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

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

Re: [cellml-discussion] UnitsML

Hi Bernard, I have thought about this a little. The biggest problem with using an ontology is that there doesn't seem to be any possibility of a mechanism for allowing user-defined units. The units ontology at present also doesn't appear to contain enough information to perform units convers

Re: [cellml-discussion] ABI Meeting minutes 2009-03-11

On 11/03/09 21:25, Dougal Cowan wrote: > I have put the minutes from yesterday's meeting up at: > > http://www.cellml.org/meeting_minutes/abi-meeting-minutes-2009-03-11 Thanks for getting the minutes up quickly. I have a comment on one item: "Randall asked whether it would be worth making the infi

Re: [cellml-discussion] Looping Cell Cycle Models

On 28/12/08 22:11, Nicolas Le novère wrote: > Catherine Lloyd wrote: > >> However, we now face a different problem... Although we can easily >> describe the switches as piece-wise equations, if we define a single >> variable more than once in a CellML model the simulation tools tell >> us that the

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

On 26/08/08 12:28, Jonathan Cooper wrote: > Andrew Miller wrote: >> 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/M

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

Andrew Miller wrote: 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 fo

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

that it better reflects the > declarative intent of CellML model descriptions. How would that work for a component like B below, which has both a public and private interface for the same variable? Jonathan. > On 2007 Dec 22, at 03:20, Jonathan Cooper wrote: > > > On Thu, Dec 2

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

this requires quite a major change in the specification, even if only to avoid user confusion. For example, I would want to deprecate the use of "in" and "out", and instead allow public_interface="yes" or public_interface="no" (perhaps a synonym for &quo

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

for instance, and I wouldn't think it'd be much harder in any other framework. Overall, I don't have a strong opinion either way on this issue. Just removing the assertion should allow my software to still work with the change. I do recall however that COR used to (and maybe still does)

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

could've sworn that wasn't the case, but I've checked, and you're right. Ho hum. I've added an option to my validator to demote units errors to warnings, so that if the only problems are with units models can still be reported as valid. It is disabled by default, however

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

ays though: 1 if it loads, 2 if it also runs, etc. Jonathan. -- Jonathan Cooper MSN: [EMAIL PROTECTED] www: jonc.me.uk/ Politics is a field where the choice lies constantly between 2 blunders. - John Morley MP ___ cellml-discussion mailing lis

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

ly check units (at least where no implicit equations are used). But it's not a simulation engine, so probably shouldn't also be displayed. Jonathan. -- Jonathan Cooper MSN: [EMAIL PROTECTED] www: jonc.me.uk/ There is no substitute for brains - but silence sometimes

[cellml-discussion] Analytic Jacobians and visibility of variables

ome up with a better mechanism for allowing limited access to encapsulated variables, in order to allow for: * setting parameters in imported models; and * creating a meta-component containing a Jacobian for use by solvers? Any suggestions? Jonathan. -- Jonathan Cooper MSN: [EMAIL PROTECTED]

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

I am curious, however, as to whether there was any particular reason not to use an XML format for MAL? Jonathan. -- Jonathan Cooper MSN: [EMAIL PROTECTED] www: jonc.me.uk/ It is astonishing what foolish things one can temporarily believe if one think

Re: [cellml-discussion] Initial units assignment

ors to make it worthwhile pursuing such a project? Anyone > interested please speak up :-) I'm not a model author, but I do find this interesting. Is there any documentation available on how JSim does this? Jonathan. -- Jonathan Cooper MSN: [EMAIL PROTECTED] www: jonc.me.uk/

[cellml-discussion] Dimensional consistency and units conversions (was [Fwd: Re: ten Tusscher model])

ipulated by the mathematical operators in the expression > before any expansion and simplification were done. eg: > > y [m] = 1000 [m/km] * x [km] = (1000 * x) [m] > > but it seems that expansion and simplification are done first, eg: > > y [m] = 1000 [m/km] * x [km

[cellml-discussion] Fwd: Re: Meeting outcome

like to point out that the mailing list link in http://www.cellml.org/notes/cleanup-of-cellml-specification-units is broken. It would also be good to link to http://www.cellml.org/pipermail/cellml-discussion/2006-October/000292.html which contains some discussion on confusions about units with offsets. Jonat

[cellml-discussion] Units in CellML

Hello all, Having spent a while grappling with the units sections of the CellML 1.0 specification whilst writing my validation tool, I have a few comments and queries on the model CellML uses for units. For the most part, I like it. However, when dealing with units with offsets, things get ra