect problems at a higher level, I can go back and look at details and possibly re- run those simulations. David Nickerson described a similar approach in an earlier post [3]. However, setting up the data structure with annotations for physical units and such is quite time-consuming

Re: [cellml-discussion] Finalising CellML Metadata 1.0 specification

2008-10-08 Thread David Nickerson
On Thu, Oct 9, 2008 at 8:55 AM, James Lawson [EMAIL PROTECTED] wrote: It appears nobody has commented on this directly within cellml-discussion. I understand you hold some opposition to finalising what you believe to be a draft specification, Andre. Could you please elaborate? I just think

Re: [cellml-discussion] CellML IRC

2008-08-20 Thread David Nickerson
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

Re: [cellml-discussion] Suggestions regarding search andbrowse utility for CellML Repository

2008-05-05 Thread David Nickerson
-discussion -- David Nickerson, PhD Research Fellow Division of Bioengineering Faculty of Engineering National University of Singapore Email: [EMAIL PROTECTED] ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo

[cellml-discussion] decompose - a model decomposition utility

2008-05-01 Thread David Nickerson
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

Re: [cellml-discussion] Call for community input: decision about theaddition of a CellML API side RDF parsing service

2008-05-01 Thread David Nickerson
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

Re: [cellml-discussion] Call for community input: final decisions on anumber of specification related issues

2008-03-04 Thread David Nickerson
___ cellml-discussion 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

Re: [cellml-discussion] Call for community input: final decisionson anumber of specification related issues

2008-03-04 Thread David Nickerson
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

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

2008-02-10 Thread David Nickerson
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

Re: [cellml-discussion] Using proposed CellML 1.2 features to createmore re-usable metabolic models

2008-01-30 Thread David Nickerson
://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] ___ cellml-discussion mailing list cellml-discussion@cellml.org

Re: [cellml-discussion] Base normative CellML Specificationfor further work

2008-01-17 Thread David Nickerson
http://www.cellml.org/mailman/listinfo/cellml-discussion ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion -- David Nickerson, PhD Research Fellow Division of Bioengineering

Re: [cellml-discussion] Survey on opinions for the backwardscompatibility levels for future CellML Specs

2008-01-08 Thread David Nickerson
://www.cellml.org/mailman/listinfo/cellml-discussion ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion -- David Nickerson, PhD Research Fellow Division of Bioengineering Faculty

Re: [cellml-discussion] CellML terminology: distinguishingCellMLmodels from the XML in which they are represented

2007-12-11 Thread David Nickerson
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

Re: [cellml-discussion] specification draft and docbook

2007-11-27 Thread David Nickerson
] 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

Re: [cellml-discussion] My specification draft in progress is nowpushed to the CellML site

2007-11-27 Thread David Nickerson
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] ___ cellml-discussion mailing list cellml-discussion

Re: [cellml-discussion] specification draft and docbook

2007-11-23 Thread David Nickerson
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

Re: [cellml-discussion] [Fwd: Re: application 'ML']

2007-11-20 Thread David Nickerson
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

Re: [cellml-discussion] Representing the next version of the CellMLSpecification

2007-11-07 Thread David Nickerson
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

Re: [cellml-discussion] Representing the next version of the CellMLSpecification

2007-11-06 Thread David Nickerson
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

Re: [cellml-discussion] Include_in_CellML_1.2 requested: [Tracker Item193] CellML namespaces policy for CellML 1.2 (and beyond)

2007-10-03 Thread David Nickerson
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

[cellml-discussion] Bug in API configure script?

2007-10-01 Thread David Nickerson
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.

[cellml-discussion] online subversion browser?

2007-10-01 Thread David Nickerson
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

Re: [cellml-discussion] online subversion browser?

2007-10-01 Thread David Nickerson
/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

Re: [cellml-discussion] Proposal: Standardised CellMLreal numberformat

2007-09-20 Thread David Nickerson
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,

Re: [cellml-discussion] CellML Versioning Strategy

2007-09-20 Thread David Nickerson
- 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

Re: [cellml-discussion] Proposal: Standardised CellML real number format

2007-09-18 Thread David Nickerson
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 or

Re: [cellml-discussion] cellml poster for ICSB 2007 conference

2007-08-29 Thread David Nickerson
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

Re: [cellml-discussion] Include_in_CellML_1.2 requested: [Tracker Item153] Allow multiple connections between the same pair of components

2007-08-28 Thread David Nickerson
--- Additional Comments from Andrew Miller [EMAIL PROTECTED] Section 3.2.4 of CellML 1.1 states, in the second sentence of the second paragraph: Only one connection may be created between any given pair of components in a model. This is a fairly pointless restriction from all fronts:

Re: [cellml-discussion] Include_in_CellML_1.2 requested: [TrackerItem153] Allow multiple connections between the same pair of components

2007-08-28 Thread David Nickerson
Andrew Miller wrote: David Nickerson wrote: --- Additional Comments from Andrew Miller [EMAIL PROTECTED] Section 3.2.4 of CellML 1.1 states, in the second sentence of the second paragraph: Only one connection may be created between any given pair of components in a model

Re: [cellml-discussion] Include_in_CellML_1.2 requested: [TrackerItem153] Allow multiple connections between the same pair of components

2007-08-28 Thread David Nickerson
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

Re: [cellml-discussion] on a CellML format

2007-08-21 Thread David Nickerson
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

[cellml-discussion] Errors building the C++ API

2007-08-19 Thread David Nickerson
Hi all, I know Andrew and I have discussed this in the past but just thought I'd raise the issue here and see if anyone has any ideas. I have just begun trying to build the C++ API implementation using the latest svn trunk code. I'm using a freshly installed Fedora 7 Linux box (gcc (GCC)

Re: [cellml-discussion] CeVAS, CUSES, MaLaES

2007-08-19 Thread David Nickerson
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

Re: [cellml-discussion] CeVAS, CUSES, MaLaES

2007-08-19 Thread David Nickerson
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

Re: [cellml-discussion] CeVAS, CUSES, MaLaES

2007-08-19 Thread David Nickerson
Andrew Miller wrote: Alan Garny wrote: 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

Re: [cellml-discussion] CellML technical question.

2007-08-01 Thread David Nickerson
/ ___ cellml-discussion 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

Re: [cellml-discussion] CellML Tracker being tested athttp://bowmore.elyt.com/bugzilla/

2007-07-20 Thread David Nickerson
on an issue to send your comment to the list. Best regards, Andrew Miller ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion -- David Nickerson, PhD Research Fellow Division

Re: [cellml-discussion] embedded stimulus currents in CellML models

2007-07-20 Thread David Nickerson
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

Re: [cellml-discussion] [Tracker Item 43] New: typo in simplified (?)interface

2007-07-20 Thread David Nickerson
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

Re: [cellml-discussion] CellML Tracker beingtested athttp://bowmore.elyt.com/bugzilla/

2007-07-20 Thread David Nickerson
Do you like the new template I just put up, which adds in Choose the area of the CellML project to which this relates: as a paragraph above the list of products? except now that I know to look in the page title bar its just duplication of information :-) isn't there some way to remove the

Re: [cellml-discussion] CellML_1.1.1 requested: [Tracker Item 48]Deprecation of the reaction element

2007-07-20 Thread David Nickerson
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] ___ cellml

Re: [cellml-discussion] CellML_1.1.1 requested: [Tracker Item48]Deprecation of the reaction element

2007-07-20 Thread 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

Re: [cellml-discussion] curation of BioModels Database

2007-07-19 Thread David Nickerson
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

Re: [cellml-discussion] embedded stimulus currents in CellML models

2007-07-18 Thread David Nickerson
Of course. And in the same sense you could simply delete the stimulus protocol component if you didn't want it. I think the issue is in fact a curation issue - we are specifying one of our curation 'levels' as model is the same as is described in the paper. If there is a stimulus protocol

Re: [cellml-discussion] [TrackerItem 42]New: CellML1.1.1specification

2007-07-18 Thread David Nickerson
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 or if it is making reaction elements invalid in a 1.1.1

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