Re: [cellml-discussion] Java error on Mac OSX10.8.2

2013-02-26 Thread Andrew Miller
On 27/02/13 10:09, Mark Cannell wrote: Hi Randall I installed the tools and the repository code does runs in OpenCell. However when I clone the distribution and edit anything I get the same java error I got before the Xcode tools were installed. I have no idea what I could be doing wrong..

[cellml-discussion] CellML API Survey

2012-11-19 Thread Andrew Miller
://cellmlapisurvey.appspot.com/survey_followup.html to participate in the survey. Yours Sincerely, Andrew Miller (ak.mil...@auckland.ac.nz, phone 09-3737599 ext 85122) Auckland Bioengineering Institute APPROVED BY THE UNIVERSITY OF AUCKLAND HUMAN PARTICIPANTS ETHICS COMMITTEE ON 7th Nov 2012

Re: [cellml-discussion] Solicitation of feedback on CellML 1.2

2012-11-04 Thread Andrew Miller
On 05/11/12 10:10, Jonathan Cooper wrote: Hi all, Just wanted to respond to a couple of points. On 30/10/2012 02:53, Andrew Miller wrote: On 29/10/12 22:36, David Nickerson wrote: In addition, we specifically ask for feedback on the issue of moving to MathML 3.0 (tracker item 67 https

[cellml-discussion] Announcing CellML API 1.12

2012-11-01 Thread Andrew Miller
Hi all, The CellML API release candidate version 1.11rc2 has been released with a minor change to correct uncertainty solvers as CellML API version 1.12. The files making up this release candidate are available here: * http://cellml-api.sourceforge.net/download.html#1.12 This release

Re: [cellml-discussion] Announcing CellML API 1.12

2012-11-01 Thread Andrew Miller
On 01/11/12 23:05, Andrew Miller wrote: Hi all, The CellML API release candidate version 1.11rc2 has been released with Sorry, that should of course be 1.12rc2. a minor change to correct uncertainty solvers as CellML API version 1.12. The files making up this release candidate

Re: [cellml-discussion] Solicitation of feedback on CellML 1.2

2012-10-29 Thread Andrew Miller
On 29/10/12 22:36, David Nickerson wrote: *Dear all, At the 5th International CellML Workshop http://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

[cellml-discussion] Announcing CellML API 1.12 release candidate 2

2012-10-22 Thread Andrew Miller
Hi all, The second release candidate for the CellML API 1.12 (1.12-rc2) has been released. This release candidate will become the CellML API 1.12 if no-one reports any problems with it by next Tuesday (New Zealand time). Please try out the the API and report any problems on the Physiome

[cellml-discussion] Announcing CellML API 1.12 release candidate 1

2012-10-09 Thread Andrew Miller
Hi all, The first release candidate for the CellML API 1.12 (1.12-rc1) has been released. This release candidate will become the CellML API 1.12 if no-one reports any problems with it by next Wednesday (New Zealand time). Please try out the the API and report any problems on the Physiome

[cellml-discussion] Auckland CellML Meeting planned for Wednesday July 4th from 9-10 AM (NZST)

2012-07-02 Thread Andrew Miller
Hi, There will be a meeting in Auckland to discuss the development of the CellML specifications tomorrow (Wednesday the 4th of July, at 9 AM NZST). The idea of this meeting is that it will allow members of the CellML community based in Auckland to express their views on development of the

Re: [cellml-discussion] Auckland CellML Meeting planned for Wednesday July 4th from 9-10 AM (NZST)

2012-07-02 Thread Andrew Miller
On 03/07/12 11:34, Lucian Smith wrote: I have one comment: * Andrew Millerak.mil...@auckland.ac.nz [2012-07-03 00:07] writes: 2. Should CellML 1.2 be an incremental change over CellML 1.1, with another version planned shortly after, or should it try to incorporate a wider set of changes?

Re: [cellml-discussion] New draft secondary specification: Uncertainty

2012-05-29 Thread Andrew Miller
prior distributions. Best wishes, Andrew kind regards, Michael On 05/29/2012 01:28 AM, Andrew Miller wrote: Hi all, I've just put up a draft secondary specification on how we could represent parameter uncertainty within the context of my CellML 1.2 draft. The secondary specification can

[cellml-discussion] New draft secondary specification: Uncertainty

2012-05-28 Thread Andrew Miller
Hi all, I've just put up a draft secondary specification on how we could represent parameter uncertainty within the context of my CellML 1.2 draft. The secondary specification can be viewed here: http://www.cellml.org/Members/miller/draft-secondary-spec-uncertainty/ The DocBook it is

Re: [cellml-discussion] trouble building on Ubuntu: for opencell build, told to build CellML API with XPCOM, but CellML API does not CMake with XPCOM support

2012-05-08 Thread Andrew Miller
On 09/05/12 16:43, Audette, Michel A. wrote: Dear CellML users, I have a recent version of Ubuntu, and when I try to build opencell, configure tells me configure: error: The CellML API directory /usr/local did not contain interfaces/ICIS.xpt. Give the path to the CellML API with

[cellml-discussion] CellML API version 1.11 has been released

2012-05-01 Thread Andrew Miller
...@auckland.ac.nz. Best wishes, Andrew Miller ___ cellml-discussion mailing list cellml-discussion@cellml.org http://lists.cellml.org/mailman/listinfo/cellml-discussion

[cellml-discussion] Announcing CellML API 1.11 release candidate 2

2012-04-17 Thread Andrew Miller
Hi all, The second release candidate for the CellML API 1.11 (1.11-rc2) has been released. This release candidate will become the CellML API 1.11 if no-one reports any problems with it by next Wednesday (New Zealand time). Please try out the the API and report any problems on the Physiome

[cellml-discussion] Announcing CellML API 1.11 release candidate 1

2012-04-10 Thread Andrew Miller
Hi all, The first release candidate for the CellML API 1.11 (1.11-rc1) has been released. This release candidate will become the CellML API 1.10 if no-one reports any problems with it by next Wednesday (New Zealand time). Please try out the the API and report any problems on the Physiome

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

2011-10-24 Thread Andrew Miller
On 25/10/11 09:14, David Nickerson wrote: Hi Maxwell, If you wrap the MathML into a CellML model/component, COR does a good job generating Matlab. OpenCell should work as well. Actually, I think OpenCell might be able to generate all the variables for you from the equation, whereas in COR you

Re: [cellml-discussion] [cellml-dev] Draft DAEs / events secondary specification for CellML 1.2

2011-09-12 Thread Andrew Miller
features needed for events. Best wishes, Andrew Also, I can't recall whether there will be any mechanism for a model document to declare which secondary specification(s) it uses, if any? Best wishes, Jonathan On 12/09/2011 03:27, Andrew Miller wrote: Hi all, The draft CellML 1.2

[cellml-discussion] CellML API 1.10rc2 available now

2011-09-06 Thread Andrew Miller
). The Linux SDK packages now include the processor type in the file name. Best wishes, Andrew Miller ___ cellml-discussion mailing list cellml-discussion@cellml.org http://lists.cellml.org/mailman/listinfo/cellml-discussion

[cellml-discussion] Proposed write-up

2011-09-05 Thread Andrew Miller
Hi all, I've written a draft CellML 1.2 Core Specification that tries to put together all the current proposals the community seems to have reached consensus on. It is available at: http://www.cellml.org/Members/miller/draft-normative-spec-andrews-preferred/toplevel.xhtml Please send any

[cellml-discussion] Minutes of Auckland CellML Meeting, 24th of August

2011-08-28 Thread Andrew Miller
Hi all, Please find the minutes at: http://www.cellml.org/community/meeting/minutes/2011/08.24 Best wishes, Andrew ___ cellml-discussion mailing list cellml-discussion@cellml.org http://lists.cellml.org/mailman/listinfo/cellml-discussion

[cellml-discussion] CellML API 1.9 released

2011-05-31 Thread Andrew Miller
with the binary releases of the API, and is available at: http://www.cellml.org/tools/api/docs/getting-started-with-the-cellml-api Best wishes, Andrew Miller ___ cellml-discussion mailing list cellml-discussion@cellml.org http://lists.cellml.org

[cellml-discussion] First unofficial draft of specification on CellML parameter uncertainty

2011-05-29 Thread Andrew Miller
Hi all, I've put together an unofficial draft specification on how uncertainty in CellML parameters could be represented. The first draft of this document is attached as a PDF; please let me know what you think. The specification is in DocBook; the source code and scripts to generate PDF

[cellml-discussion] SBML L3 dist package

2011-05-24 Thread Andrew Miller
Hi Darryl, I'm working on approaches for representing parameter uncertainty in CellML, and was wondering if you had any more recent draft specifications for the SBML dist package than the 2005 version on the SBML site (which currently only seems to have the 2005 draft and your presentation

[cellml-discussion] CellML API Release Candidate 4 out

2011-05-23 Thread Andrew Miller
with the release candidate are identified, a release of CellML API 1.9 will be made shortly. Please report any bugs you find on the tracker at https://tracker.physiomeproject.org/, or failing that to cellml-tools-develop...@cellml.org, or to ak.mil...@auckland.ac.nz. Best wishes, Andrew

[cellml-discussion] CellML API 1.9 release candidate 3 out

2011-05-17 Thread Andrew Miller
Hi all, A further release candidate for CellML API version 1.9 has just been released, and can be seen at: http://www.cellml.org/tools/downloads/cellml_api/releases/1.9rc3 The SDK binaries have been tested to work for compiling a simple program (in both C++ and Java), as documented at:

[cellml-discussion] CellML API 1.9 Release Candidate 2 available now

2011-05-03 Thread Andrew Miller
Hi all, Release candidate 2 for the CellML API 1.9 has been released, and can be downloaded from: * http://www.cellml.org/tools/downloads/cellml_api/releases/1.9rc2 The following are provided with this release candidate: * Source code * Binary CellML API SDK packages for: * Linux

[cellml-discussion] CellML API 1.9 Release Candidate 1 available now

2011-04-26 Thread Andrew Miller
Hi all, Release candidate 1 for the CellML API 1.9 has been released, and can be downloaded from: * http://www.cellml.org/tools/downloads/cellml_api/releases/1.9rc1 The following are provided with this release candidate: * Source code * Binary CellML API SDK packages for: * Linux

[cellml-discussion] Unofficial draft CellML specification - backwards compatibility, type attributes on variables

2011-02-01 Thread Andrew Miller
Hi all, I've just put up an unofficial draft CellML specification up at http://www.cellml.org/Members/miller/draft-normative-spec-andrews-preferred/toplevel.xhtml to prototype what some of the new features could look like. This version has the following features: Backwards and forwards

[cellml-discussion] ABI CellML Meeting Minutes, 15th December 2010

2010-12-16 Thread Andrew Miller
Hi all, I have put the minutes from this week's meeting up at: http://www.cellml.org/community/meeting/minutes/2010/12.15 Best wishes, Andrew ___ cellml-discussion mailing list cellml-discussion@cellml.org

Re: [cellml-discussion] Exponentiating in OpenCell

2010-09-07 Thread Andrew Miller
On 08/09/10 08:38, Erin wrote: Hello, I'm trying to use OpenCell to structure a model, but I'm having trouble using the equation editor. I'm typing in equations like the tutorial recommends and I'm using the character ^ to exponentiate. OpenCell doesn't seem to recognize that character, so

[cellml-discussion] Fwd: Multiple independent parameter support in the CellML API

2010-07-20 Thread Andrew Miller
Hi all, This may be of interest to some people on this list. Best wishes, Andrew Original Message Subject: Multiple independent parameter support in the CellML API Date: Thu, 15 Jul 2010 12:05:40 +1200 From: Andrew Miller ak.mil...@auckland.ac.nz To: Chris Bradley c.brad

Re: [cellml-discussion] Fwd: Haugh 2004b

2010-03-10 Thread Andrew Miller
Catherine Lloyd wrote: Hi Andrew and Randall This has gone beyond a curation question... Can one of you please explain daes to Lucian and also how OpenCell handles them? In a CellML model, if you have two equations: f(x, y, z, a, b, c) = g(x, y, z, a, b, c) h(x, y, z, a, b, c) = i(x, y,

Re: [cellml-discussion] ABI CellML meeting minutes 2009-12-16

2009-12-18 Thread Andrew Miller
alan.ga...@dpag.ox.ac.uk wrote: James Lawson wrote: We (Catherine, Poul and I) were thinking that there are basically three places where you'd want to display / store this information within PMR2: in the metadata itself (thereby allowing it to be rendered by software, indexed and searched

[cellml-discussion] Tracker / subversion outage tonight 9:30 PM to 11:30 PM

2009-12-16 Thread Andrew Miller
Hi all, The Physiome tracker and Subversion repositories containing software snapshots will be unavailable tonight from 9:30 PM until 11:30 PM NZDT (8:30 AM - 10:30 AM GMT) when power will be switched from the generator to mains power, following the power failure last night affecting the

Re: [cellml-discussion] Description of CellML groupings

2009-12-08 Thread Andrew Miller
groupings and also a CellML 1.1 model building tutorial at today's team meeting. Regarding the first comment, Andrew Miller has been working on the CellML 1.2 specification (currently a draft) and he will send you a link to it - asking if the description is any clearer in the new spec

Re: [cellml-discussion] Stochastic support / non-exclusion in CellML 1.2

2009-10-13 Thread Andrew Miller
Michael Cooling wrote: Hi I'm still interested in the below. Does anyone have any information beyond the comment I cite below? In particular, might I be able to read the document that Andrew wrote? Hi Mike, We don't have much in the way of a well-developed document; but a brief proposal

Re: [cellml-discussion] The CellML library basics

2009-07-27 Thread Andrew Miller
Lucian Smith wrote: * Justin Marsh j.ma...@auckland.ac.nz [2009-07-28 00:31] writes: Hi Lucian, The basic C++ should have two functions for each member attribute, named after the attribute; one with no arguments, which returns the value of the attribute, and one with one argument which

Re: [cellml-discussion] 'Model' has pure virtual functions

2009-07-23 Thread Andrew Miller
Lucian Smith wrote: I am just starting to use the CellML DOM API in C++, and am running into problems. Everything compiled fine (I'm using v1.6), but I seem to be unable to declare 'Model' objects because they contain pure virtual functions: This code: cellml_api::Model model; Hi Lucian,

Re: [cellml-discussion] ABI Meeting minutes 2009-05-06

2009-05-06 Thread Andrew Miller
Dougal Cowan wrote: I have put the minutes from Wednesday's meeting up at: http://www.cellml.org/meeting_minutes/abi-meeting-minutes-2009-05-06/ It is worth noting that the changes I sent earlier today weren't included in the minutes: Hi all, A few extra things: 4) Andrew will add a

[cellml-discussion] ABI Meeting minutes 2009-04-29

2009-05-05 Thread Andrew Miller
Hi all, I have put the minutes from last Wednesday's meeting up at: http://www.cellml.org/meeting_minutes/abi-meeting-minutes-2009-04-29/ Apologies to those who would have liked to see these sooner. Best wishes, Andrew ___ cellml-discussion mailing

[cellml-discussion] Using a functional programming language to express models

2009-04-21 Thread Andrew Miller
Hi all, I have created a tracker item to discuss the possibility of using a functional programming language to express models. Please see my description of how it could be done, add any comments you have on the idea there. Best wishes, Andrew ___

Re: [cellml-discussion] Using a functional programming language to express models

2009-04-21 Thread Andrew Miller
Andrew Miller wrote: Hi all, I have created a tracker item to discuss the possibility of using a functional programming language to express models. Please see my description of how it could be done, add any comments you have on the idea there. My apologies, I missed out the tracker item

[cellml-discussion] Proposal to re-structure CellML mailing lists

2009-04-21 Thread Andrew Miller
Hi all, I have created a tracker item for the proposal to restructure the CellML mailing lists, as the current structure of team and cellml-discussion (originally intended to avoid conflating technical and non-technical issues on the same list) isn't necessarily working as well as we would

Re: [cellml-discussion] cellml namespaces

2009-03-18 Thread Andrew Miller
Alan Garny wrote: Agreed, that wouldn't harm. A link to the CellML specification and some of the other existing content should be sufficient. Best wishes, Andrew Alan -Original Message- From: cellml-discussion-boun...@cellml.org [mailto:cellml-discussion- boun...@cellml.org]

[cellml-discussion] Example models using possible CellML 1.2 lambda calculus type system notation

2009-02-17 Thread Andrew Miller
Hi all, In response to a request by Poul Nielsen, I have produced a model demonstrating how this functionality might be used. type_library.cellml is the beginnings of a type library, which provides a complex number type and some other types needed to support it. The complex number type is

[cellml-discussion] Prototype SBML to CellML converter

2009-01-14 Thread Andrew Miller
Hi all, I have recently coded up a prototype designed to demonstrate how a program to convert from SBML to CellML might work. This prototype is written in Ruby using the REXML XPath parser, which was rapid to develop but makes it very slow to run - the intention is that once the algorithms

Re: [cellml-discussion] installation of CellML DOM API: Core implementation for all platforms

2008-10-07 Thread Andrew Miller
song zhen wrote: Hi Alan, I have read those documentations, but I am not familiar with this kind stuff, and the problem is that I don't really know what kind of the Linux systems I am using. Here is the information for my iMac: Mac OS X Version 10.4.11 (Tiger), Fink installed. Could you tell

[cellml-discussion] Finalising CellML Metadata 1.0 specification

2008-09-30 Thread Andrew Miller
Dear all, I would like to draw your attention to tracker item 1405, which can be viewed at https://tracker.physiomeproject.org/show_bug.cgi?id=1405 . This tracker item proposes that a decision on finalising the CellML Metadata Specification be made on the 15th of October 2008. Please add any

Re: [cellml-discussion] A typed lambda calculus system for CellML

2008-08-05 Thread Andrew Miller
Alan Garny wrote: Hi Andrew, I have been looking into how we could define a typed lambda calculus system in CellML, and have written up a document to collect ideas on this: http://www.cellml.org/Members/miller/outline-of-a-typed-lambda-calculus- system This is a good starting

Re: [cellml-discussion] A typed lambda calculus system for CellML

2008-07-31 Thread Andrew Miller
Randall Owen wrote: Andrew: This seems like a very good idea. How much work has actually been done in this area? Hi Randy, I presume you are only asking about work in relation to CellML? The document I linked is pretty much it in terms of actual written up documents... once we allow

[cellml-discussion] A typed lambda calculus system for CellML

2008-07-23 Thread Andrew Miller
Hi all, I have been looking into how we could define a typed lambda calculus system in CellML, and have written up a document to collect ideas on this: http://www.cellml.org/Members/miller/outline-of-a-typed-lambda-calculus-system This document does not yet aim to be a formal specification, but

Re: [cellml-discussion] CellML DOM API 1.4, CORBA and Java help

2008-06-18 Thread Andrew Miller
Randall Britten wrote: 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

Re: [cellml-discussion] unit conversion

2008-06-02 Thread Andrew Miller
' setting for the integrator in Jsim will not run the model - the CVode integrator must be selected manually. Kind regards, James Lawson Erik Butterworth wrote: On Thu, 29 May 2008, Andrew Miller wrote: I think James had something more along the lines of: I_inter_fibro = 10^6

Re: [cellml-discussion] [Fwd: Re: CellML model of Electrophysiological Modeling of Fibroblasts and their Interaction with Myocytes]

2008-05-28 Thread Andrew Miller
James Lawson wrote: Hi Andrew, I have to confess I really didn't understand Erik Butterworth's email. However this is a forward of a reply I just got from Frank Sachse, the original model author. I think he has a point - it seems that Jsim does do the dimensional conversion but PCEnv

[cellml-discussion] Representing stochastic models in CellML

2008-04-22 Thread Andrew Miller
Hi all, I have spent some time looking into how we might be able to represent stochastic models in CellML. This is something that would be useful to ensure we have properly contemplated for CellML 1.2. I have pasted in the notes I wrote on this below. Please let me know if you have any

Re: [cellml-discussion] Identifying smaller subsystems of simultaneous equations in differential-algebraic models

2008-04-21 Thread Andrew Miller
Randall Britten wrote: 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,

[cellml-discussion] Identifying smaller subsystems of simultaneous equations in differential-algebraic models

2008-04-15 Thread Andrew Miller
Hi all, One issue which has recently been discussed amongst those of us working on CellML tools is the best way to handle models which require systems of equations to be solved efficiently. For example, if a model has equations like: f1(a, b, c) = 0 f2(a, b, c) = 0 f3(a, c) = 0 f4(b, c, d, e)

[cellml-discussion] Specifying the variable(s) of integration / independent variable(s) in MIASE

2008-03-11 Thread Andrew Miller
Dear all, Based off the UML diagram at http://miase.cvs.sourceforge.net/*checkout*/miase/miaseOM/miaseOM/miaseOM.pdf?revision=1.5 , I notice that the UniformTimeCourse UML class makes the assumption that the model is being evaluated across a time variable (in other words, that time is

[cellml-discussion] Proposed CellML 1.2 change: removing group and replacing it with an encapsulation element

2008-03-04 Thread Andrew Miller
Hi all, As has been previously discussed on this mailing list, grouping in the general sense can be used to represent information such as containment which would more appropriately be treated as metadata and represented in RDF/XML. The overall process of moving this information out into

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

2008-03-04 Thread Andrew Miller
Hi all, There are a number of items in the CellML tracker regarding decisions about the next version of the CellML specification, which have been discussed in the past and around which consensus seems to have been reached, but on which we have yet to declare a final decision. By making a

Re: [cellml-discussion] CellML 1.1 to draft CellML 1.2 normative specification mapping

2008-02-20 Thread Andrew Miller
Alan Garny wrote: Hi Andrew, I have now defined a mapping between CellML 1.1 and one draft of CellML 1.2. I have put this up at: http://www.cellml.org/Members/miller/mapping-1-1-to-draft-1.2/mapping It currently has all the mappings from 1.1 to a particular 1.2 draft, although it may

Re: [cellml-discussion] Time delays in CellML models

2008-02-12 Thread Andrew Miller
Rui Zhu wrote: Dear Catherine, Thank you so much for your reply! It is very helpful! Learning CellML modeling from an expert is a really delightful experience. I am having another thought. I searched online, and it says SBML level2 can deal with the time delay term, Hi Rui, I have

[cellml-discussion] CellML 1.1 to draft CellML 1.2 normative specification mapping

2008-02-12 Thread Andrew Miller
Hi all, I have now defined a mapping between CellML 1.1 and one draft of CellML 1.2. I have put this up at: http://www.cellml.org/Members/miller/mapping-1-1-to-draft-1.2/mapping It currently has all the mappings from 1.1 to a particular 1.2 draft, although it may be missing some of the reverse

[cellml-discussion] Proposal: Simplification of connections - removal of directionality and map_components

2008-02-06 Thread Andrew Miller
Hi all, I am proposing that in CellML 1.2, we make connections between variables undirected (that is, we don't have an in or out on public or private interfaces for variables). I am also proposing that we remove the map_components element and move the component_1 and component_2 attributes

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

2008-01-30 Thread Andrew Miller
if connections don't have directionality, then it makes no sense in the language to say that a connection is from A to B, as opposed to from B to A, and we wouldn't want to force users to duplicate information and provide both directions. Best regards, Andrew Cheers, Quoting Andrew Miller [EMAIL

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

2008-01-30 Thread Andrew Miller
Michael Cooling wrote: because if connections don't have directionality, then it makes no sense in the language to say that a connection is from A to B, as opposed to from B to A, and we wouldn't want to force users to duplicate information and provide both Oops I didn't mean to

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

2008-01-30 Thread Andrew Miller
Michael Cooling wrote: if both state variables have the same initial values and rates (which they would... why should they have the same initial values? I agree if they did then it makes no difference to the correctness of the model but it seems very possible to create a model of

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

2008-01-30 Thread Andrew Miller
David Nickerson wrote: Hi Andrew, This looks quite intriguing. As you mention later in this thread I currently take the approach of adding an extra real scalar term and exposing that as a way to hook future (in my case) currents into ion concentration rate equations. Such and approach

[cellml-discussion] Proposal: Secondary specifications in CellML

2008-01-29 Thread Andrew Miller
Hi all, I am proposing that we define CellML 1.2 such that 'secondary CellML specifications' can be created. The primary CellML 1.2 specification will then define the core structure of CellML and the semantics of how models are created, with the secondary specifications narrowing it down to

[cellml-discussion] Using proposed CellML 1.2 features to create more re-usable metabolic models

2008-01-29 Thread Andrew Miller
Hi all, To aid in working out what features we should include in CellML 1.2, I have been looking into one of the major difficulties with creating re-usable metabolic models at the moment: that to compute a derivative, you need to know all the fluxes, but when a model is extended, new fluxes

[cellml-discussion] New Tracker Item: Describe how we can create secondary specifications to narrow CellML

2008-01-22 Thread Andrew Miller
Hi all, I filed a tracker item on the creating of a secondary specifications on how to narrow CellML to support particular types of models. https://tracker.physiomeproject.org/show_bug.cgi?id=332 Please feel free to comment on the tracker item. Best regards, Andrew

[cellml-discussion] Should RDF be allowed / required to be processed from extension elements?

2008-01-22 Thread Andrew Miller
Hi all, I filed a tracker item on where RDF/XML should be allowed in CellML Infosets. https://tracker.physiomeproject.org/show_bug.cgi?id=331 Please feel free to comment on the tracker item. Best regards, Andrew ___ cellml-discussion mailing list

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

2008-01-17 Thread Andrew Miller
-discussion- [EMAIL PROTECTED] On Behalf Of Andrew Miller Sent: 16 January 2008 23:30 To: For those interested in contributing to the development of CellML. Subject: [cellml-discussion] Base normative CellML Specification for further work Hi all, I have recently been working on developing

[cellml-discussion] Base normative CellML Specification for further work

2008-01-16 Thread Andrew Miller
Hi all, I have recently been working on developing an unofficial 'base' normative CellML specification to provide something off which proposed changes can be based and merged into. The aim of this unofficial draft specification is to provide a minimalistic, and normative, specification of all

[cellml-discussion] Identifying features for CellML from the SBML level 3 proposals

2008-01-15 Thread Andrew Miller
Hi all, I have had a look through the proposals at http://sbml.org/wiki/SBML_Level_3_Efforts . I don't know if there is a draft for the 'core' of SBML level three yet, although it seems the plan is that it will not change much from level 2. I think that under the current approach of splitting

Re: [cellml-discussion] A list of proposed changes to semantics to makein CellML 1.2

2008-01-09 Thread Andrew Miller
Randall Britten wrote: 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. The usage of the words public and private in CellML is conceptually different

Re: [cellml-discussion] A list of proposed changes to semantics to makein CellML 1.2

2008-01-09 Thread Andrew Miller
- [EMAIL PROTECTED] On Behalf Of Andrew Miller Sent: Thursday, 10 January 2008 1:39 p.m. ... For example, the total sodium current in the Beeler-Reuter model is meaningless to the parts which contribute to the sodium current, and isolating them properly from each other helps prevent

[cellml-discussion] Survey on opinions for the backwards compatibility levels for future CellML Specs

2008-01-08 Thread Andrew Miller
Hi all, There have recently been some discussions of changes which would drastically break forwards or backwards compatibility of CellML (for example, changing the way that connections work). I think that it is important that we come to some consensus on what the policy for inter-version

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

2008-01-08 Thread Andrew Miller
wishes Poul On 2008 Jan 09, at 11:58, Andrew Miller wrote: Hi all, There have recently been some discussions of changes which would drastically break forwards or backwards compatibility of CellML (for example, changing the way that connections work). I think that it is important

[cellml-discussion] Should groups be allowed to imply metadata information?

2007-12-11 Thread Andrew Miller
Hi all, The CellML 1.1 specification says: 6.5.3 Groups must not imply metadata information Modellers must not use CellML groups to associate properties or classification information with sets of components. The metadata functionality is the proper method for making such associations. This

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

2007-12-11 Thread Andrew Miller
Model, and Mathematical Model? Best regards, Andrew Andre. Andrew Miller wrote: Hi all, I have been working on resolving the current terminology issues in CellML 1.1 where 'model' is used to mean both the XML file in which the model element resides, and the abstract mathematical

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

2007-12-11 Thread Andrew Miller
David Nickerson wrote: Andrew Miller wrote: ... How about CellML Infoset, CellML Model, and Mathematical Model? That sounds good to me. While I guess this use of infoset is pretty common in the XML world, it might be useful to refer to the CellML XML Infoset? Or is it safe

Re: [cellml-discussion] specification draft and docbook

2007-11-27 Thread Andrew Miller
David Nickerson wrote: Hi Andrew, 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 -

Re: [cellml-discussion] specification draft and docbook

2007-11-23 Thread Andrew Miller
David Nickerson wrote: Hi Andrew, 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

[cellml-discussion] Question on community's preferred way to resolve CellML 1.1 identifier contradiction

2007-11-21 Thread Andrew Miller
Hi all, I have been working on writing up a purely normative, unambiguous draft of the CellML specification to facilitate discussions of how to improve CellML in the future. As part of this, I have been rewriting most of the text of the specification to follow good practices for normative

Re: [cellml-discussion] Proof of concept: using git for specification development

2007-11-11 Thread Andrew Miller
Alan Garny wrote: git is also a distributed version control system - the two tools have a fairly similar conceptual model in terms of how they work, with a lot of flow of ideas between the too tools. I have found git slightly faster and a bit more extensible (and with a larger set of commands

Re: [cellml-discussion] Proof of concept: using git for specification development

2007-11-11 Thread Andrew Miller
Alan Garny wrote: Andrew Miller wrote: Alan Garny wrote: There are viewable web interfaces for git - see the gitweb at e.g. http://repo.or.cz/w/cellml-draft- miller.git?a=tree;h=normative;hb=normative How does it work? Using Opera, if I click on blob for abstract.xml, I

Re: [cellml-discussion] Proof of concept: using git for specification development

2007-11-10 Thread Andrew Miller
, and if the community agrees, we will have a specification, complete with the merged revision histories from everyone who worked on it. Best regards, Andrew Bob G On Thu, 2007-11-08 at 13:44 +1300, Andrew Miller wrote: Hi all, As a proof of concept, I have set up an unofficial CellML

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

2007-11-07 Thread Andrew Miller
Matt wrote: On 8/11/2007, at 10:27 AM, Randall Britten wrote: Hi all Another option to add to the mix: using a Wiki. In this case, I would specifically suggest MediaWiki (a la Wikipedia). Pros: -Widely used, lots of user familiarity. -Easy collaboration: edits done via web interface.

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

2007-11-07 Thread Andrew Miller
Randall Britten wrote: Hi all Another option to add to the mix: using a Wiki. In this case, I would specifically suggest MediaWiki (a la Wikipedia). Hi Randall, Pros: -Widely used, lots of user familiarity. Although MediaWiki mark-up is similar to MoinMoin and other wiki software

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

2007-11-06 Thread Andrew Miller
of the markup (although perhaps easier than XML, depending on taste and familiarity with each markup language). Best regards, Andrew On 7/11/2007, at 2:16 PM, Andrew Miller wrote: Hi, One issue which came up at today's meeting for people at Auckland involved with CellML is how we will represent

Re: [cellml-discussion] online subversion browser?

2007-10-01 Thread Andrew Miller
David Nickerson wrote: Thanks Matt. Would be nice to get a permanent solution soon... Hi Andre, This is one of a list of services that I also would like to have. I have discussed this with Randall recently and I believe he intends to follow them up one-by-one with IT: 1) Bug tracker

Re: [cellml-discussion] FW: r1756 - pce/trunk/chrome/content/ui

2007-09-19 Thread Andrew Miller
Randall Britten wrote: Don't you think we should put a test in somewhere for this? (Perhaps a manual test for it is already in Litmus?). It is already in Litmus, although we could probably do automated testing of PCEnv too (it requires running Javascript as part of the tests, but Mozilla

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

2007-09-19 Thread Andrew Miller
Alan Garny wrote: 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

Re: [cellml-discussion] CellML Versioning Strategy

2007-09-19 Thread Andrew Miller
Matt Halstead wrote: Otherwise, Matt wrote: ... You might want to scan a document to see what versions the model conforms up to, but one of the nice things about pushing these new elements/attributes into new namespaces is that you can still treat a model as say 1.1 even if it contains

Re: [cellml-discussion] CellML Versioning Strategy

2007-09-19 Thread Andrew Miller
Alan Garny wrote: At the break-away session on the versioning strategy for CellML (which followed the Auckland CellML meeting today) we discussed the future of how we would version CellML, including whether we would put all elements for the next version of CellML in a completely different

Re: [cellml-discussion] r1755 - in pce/trunk/chrome/content: controls ui util

2007-09-18 Thread Andrew Miller
Hi, A few review comments for this commit are inline. CellML Automated Notifications wrote: Author: agarny Date: 2007-09-19 05:47:09 +1200 (Wed, 19 Sep 2007) New Revision: 1755 Modified: pce/trunk/chrome/content/controls/graph.xml pce/trunk/chrome/content/controls/model.xml

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

2007-09-18 Thread Andrew Miller
Hi all, The CellML Specification does not define the format in which real numbers will be represented at all (it just says, for initial_value: The value of the |initial_value| attribute may be a real number or a variable). The MathML specification defines A real number is presented in decimal

[cellml-discussion] CellML Versioning Strategy

2007-09-18 Thread Andrew Miller
Hi all, At the break-away session on the versioning strategy for CellML (which followed the Auckland CellML meeting today) we discussed the future of how we would version CellML, including whether we would put all elements for the next version of CellML in a completely different namespace, or

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