Re: [cellml-discussion] [team-cellml] Linux functional test buildof PCEnv available

2006-10-01 Thread David Nickerson
remains to be seen. And not that such functionality is currently required (or expected) from the CellML API implementation. David. -- David Nickerson, PhD Research Fellow Division of Bioengineering Faculty of Engineering National University of Singapore Email: [EMAIL PROTECTED

Re: [cellml-discussion] [team-cellml] Linux functional test buildofPCEnv available

2006-10-01 Thread David Nickerson
I'm not sure we would name them so the URL needed a query portion, because that would mean that browsers would save the model wrong. A hierarchy (perhaps a subset of an existing ontology restricted so it becomes a tree) could be used to locate the model from the path rather than query,

Re: [cellml-discussion] [team-cellml] Linux functionaltestbuildofPCEnv available

2006-10-03 Thread David Nickerson
There may also be requirements for some of the metadata you describe in terms of model curation. Andre. Andrew Miller wrote: David Nickerson wrote: I agree that we need to only ever have a single URL for a given model and you have pretty much convinced me that we don't want to start

Re: [cellml-discussion] API with relative URLs

2006-10-08 Thread David Nickerson
-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 mailing

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

2006-10-18 Thread David Nickerson
/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 http://www.cellml.org

Re: [cellml-discussion] Binary and source snapshots for PCEnv onWin32and Linux

2006-10-18 Thread David Nickerson
Assuming that there is an exception, the most likely cause is that you are still using an old version of cellml_corba_server, with a new version of PCEnv. This could happen if you ran the old functional test build, and then installed the latest snapshot. If you are changing from one

[cellml-discussion] pcenv and cellml_corba_server

2006-10-19 Thread David Nickerson
application for people to run. Why does it need to start up a independent server of any kind and why does it then leave that server running once you exit the application? -- David Nickerson, PhD Research Fellow Division of Bioengineering Faculty of Engineering National University of Singapore

Re: [cellml-discussion] Binary and source snapshots for PCEnvonWin32and Linux

2006-10-19 Thread David Nickerson
I have now grabbed to 20061020 snapshot release (linux) and I'm getting this error when I click the integrate button: /path/to/pcenv-snap20061020/gcc/bin/../libexec/gcc/i386-linux/3.4.3/ld:/usr/lib/libc.so: file format not recognized; treating as linker script

Re: [cellml-discussion] pcenv and cellml_corba_server

2006-10-19 Thread David Nickerson
Andrew Miller wrote: David Nickerson wrote: Ok - you have some reasonable arguments for why this approach has been used. But if we accept that this is the correct way to be doing this, then I think the way pcenv is being distributed needs to be changed. The fact

Re: [cellml-discussion] Binary and source snapshots for PCEnvonWin32and Linux

2006-10-20 Thread David Nickerson
a parameter and plotting the results together. David Nickerson wrote: I have now grabbed to 20061020 snapshot release (linux) and I'm getting this error when I click the integrate button: /path/to/pcenv-snap20061020/gcc/bin/../libexec/gcc/i386-linux/3.4.3/ld:/usr/lib/libc.so: file format

Re: [cellml-discussion] CellML meetings - can we shift toconference calls?

2006-10-26 Thread David Nickerson
-- 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

[cellml-discussion] pcenv development priorities

2006-10-29 Thread David Nickerson
plugging CVODE in will result in comparable performance - in which case it would then seem a good time to make an initial official release. David. -- David Nickerson, PhD Research Fellow Division of Bioengineering Faculty of Engineering National University of Singapore Email: [EMAIL PROTECTED

Re: [cellml-discussion] pcenv development priorities

2006-10-30 Thread David Nickerson
possible I have either missed some relative links or left out some required files... Andrew Miller wrote: David Nickerson wrote: Hi all, From today's meeting minutes the following priorities were set for the development of pcenv: 1. Make an official release of what we have now, instead

Re: [cellml-discussion] pcenv development priorities

2006-10-30 Thread David Nickerson
] On Behalf Of David Nickerson Sent: 30 October 2006 10:14 To: For those interested in contributing to the development of CellML. Subject: Re: [cellml-discussion] pcenv development priorities Just thought it might be useful to establish some benchmarks for comparison of performance amongst

[cellml-discussion] Graphing metadata

2006-10-30 Thread David Nickerson
? Thanks, David. -- 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

Re: [cellml-discussion] Graphing metadata

2006-10-30 Thread David Nickerson
Andrew Miller wrote: David Nickerson wrote: Thanks Andrew, cleared a few things up. So now for some more ideas/questions... When defining a graph outside the scope of a single model or when combining results from multiple model's, does it still make sense to use the about=modelid ? I

Re: [cellml-discussion] Graphing metadata

2006-10-31 Thread David Nickerson
I wouldn't be opposed, however, to adding a style guideline recommending that graph nodes be given an explicit URL (we actually say that they would normally be an anonymous node at the moment), so they can be referenced. The only disadvantages of this is that the resulting RDF/XML is

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

2006-11-08 Thread David Nickerson
-- 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

Re: [cellml-discussion] Quick questions about units...

2006-11-09 Thread David Nickerson
CellML processing software is not required to check for dimensional consistency at the equation level (but validating software would probably want to). Software is also not strictly required to convert at the connection level, although appendix C defines how to do this if software

Re: [cellml-discussion] Quick questions about units...

2006-11-09 Thread David Nickerson
eye...for example, this sort of equation can give you widely different results without the need for any units corrections at the connection level: a [mM] = b [uM] + c [mM] but would presumably result in (b*0.001) within the equation... David. -- David Nickerson, PhD Research Fellow Division

[cellml-discussion] cmeta:id's and the CCGS

2006-12-25 Thread David Nickerson
, but the general idea seems sound to me. What do people think? Perhaps there is already a way to do this or something similar, but I couldn't find it. Or maybe I'm just going about this in completely the wrong way? David. -- David Nickerson, PhD Research Fellow Division of Bioengineering Faculty

Re: [cellml-discussion] Switching between graphs in PCEnv: Opinionssought

2007-02-27 Thread David Nickerson
Regarding the setups for a model, there is a minor UI inconsistency here, because PCEnv adopts a many to many relationship between models and graph panels (otherwise you wouldn't, for example, be able to compare two model runs on the same set of axes). However, this conflicts with the

Re: [cellml-discussion] [team-cellml] corrections for the minutes

2007-03-04 Thread David Nickerson
Andrew Miller wrote: David Nickerson wrote: Just to note that the page for the website has been ready for a while now, it is only the programme which is not finalised and can't be until we know who can make itand we are running out of time to promote the event... Thanks

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

2007-03-15 Thread David Nickerson
a reason why this would ever be required? David. -- 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] PCEnv questions

2007-03-22 Thread David Nickerson
Three queries: 1. Regarding the saved session facility - if it is now possible to save a session that includes the model as well as the graph layout, could we not just load a session containing the model when you click on the website link to a model? Hi Peter, I have already asked

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

2007-04-11 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

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

2007-04-11 Thread David Nickerson
. cheers Matt ___ 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

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

2007-04-11 Thread David Nickerson
Another alternative in the short term would to simply name the models as separate models (which they are) That's an interesting proposal. Given the current way that the models are listed, that would be a good way of displaying that the models are variants. If you upload two variants of a

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

2007-04-11 Thread David Nickerson
e.g. model-1/generic/1.xml model-1/parameterisations/1.xml model-1/parameterisations/2.xml but should that be parameterisations or parameterizations? :-) Anyway, yes. Needs a working group, but also needs a starting document that at least lists the objectives of this before we all throw in

[cellml-discussion] Initial units assignment

2007-04-16 Thread David Nickerson
CellML model authors to make it worthwhile pursuing such a project? Anyone interested please speak up :-) David. -- David Nickerson, PhD Research Fellow Division of Bioengineering Faculty of Engineering National University of Singapore Email: [EMAIL PROTECTED

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

2007-04-17 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] Identifying time-points at which themodelbecomes stiff

2007-04-19 Thread David Nickerson
I was actually thinking more along the lines of when stiff_indicator is zero, a transition to stiffness occurs. stiff_indicator would be expected to be defined in such a way that it gradually approaches zero, rather than suddenly falls to zero, or it is stiff too and so not much help. The

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

2007-04-20 Thread David Nickerson
going back to the following equation Andrew supplied: amount_Na [nmol] = 10^-6 [dimensionless] * conc_Na [nmol / L] * vol[microL] How do you make this more 'valid'? (it is already valid dimensionally and numerically). but it is not consistent or valid dimensionally. The specification

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

2007-04-22 Thread David Nickerson
So where does the problem lie? This says that all you supposedly dimensionless constants should have units. Does it need to be clearer that you are not allowed to simplify them out into dimensionless yourself? yes - I think this is the issue. Also that tools shouldn't simplify them into

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

2007-04-23 Thread David Nickerson
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. so you

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

2007-04-24 Thread David Nickerson
on. Best regards, Andrew ___ 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

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

2007-05-01 Thread David Nickerson
) ^ (#expr2 != 0) Best regards, Andrew ___ 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

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

2007-05-01 Thread David Nickerson
The intention is that MaLaES is a lower-level API, in the sense that it only describes how to convert MathML into some sort of flat text-based representation of the equations. It does not define any semantics for the interpretation of the results, because the semantics are up to the user

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

2007-05-10 Thread David Nickerson
options would. I welcome any opinions on what approach would be best. Best regards, Andrew Miller ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion -- David Nickerson

[cellml-discussion] broken tabs on the repository pages

2007-05-14 Thread David Nickerson
The model metadata, curation, and procedural code tabs on the model repository model pages seem to be currently broken. For all the models I try I get plone errors for each of them... model metadata: Error Type AttributeError Error Value CellMLMetadata instance has no attribute

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

2007-05-14 Thread David Nickerson
Procedural code relies on the CCGS server provided by the CellML API, and if the server is down or being restarted that happens. So I managed to find the tiny window when it was down or being restarted? cool! :-) As for the model metadata and curation, they don't always have data populated

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

2007-05-14 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] Proposed backward-incompatible changes to theCCGS.

2007-05-15 Thread David Nickerson
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, and CUSES. Due to the large scale

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

2007-05-16 Thread David Nickerson
While I haven't followed through with any changes, I'm hoping that modifying a model's name or curation level will force the editor to also add modification metadata to the model? You could perhaps pre-populate the modification fields based on the changes the user is making... I am

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

2007-05-16 Thread David Nickerson
excellent, thanks for the explanations Andrew - it all makes sense now :-) Andre. Andrew Miller wrote: 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

Re: [cellml-discussion] Analytic Jacobians and visibility of variables

2007-05-21 Thread David Nickerson
Hi Jonathan, I've recently been working on a tool to symbolically compute an analytic Jacobian for (parts of) cardiac electrophysiological models described in CellML. Those of you at the CellML workshop may remember a few slides on this in the Oxford talk. The tool determines the Jacobian

[cellml-discussion] altering existing currents in an electrophysiology model

2007-05-30 Thread David Nickerson
to alter some of the potentially deeply encapsulated variables. The page is http://www.cellml.org/wiki/ModelReuse and I'd be keen on any thoughts people might have on this... Andre. -- David Nickerson, PhD Research Fellow Division of Bioengineering Faculty of Engineering National University

Re: [cellml-discussion] PMR categories

2007-06-05 Thread David Nickerson
@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 mailing list

Re: [cellml-discussion] PMR categories

2007-06-05 Thread David Nickerson
James Lawson wrote: David Nickerson wrote: Would I be correct in assuming that these terms will be key words added to the model metadata and that the division into categories on the main repository page will be assembled from queries on each of these predefined key words? Well

Re: [cellml-discussion] PMR categories

2007-06-05 Thread David Nickerson
And what are the consequences for a model not fitting into any of these categories? It has to fit somewhere, I don't think the list is easily determined from the top down like this. I would prefer that keywords were added for each model and then we look at the accumulation of terms post

Re: [cellml-discussion] PMR categories

2007-06-05 Thread David Nickerson
, and as a broad category filter for the main repository listing. Users would still be able to add or search by other keywords (from the advance search interface) if they wish. Tommy. Matt wrote: On 6/6/07, David Nickerson [EMAIL PROTECTED] wrote: James Lawson wrote: David Nickerson wrote

Re: [cellml-discussion] PMR categories

2007-06-07 Thread David Nickerson
appropriate terms or additional ones, then I'll ask Tommy to implement it. I'm happy to then go through and classify all current models in the repository into these categories. Cheers, Peter David Nickerson wrote: One thing I have found useful in other taxonomy/keyword type web

Re: [cellml-discussion] clarification required?

2007-06-10 Thread David Nickerson
number of models in the repository is no longer given? Thanks, David. ___ 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] clarification required?

2007-06-10 Thread David Nickerson
True, that does present a point of confusion. What we (perhaps not so obviously) meant was that there are that number of models that are based on peer reviewed papers. I see the repository has now been updated, but the new statement is even more confusing and putting more emphasis on the peer

Re: [cellml-discussion] PMR categories

2007-06-11 Thread David Nickerson
Tommy Yu wrote: David Nickerson wrote: Actually they are. Keywords are defined in the CellML metadata specifications and are already being used in various files. Feel free to check the CellML files of the old repository and scroll down the to keyword section. An example follows. From

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

2007-06-20 Thread David Nickerson
I don't know what has been used for checking the models, but my validator (https://chaste.ediamond.ox.ac.uk/cellml/) can thoroughly check units (at least where no implicit equations are used). But it's not a simulation engine, so probably shouldn't also be displayed. whoops, knew there was

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

2007-06-20 Thread David Nickerson
I haven't been using Jsim, I've mainly been using PCEnv. It is my understanding that I can't use Jsim yet, from what others have told me, but I haven't checked that out myself. I can't recall any reason why you couldn't use JSim - just like Jonathan's validator it will give you errors for

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

2007-06-20 Thread David Nickerson
OK - now I'm really confused by all this talk of stars and simulation tools. Perhaps the key is to separate the model curation status from the simulation tools - i.e., to have a distinct Curation Level field at the top of the model page separate to the current Download options section. I think

Re: [cellml-discussion] a detailed curation specification

2007-06-20 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] curation status of models in the repository

2007-06-20 Thread David Nickerson
James Lawson wrote: David Nickerson wrote: OK - now I'm really confused by all this talk of stars and simulation tools. Perhaps the key is to separate the model curation status from the simulation tools - i.e., to have a distinct Curation Level field at the top of the model page separate

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

2007-06-21 Thread David Nickerson
Jonathan Cooper wrote: On Thu, Jun 21, 2007 at 02:12:38PM +0800, David Nickerson wrote: Wilfred Li wrote: Maybe instead of the star system, which may be open to interpretation at first sight, an abbreviation or a specific word may be used to represent its status? I guess that if you use

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

2007-06-21 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

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

2007-06-21 Thread David Nickerson
No, there are no stars, anywhere, that are on by default. They are all off by default until someone, probably me, certifies that the model meets the requirements to get itself a star, or two. Or maybe three. ok - good to know. ___ cellml-discussion

Re: [cellml-discussion] a detailed curation specification

2007-06-21 Thread David Nickerson
I have been thinking about this and I think it's worth proposing formally. But is having a whole level all about units consistency justified? Perhaps there are other things we could add to this level that could similarly require the intervention/expertise of the model author? I can't think of

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

2007-06-22 Thread David Nickerson
Do we really want to proxy remote repositories? Can we start smaller for now but keep that in mind? I think this will be an essential feature of the model repository as we move forward. We are trying to present model authors with a common platform for the distribution and archiving of their

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

2007-06-22 Thread David Nickerson
and/or build on top of it. Cheers, Tommy. ___ 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

[cellml-discussion] model upload problems

2007-06-22 Thread David Nickerson
since I can run simulations of the model fine using my tool based on the CCGS and API and the code generation tab works fine and gives me the expected C code. Anyone have any suggestions? Thanks, Andre. -- David Nickerson, PhD Research Fellow Division of Bioengineering Faculty

[cellml-discussion] Draft graphing metadata specification updated

2007-06-22 Thread David Nickerson
and the expected outputs. David. -- 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

Re: [cellml-discussion] model upload problems

2007-06-24 Thread David Nickerson
element of model in the CellML 1.0 namespace and give the user an error and not accept the model? Andre. James Tommy Yu wrote: David Nickerson wrote: Hi, I just tried to load the attached model into the model repository to use as an example with the graphing metadata specification

Re: [cellml-discussion] model upload problems

2007-06-24 Thread David Nickerson
Loading http://www.cellml.org/models/sine-approximations_version01 in PCEnv, the graph has three traces, but only one of them shows (sin1). Is this supposed to happen? not sure - I think that because the graphing metadata is still under development PCEnv, I think, uses a combination of

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

2007-06-24 Thread David Nickerson
In terms of the policy for allocating addresses, we don't want to become a free e-mail redirection host for anyone on the Internet, but I think as long as someone at least has some connection with CellML, they should be allowed an alias (subject to review of what that alias is to ensure

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

2007-06-25 Thread David Nickerson
Matt wrote: On 6/25/07, David Nickerson [EMAIL PROTECTED] wrote: Matt wrote: This seems like it's going in circles. I'm not really sure why anyone would want to contact us personally with something they didn't want to send to the list. Thinking about this more we should probably try: 1

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

2007-06-25 Thread David Nickerson
a catchall for the whole team for example, I don't really know who I would want to bother personally if I had a personal problem with the sbml site or wanted to invite the team to a conference, or was rejected from the mailing list, etx; I would just use the Email: [EMAIL PROTECTED] link

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

2007-06-25 Thread David Nickerson
Matt wrote: This seems like it's going in circles. I'm not really sure why anyone would want to contact us personally with something they didn't want to send to the list. Thinking about this more we should probably try: 1) cellml-discussion@cellml.org 2) [EMAIL PROTECTED] - for specific

Re: [cellml-discussion] Tracker for Roadmap

2007-06-26 Thread David Nickerson
with it for now. Your feedback would be appreciated. Thanks. Regards, Randall ___ 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] CellML tracker

2007-06-26 Thread David Nickerson
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 for some input from the wider

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

2007-06-26 Thread David Nickerson
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 is that these lists only be used for messages like

Re: [cellml-discussion] CellML2Dot

2007-06-27 Thread David Nickerson
Hi James, James Lawson wrote: Hi Andre, In the workshop you showed us a slide of a program you'd made for debugging models that showed all the connections etc. Is this that program? I tried to get the source off subversion but it didn't work. Do you have any tips on getting this tool to

Re: [cellml-discussion] CellML2Dot

2007-06-27 Thread David Nickerson
to keep current value): Variable Name: LIBRARY_OUTPUT_PATH Description: Single output directory for building all libraries. Current Value: New Value (Enter to keep current value): Please wait while cmake processes CMakeLists.txt files David Nickerson wrote: Hi James, James Lawson

Re: [cellml-discussion] CellML2Dot

2007-06-27 Thread David Nickerson
PS - as you go through this if you can think of anything that would make the process easier for you can you please file them under the tracker at http://sourceforge.net/projects/cellml, thanks! ___ cellml-discussion mailing list

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

2007-07-17 Thread David Nickerson
I think the current use of an embedded stimulus current is due to the repository being limited to CellML 1.0 models. The correct way to approach this problem is this: (1) define the mathematical model independent of parameter values and boundary/initial conditions; (2) (this is an optional

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

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

2007-07-18 Thread David Nickerson
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 intention to deprecate reaction elements

Re: [cellml-discussion] CellML 1.1.1 specification

2007-07-18 Thread David Nickerson
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 erratum would be

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] 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] 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

[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] 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

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

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