Re: [cellml-discussion] API with relative URLs

2006-10-08 Thread Andrew Miller
David Nickerson wrote: What is your xml:base URL on the importing model (this is set automatically to the absolute URI being loaded by the API if you do a synchronous load, and it isn't already set)? Obviously the process of resolving a relative URL by an absolute URI is getting the wrong

[cellml-discussion] [Fwd: AUTH48 [SG]: RFC 4708 draft-miller-media-type-cellml-05.txt NOW AVAILABLE]

2006-10-09 Thread Andrew Miller
Original Message Subject:AUTH48 [SG]: RFC 4708 NOW AVAILABLE Date: Mon, 9 Oct 2006 16:38:51 -0700 From: rfc-editor@rfc-editor.org To: [EMAIL PROTECTED] CC: rfc-editor@rfc-editor.org IMPORTANT* Updated 2006/10/09 RFC AUTHOR(S): --

Re: [cellml-discussion] AUTH48 [SG]: RFC 4708 draft-miller-media-type-cellml-05.txt NOW AVAILABLE

2006-10-09 Thread Andrew Miller
) : Area Director(s) : Best regards, Andrew Miller ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion

[cellml-discussion] Binary and source snapshots for PCEnv on Win32 and Linux

2006-10-18 Thread Andrew Miller
, please send your system details (and any error messages) to [EMAIL PROTECTED], so they can be fixed before the stable release. * Feedback about the functionality of PCEnv is welcomed. Please send this to [EMAIL PROTECTED], or to the mailing list [EMAIL PROTECTED] Best regards, Andrew Miller

Re: [cellml-discussion] Binary and source snapshots for PCEnv on Win32and Linux

2006-10-18 Thread Andrew Miller
David Nickerson wrote: Hi Andrew, Using the linux snapshot given below I try to load my model (CellML 1.1) and I get some messages flash up in the status bar about loading the files and looking for further imports - the only URI I see is that of the units model which is imported by all

Re: [cellml-discussion] Questions about the CCGS, and 3 possible bugs

2006-10-25 Thread Andrew Miller
Jonathan Cooper wrote: Many thanks for your swift and thorough response. * Andrew Miller [EMAIL PROTECTED] [2006-10-24 22:51]: Jonathan Cooper wrote: Hi Andrew, You may be aware that a group of people are writing a review article on CellML and associated tools, for a special

Re: [cellml-discussion] Graphing metadata

2006-10-30 Thread Andrew Miller
David Nickerson wrote: Hi all, I have just been looking through the graphing metadata specification (http://www.cellml.org/specifications/metadata/graphs) and have a couple of questions (pretty much due to my continuing RDF ignorance). This specification seems to have dropped behind the

[cellml-discussion] application/cellml+xml media type now official

2006-10-30 Thread Andrew Miller
Hi all, The RFC defining the correct media type for CellML documents to be application/cellml+xml has now been published, as RFC4708. It can now be viewed at ftp://ftp.rfc-editor.org/in-notes/rfc4708.txt. Best regards, Andrew Miller ___ cellml

Re: [cellml-discussion] Graphing metadata

2006-10-31 Thread Andrew Miller
David Nickerson wrote: Therefore, you have to be aware of the relationship between RDF/XML and the RDF data model, and make sure you put your rdf:ID in the right place (as with any other attribute in RDF). ok - I think something just dropped into place. So in this case what I would

Re: [cellml-discussion] pcenv development priorities

2006-10-31 Thread Andrew Miller
This is with the main program / SUNDIALS compiled with -O2, and the generated code compiled with -O3 -ffast-math. I have disassembled the computation functions in the -O3 -ffast-math code, and it looks reasonable, there are no CALL instructions anymore (the built-in exp and log from gcc

[cellml-discussion] Release process for XPCORBA, CellML API, xpcellml_api, and PCEnv

2006-11-01 Thread Andrew Miller
Hi all, I have been codifying the recent discussions on team-cellml into a shell script which can be used to control the build process. This shell script will be sourced into the scripts used launch automated builds, and also into the scripts which package snapshots and put them onto the FTP

[cellml-discussion] CellML API 1.0rc1 (release candidate for CellML API 1.0) out

2006-11-05 Thread Andrew Miller
with the release candidate are identified, the API will be released. Please report any bugs you find at http://www.cellml.org/tools/api/api_tracker, or to this list, or directly to [EMAIL PROTECTED] Best regards, Andrew Miller ___ cellml-discussion mailing list

Re: [cellml-discussion] CellML API 1.0rc1 (release candidate for CellML API 1.0) out

2006-11-05 Thread Andrew Miller
Andrew Miller wrote: Hi all, The first release candidate for CellML API, version 1.0, has been released Information about the released files is available at http://www.cellml.org/tools/api/downloads/cellml-dom-api-core-implementation/releases/1.0rc1 . If you would like to ensure that your

[cellml-discussion] xpcellml_api 1.0rc1 (release candidate for xpcellml_api 1.0) out

2006-11-05 Thread Andrew Miller
API is released), xpcellml_api will be released. Please report any bugs you find at http://www.cellml.org/tools/api/api_tracker, or to this list, or directly to [EMAIL PROTECTED] Best regards, Andrew Miller ___ cellml-discussion mailing list cellml

[cellml-discussion] PCEnv 0.1rc1 (release candidate for PCEnv 1.0) out

2006-11-05 Thread Andrew Miller
report any bugs you find at http://www.cellml.org/tools/pcenv/tracker, or to this list, or directly to [EMAIL PROTECTED] Best regards, Andrew Miller ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo

[cellml-discussion] New Draft: Custom Subset Metadata specification

2006-11-05 Thread Andrew Miller
are solicited, please send them to cellml-discussion@cellml.org Best regards, Andrew Miller ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion

Re: [cellml-discussion] CellML API 1.0rc1 (release candidate forCellMLAPI 1.0) out

2006-11-13 Thread Andrew Miller
David Nickerson wrote: Andrew Miller wrote: David Nickerson wrote: I just grabbed the CellML API 1.0rc1 and found that it does not have a configure file. The README that comes with the distribution says to follow the instructions in the INSTALL which talk about the standard

[cellml-discussion] CellML API 1.0r2 (release candidate for CellML API 1.0) out

2006-11-13 Thread Andrew Miller
enhancements to the CellML, DOM. MathML and CCGS implementations, to fix the performance problems seen in the CCGS with 1.0rc1. Best regards, Andrew Miller ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo

Re: [cellml-discussion] [team-cellml] CellML Spec: Non-mandatory units on connections + option of conversions at math level

2006-11-13 Thread Andrew Miller
Matt wrote: Sure. I replied to that earlier thread last night. I haven't seen your post on the list, so I guess it got lost somewhere (the mailman has been delaying my messages for rather random periods of time recently, so I am guessing there is some bottleneck that could also be timing

[cellml-discussion] Mac OSX PCEnv: Is it a problem to depend on a system gcc?

2006-11-15 Thread Andrew Miller
Hi all, I have put some more work into getting cctools to compile on OS X (the Mac port needs this, in order to be able to run the generated code). We can't use the official binaries for licensing reasons (and also, for portability reasons, see below). There are numerous known problems

[cellml-discussion] CellML API 1.0rc3 (release candidate for CellML API 1.0) out

2006-11-15 Thread Andrew Miller
being lost when using CORBA (due to CORBA message size limits being exceeded) was fixed. You can download the source code for the CellML API 1.0rc3 from http://www.cellml.org/tools/api/downloads/cellml-dom-api-core-implementation/releases/1.0rc3 Best regards, Andrew Miller

[cellml-discussion] User input language for MathML in CellML

2006-11-16 Thread Andrew Miller
Hi all, I am looking at what sort of grammar can be used to represent and edit the content MathML included inside components and reactions in CellML models. I propose the following grammar (this is a valid and unambiguous bison grammar). This has been designed to be intuitive to people who

Re: [cellml-discussion] simulation metadata editing

2006-12-04 Thread Andrew Miller
Bob Gustafson wrote: Are the models/metadata/simulation-results in any sort of Version Control System (Subversion comes to mind)? Models are assigned a 'version' and a 'variant', and the model curation workflow means that models are never changed or deleted, instead a copy of the model

Re: [cellml-discussion] import bug in the CCGS?

2006-12-21 Thread Andrew Miller
David Nickerson wrote: I have attached two implementations of the same equation, y = sin(x). In the case where the equation is given in a component within the same model as its parent in the encapsulation hierarchy (import_bug-ok.xml) everything works fine and CellML2C gives me the expected

Re: [cellml-discussion] BioModels qualifiers in CellML and references to external data

2006-12-28 Thread Andrew Miller
David Nickerson wrote: Hi all, Just wanted to see what people think about using the BioModels qualifiers (http://biomodels.net/index.php?s=Qualifiers) in CellML models? i.e., following the SBML annotation specification (see section 6 of the SBML level 2 version 2 specification). The

Re: [cellml-discussion] Session specs for PCEnv

2007-03-11 Thread Andrew Miller
difference as to how this case is handled. Best regards, Andrew Miller ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion

[cellml-discussion] Proposal: BCP for including external code in CellML models

2007-03-14 Thread Andrew Miller
protect the utility of CellML as a model interchange format? 5) Does the proposed approach fit well with the design of CellML? Thanks and Best regards, Andrew Miller ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org

Re: [cellml-discussion] Proposal: BCP for including external code inCellML models

2007-03-15 Thread Andrew Miller
) CellML with external (non-standardised) code. Best regards, Andrew Miller ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion

Re: [cellml-discussion] Proposal: BCP for including external codeinCellML models

2007-03-17 Thread Andrew Miller
David Nickerson wrote: ECMAScript is not practical for use in modelling, because it is an interpreted, non-typed language, which necessarily means that it cannot be compiled and will be slower than compiled code. But CellML is an language for the description and exchange of

Re: [cellml-discussion] Proposal: BCP for including external codeinCellML models

2007-03-18 Thread Andrew Miller
Matt wrote: I have often thought referencing external code through a clearly defined interface would be useful, and mostly because procedural code is another natural way to solve problems. But I have always banged my head up against validation. With procedural code this amounts to passing

[cellml-discussion] Biological and other non-model citations in CellML metadata?

2007-03-28 Thread Andrew Miller
Hi, As discussed at the last CellML meeting, there are some models which reference both the paper about the model, and a reference about the biology. Since there is no way to determine between them, this creates problems for CellML metadata processing tools which want to identify the paper

Re: [cellml-discussion] Identifying time-points at which the modelbecomes stiff

2007-04-17 Thread Andrew Miller
David Nickerson wrote: Hi Andrew, Are you thinking that you'd have metadata like when variable IStim is non-zero reduce maxDt to x or more like when variable IStim is non-zero system becomes stiff and let the software decide the best way to handle that? I was actually thinking more along

[cellml-discussion] Using CellML to represent huge CellML models: Has anyone worked on this already?

2007-04-23 Thread Andrew Miller
Hi, I am working on developing a CellML model (using external code) of transcriptional control in yeast which is 23 MB in size. I hope to eventually do a similar thing for organisms which have much more complicated sets of interactions, in which case this size may grow substantially. If

Re: [cellml-discussion] Using CellML to represent huge CellML models:Has anyone worked on this already?

2007-04-23 Thread Andrew Miller
David Nickerson wrote: I am working on developing a CellML model (using external code) of transcriptional control in yeast which is 23 MB in size. I hope to eventually do a similar thing for organisms which have much more complicated sets of interactions, in which case this size may grow

[cellml-discussion] Proposal: Refactoring the CCGS into smaller, re-usable components

2007-04-23 Thread Andrew Miller
Hi, I have been wanting to use some functionality present in the CellML Code Generation Service, for a quite different type of problem (not a system of ODEs). The problem is, the functionality isn't exposed. I think there is actually quite a lot of useful functionality in the CCGS which could

Re: [cellml-discussion] Using CellML to represent huge CellML models: Has anyone worked on this already?

2007-04-25 Thread Andrew Miller
Randall Owen wrote: In message [EMAIL PROTECTED] CellML Discussion List cellml-discussion@cellml.org writes: Hi, I am working on developing a CellML model (using external code) of transcriptional control in yeast which is 23 MB in size. I hope to eventually do a similar thing for

[cellml-discussion] Describing rules for translating expressions into arbitrary languages

2007-04-29 Thread Andrew Miller
Hi, I am looking at refactoring the CCGS into several components, as discussed in an earlier e-mail. As part of this, I am looking at how I can separate out the language specific parts of code generation. At this stage, I am focusing on how expressions get generated, rather than entire

Re: [cellml-discussion] Describing rules for translating expressionsinto arbitrary languages

2007-05-01 Thread Andrew Miller
at the level of the format specification. Best regards, Andrew Andre. Andrew Miller wrote: Hi, I am looking at refactoring the CCGS into several components, as discussed in an earlier e-mail. As part of this, I am looking at how I can separate out the language specific parts of code

[cellml-discussion] CCGS Refactoring Branch

2007-05-02 Thread Andrew Miller
with CellML, and any suggested improvements (or patches :) ). Best regards, Andrew Miller ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion

[cellml-discussion] Implications of MathML 3.0 for CellML

2007-05-08 Thread Andrew Miller
Hi, There was a brief discussion of the implications of the recent MathML 3.0 public draft on CellML at today's CellML meeting. I noted that the following changes from MathML 2.0 to the canonical form of MathML 3.0 would be likely to affect us if we were to allow MathML 3.0 in CellML: 1)

Re: [cellml-discussion] Describing rules for translating expressions into arbitrary languages

2007-05-08 Thread Andrew Miller
Jonathan Cooper wrote: * Andrew Miller [EMAIL PROTECTED] [2007-04-29 23:51]: I have defined a file format specification, called MAL (or MathML-language mapping) designed to contain all the information needed to generate expressions for a specific programming language. I would welcome

[cellml-discussion] Interactions between SVG diagrams and PCEnv.

2007-05-09 Thread Andrew Miller
be edited in something other than a text editor. However, they do not give the same flexibility as the other options would. I welcome any opinions on what approach would be best. Best regards, Andrew Miller ___ cellml-discussion mailing list cellml

Re: [cellml-discussion] Proposed backward-incompatible changes to theCCGS.

2007-05-16 Thread Andrew Miller
David Nickerson wrote: Hi Andrew, I think the advantages offered by this transition outweigh the lack of backwards compatibility and have no objections to your proposal, just a few clarifications below... I am planning on completely updating the CCGS to make use of CeVAS, MaLaES,

Re: [cellml-discussion] removal of reaction components from models

2007-05-16 Thread Andrew Miller
@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion Best regards, Andrew Miller ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion

[cellml-discussion] PCEnv 0.2 released

2007-06-12 Thread Andrew Miller
are encouraged to upgrade. Should you find a bug in PCEnv, please report it at http://www.cellml.org/tools/pcenv/bugs . Best regards, Andrew Miller ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml

Re: [cellml-discussion] PCEnv sessions description

2007-06-18 Thread Andrew Miller
regards, Andrew Miller ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion

Re: [cellml-discussion] curation status of models in the repository

2007-06-20 Thread Andrew Miller
James Lawson wrote: Hi David, ... Because of the way this model is built, getting the units to match would require drastically remaking it, and I don't think I'd know how to do it. I have some ideas, but only because this is a particularly simple model, with 3 differential equations and

Re: [cellml-discussion] Cellml website access speed and IE7 warning

2007-06-20 Thread Andrew Miller
Wilfred Li wrote: Hi, everyone, It seems that the access speed from North America to the website is rather slow, Network latencies and throughputs from New Zealand - US are always going to be slower than the typical speeds within each respective country, so I'm not sure if this is normal or

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

2007-06-21 Thread Andrew Miller
Tommy Yu wrote: 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

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

2007-06-21 Thread Andrew Miller
Matt wrote: - Version/Variant It already clogged up the system. There is no proper revision control mechanism, what we have now is an ad-hoc emulated system. I don't think it has clogged the system I just think it has been improperly used both by authors and by the user interface.

Re: [cellml-discussion] [team-cellml] @cellml.org addresses

2007-06-24 Thread Andrew Miller
James Lawson wrote: See below... Andrew Miller wrote: David Nickerson wrote: I see the project team is being the core management team for the CellML project - essentially the group that should be making the decisions when consensus can't be reached and setting the goals

Re: [cellml-discussion] [team-cellml] @cellml.org addresses

2007-06-24 Thread Andrew Miller
David Brooks wrote: See below... On 25/06/2007 4:32 p.m., Andrew Miller wrote: James Lawson wrote: Andrew Miller wrote: I don't think we should use the word 'project team' because there is no formal project team. Perhaps we can just have a list of people categorised

Re: [cellml-discussion] [team-cellml] @cellml.org addresses

2007-06-25 Thread Andrew Miller
Matt wrote: I still don't like the idea of a 'core project team' simply because that would require defining what the core project is, and it would appear to then give exclusive domain over such aspects to a limited set of people. In some sense, my objection is that the CellML 'project' is not

[cellml-discussion] Proposal: Local CellML team e-mail addresses

2007-06-26 Thread Andrew Miller
rules for the list. 5) Transitional measures for the Auckland group: a) A list [EMAIL PROTECTED] will be created. b) All members of the list [EMAIL PROTECTED] will be subscribed to [EMAIL PROTECTED] c) Andrew Miller will be the initial designated administrator of [EMAIL PROTECTED] d

Re: [cellml-discussion] Tracker for Roadmap

2007-06-26 Thread Andrew Miller
David Nickerson wrote: Hi Randall, Two quick points. PCEnv is an Auckland tool and as discussed previously it should be kept quite distinct from the community sections of cellml.org - i.e., there shouldn't be a common tracker for PCEnv and the specifications and cellml.org etc. I

Re: [cellml-discussion] Proposal: Local CellML team e-mail addresses

2007-06-26 Thread Andrew Miller
, and the people who make the final decision can do so on the basis of discussions (which may include them) on the list. I don't see any need for a second mailing list for this. Andre. Andrew Miller wrote: Hi, There has been some discussion recently about how best to handle local CellML

Re: [cellml-discussion] CellML tracker

2007-06-26 Thread Andrew Miller
David Nickerson wrote: Andrew Miller wrote: Hi, At the Auckland CellML meeting today, we discussed the possibility of changing to a better tracker and moving some of the mailing list discussions onto that tracker. Everyone at the meeting agreed with this idea, so I am now looking

Re: [cellml-discussion] Proposal: Local CellML team e-mail addresses

2007-06-26 Thread Andrew Miller
David Nickerson wrote: Andrew Miller wrote: David Nickerson wrote: Hi Andrew, I think this is an excessive response to a very minor problem. I very easily see this evolving into many separate and distinct local communities with little interaction. The intention

Re: [cellml-discussion] CellML tracker

2007-06-26 Thread Andrew Miller
David Nickerson wrote: Michael Dunstan just suggested Trac and Poi as being worth looking at too. I don't think Poi has the same level of features as Bugzilla (e.g. CC lists, etc...). are these CC lists any different to the subscription feature of the current plone

[cellml-discussion] Expanding the CellML abbreviation

2007-07-02 Thread Andrew Miller
Hi, I have noticed that a lot of people who refer to CellML (generally people who don't use CellML, but reference it) feel obliged to expand the abbreviation, and they generally expand it as Cell Markup Language. As far as I am aware, we have never actually said that CellML stands for Cell

[cellml-discussion] [Fwd: Re: [team-cellml] Agenda items]

2007-07-16 Thread Andrew Miller
Andre's post crossed with mine, but he is right, this should be on CellML Discussion, so I am forwarding my message there too... Original Message Subject:Re: [team-cellml] Agenda items Date: Tue, 17 Jul 2007 17:53:59 +1200 From: Andrew Miller [EMAIL PROTECTED] Reply

Re: [cellml-discussion] information_cellml_simulator

2007-07-18 Thread Andrew Miller
of these program send simulations to run on remote servers, although I am not aware of any of them requiring accounts for normal use. Best regards, Andrew Miller ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org

[cellml-discussion] CellML 1.1.1 specification

2007-07-18 Thread Andrew Miller
David Nickerson wrote: Andrew Miller wrote: David Nickerson wrote: 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

Re: [cellml-discussion] CellML 1.1.1 specification

2007-07-18 Thread Andrew Miller
David Nickerson wrote: Correct me if I am wrong, but I believe that nothing in the text of the CellML 1.1 specification says that reactions will or will not be deprecated in any future version of CellML, and therefore there is no need for an erratum to CellML 1.1 (and indeed, such an

[cellml-discussion] CellML version interoperability strategy

2007-07-18 Thread Andrew Miller
David Nickerson wrote: I think that we disagree about how the specification process should work and what it aims to address. I see a given version of a CellML specification as being a 'protocol' which both tools and model authors speak, therefore allowing them to interwork. All I'm

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

2007-07-20 Thread Andrew Miller
/ security issue options), and you also have the option when commenting 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

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

2007-07-20 Thread Andrew Miller
to change this - I am just not sure how to make it less confusing - perhaps once we have at least one duplicate in statistics for the database it won't be as confusing? Best regards, Andrew Thanks, David. Andrew Miller wrote: Hi all, Following discussions with the IT group yesterday

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

2007-07-20 Thread Andrew Miller
David Nickerson wrote: What does this mean? I guess that CellML_1.1.1 is a bad name for the flag. Flags are a generic facility in Bugzilla which are requested and then granted or denied. I intended for this to be used for proposals to be requested for CellML 1.1.1 (i.e. suggested for a

Re: [cellml-discussion] CellML technical question.

2007-08-01 Thread Andrew Miller
for your feedback on PCEnv. Best regards, Andrew Thanks again. From: Andrew Miller [EMAIL PROTECTED] To: CellML Discussion List cellml-discussion@cellml.org CC: [EMAIL PROTECTED] Subject: Re: [cellml-discussion] CellML technical question. Date: Wed, 01 Aug 2007 09:30:26 +1200

Re: [cellml-discussion] how to units make a difference to simulation

2007-08-06 Thread Andrew Miller
Alan Garny wrote: As you know we (Catherine, you and I) spent a bit of time this morning trying to understand some models. One of the models that Catherine has been working on had problems with units. My understanding is that PCEnv didn't pick those problems up, while COR did. Correcting the

Re: [cellml-discussion] how to units make a difference to simulation

2007-08-06 Thread Andrew Miller
Alan Garny wrote: Again, this is a feature that it would be useful to be able to turn on and off. However I think in most cases the software will not be smart enough to figure out what the units should be. Wrong, it can easily be done. I was about to work on that in COR when Peter got

Re: [cellml-discussion] automated connection creation

2007-08-07 Thread Andrew Miller
James Lawson wrote: Hi all, I was sitting in bed last night, and this idea came to me: It would be really easy to create some kind of script / automation process that automatically connects up variables of the same name if they have matching interfaces. Say you have a component A with

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

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

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

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

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

2007-08-19 Thread Andrew Miller
. Andrew Miller wrote: David Nickerson wrote: Hi all, I have just done an update on my working copy of the CellML API C++ implementation and have found that new version of the code generation services (?) have arrived. While I presume the CCGS code is still complete and working

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

2007-08-19 Thread Andrew Miller
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 right, so you need

Re: [cellml-discussion] Include_in_CellML_1.2 requested: [Tracker Item 153] Allow multiple connections between the same pair of components

2007-08-28 Thread Andrew Miller
Hi all, Are there any objections to marking this as something we should include in CellML 1.2? Best regards, Andrew [EMAIL PROTECTED] wrote: Andrew Miller [EMAIL PROTECTED] has asked for Include_in_CellML_1.2: Tracker Item 153: Allow multiple connections between the same pair of components

[cellml-discussion] Removing PCEnv snapshots from ftp.bioeng.auckland.ac.nz

2007-09-09 Thread Andrew Miller
Hi, Due to space limitations on the bioengineering FTP server, I have recently migrated all snapshots into Subversion so we can take advantage of the binary diff functionalities to store them more efficiently. The plan is that all new snapshots will only go into Subversion. I updated the

[cellml-discussion] Changing component import semantics

2007-09-11 Thread Andrew Miller
9.4.1.2: * An import element may not contain any pair of components which are related by encapsulation. Please send any comments you have about this proposed changed to [EMAIL PROTECTED] Best regards, Andrew Miller ___ cellml-discussion mailing

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

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

2007-09-18 Thread Andrew Miller
David Nickerson 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

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] 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] 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] 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] 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] 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

[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] 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

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 -

[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

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