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I should mention that the staging instance will not persist its data whenever
I stage a new major feature. Please do not use it to keep your sole copy of
any models.

Do push it to the main instance, and keep a copy on your system for peace of
mind.


----- Reply message -----
From: "Randall Britten" <r.britten at auckland.ac.nz>
Date: Thu, Nov 24, 2011 12:42
Subject: [cellml-discussion] cellml-discussion Digest, Vol 87, Issue 10
To: "CellML Discussion List" <cellml-discussion at cellml.org>

Hi

Probably the easiest way to get MATLAB code for CellML models that are in the
CellML model repository if via the generated code link available for each
exposed cellml model. However, models.cellml.org uses a buggy version of the
API, but this has already been fixed by Tommy, and is staged at
http://50.18.64.32/ (see
https://tracker.physiomeproject.org/show_bug.cgi?id=3078#c4 ). This is due
to be deployed to the live site in the within about a month.

So, if your model is in the repository, you should be able to get valid
MATLAB code for it, and if not, just create an account for yourself on the
staged instance, create a workspace, upload your model, and create an
exposure (which will initially only be visible to you, i.e. you can keep it
private if you want).

Regards,
Randall


> -----Original Message-----
> From: cellml-discussion-bounces at cellml.org [mailto:cellml-discussion-
> bounces at cellml.org] On Behalf Of Andrew Miller
> Sent: Tuesday, 25 October 2011 9:41 a.m.
> To: cellml-discussion at cellml.org
> Subject: Re: [cellml-discussion] cellml-discussion Digest, Vol 87, Issue 10
>
> 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 might also have to create the variables
> > before it will let you export to Matlab.
>
> To add to what David said, the CellML API includes a general facility
> for translating CellML into imperative languages, and a specific
> description of how to do this for MATLAB, and this was exposed in
> OpenCell.
>
> There are a few problems with the generated MATLAB that have been
> found
> since the final release of OpenCell (which is no longer maintained in
> Auckland) that have been fixed in the API.
>
> There is a program that comes with the API (and which exists purely for
> testing the API, rather than as a user friendly program) - if you build
> the CellML API from source code, you can run it as follows:
>
> cd cellml-api
> ./testCeLEDS urlToModelHere ./CeLEDS/languages/MATLAB.xml
>
> Hopefully OpenCOR, which is based on the CellML API, and being developed
> in Oxford, will expose this functionality in a user friendly way.
>
> Best wishes,
> Andrew
>
> >
> > Cheers,
> > David.
> >
> > On Tue, Oct 25, 2011 at 7:58 AM, Maxwell Neal<mneal at u.washington.edu>
> wrote:
> >> Hi all,
> >>
> >> Does anyone know of a good java package for translating MathML into
> MATLAB?
> >> Many thanks,
> >>
> >> M
> >>
> >> ---------------------------------
> >> Maxwell Neal
> >>
> >> Post-doctoral researcher
> >> University of Washington
> >> mneal at uw.edu
> >> (206) 543-8769
> >> ---------------------------------
> >>
> >>
> >>
> >>
> >> On Oct 23, 2011, at 4:00 PM, cellml-discussion-request at cellml.org
> >> wrote:
> >>
> >>> Send cellml-discussion mailing list submissions to
> >>> cellml-discussion at cellml.org
> >>>
> >>> To subscribe or unsubscribe via the World Wide Web, visit
> >>> http://lists.cellml.org/mailman/listinfo/cellml-discussion
> >>> or, via email, send a message with subject or body 'help' to
> >>> cellml-discussion-request at cellml.org
> >>>
> >>> You can reach the person managing the list at
> >>> cellml-discussion-owner at cellml.org
> >>>
> >>> When replying, please edit your Subject line so it is more specific
> >>> than "Re: Contents of cellml-discussion digest..."
> >>>
> >>>
> >>> Today's Topics:
> >>>
> >>> 1. Re: cellml-discussion Digest, Vol 87, Issue 9 (Maxwell Neal)
> >>>
> >>>
> >>> ----------------------------------------------------------------------
> >>>
> >>> Message: 1
> >>> Date: Sat, 22 Oct 2011 19:02:16 -0700
> >>> From: Maxwell Neal<mneal at u.washington.edu>
> >>> Subject: Re: [cellml-discussion] cellml-discussion Digest, Vol 87,
> >>> Issue 9
> >>> To: cellml-discussion at cellml.org
> >>> Message-ID:<28198366-57CF-471F-8882-
> 34E73FC05C35 at u.washington.edu>
> >>> Content-Type: text/plain; charset=us-ascii
> >>>
> >>> Great. Thanks, Lucian and David.
> >>>
> >>> M
> >>>
> >>> ---------------------------------
> >>> Maxwell Neal
> >>>
> >>> Post-doctoral researcher
> >>> University of Washington
> >>> mneal at uw.edu
> >>> (206) 543-8769
> >>> ---------------------------------
> >>>
> >>>
> >>>
> >>>
> >>> On Oct 22, 2011, at 4:00 PM, cellml-discussion-request at cellml.org
> wrote:
> >>>
> >>>> Send cellml-discussion mailing list submissions to
> >>>> cellml-discussion at cellml.org
> >>>>
> >>>> To subscribe or unsubscribe via the World Wide Web, visit
> >>>> http://lists.cellml.org/mailman/listinfo/cellml-discussion
> >>>> or, via email, send a message with subject or body 'help' to
> >>>> cellml-discussion-request at cellml.org
> >>>>
> >>>> You can reach the person managing the list at
> >>>> cellml-discussion-owner at cellml.org
> >>>>
> >>>> When replying, please edit your Subject line so it is more specific
> >>>> than "Re: Contents of cellml-discussion digest..."
> >>>>
> >>>>
> >>>> Today's Topics:
> >>>>
> >>>> 1. Re: nested components in CellML (David Nickerson)
> >>>>
> >>>>
> >>>> ----------------------------------------------------------------------
> >>>>
> >>>> Message: 1
> >>>> Date: Sat, 22 Oct 2011 14:30:37 +1300
> >>>> From: David Nickerson<david.nickerson at gmail.com>
> >>>> Subject: Re: [cellml-discussion] nested components in CellML
> >>>> To: CellML Discussion List<cellml-discussion at cellml.org>
> >>>> Message-ID:
> >>>> <CADizRjhqHMOpDDm=8xoZLAD=BCOGNSm0XdLFma6Yeox20K-
> R4Q at mail.gmail.com>
> >>>> Content-Type: text/plain; charset=ISO-8859-1
> >>>>
> >>>> On Sat, Oct 22, 2011 at 10:10 AM, Lucian Smith<lpsmith at spod-
> central.org> wrote:
> >>>>> * Maxwell Neal<mneal at u.washington.edu> [2011-10-21 22:03]
> writes:
> >>>>>> Hi all,
> >>>>>>
> >>>>>> I was wondering - can CellML models have nested
> components? ?That is, are there instances where some model component is
> a component in another model component?
> >>>>>> Thanks,
> >>>>>
> >>>>> Yes--this is covered by the concept of encapsulation. ?See
> >>>>> http://www.cellml.org/getting-
> started/tutorials/tutorial/best_practice/#grouping
> >>>>> for more detail, but basically you set up a whole tree of nested
> >>>>> components, and this nesting determines the rules for how you can
> connect
> >>>>> the variables in those components.
> >>>>>
> >>>>> Also, an imported component from another file that encapsulates
> other
> >>>>> components brings those components (and corresponding
> connections) with
> >>>>> it in the import.
> >>>>>
> >>>>> Is that a reasonable summary, list denizens?
> >>>>
> >>>> yep, I think that summarises it nicely. Importing along with
> >>>> encapsulation allows the definition of models where some
> components
> >>>> are components from another model.
> >>>>
> >>>>
> >>>> Cheers,
> >>>> Andre.
> >>>>
> >>>>
> >>>> ------------------------------
> >>>>
> >>>> _______________________________________________
> >>>> cellml-discussion mailing list
> >>>> cellml-discussion at cellml.org
> >>>> http://lists.cellml.org/mailman/listinfo/cellml-discussion
> >>>>
> >>>>
> >>>> End of cellml-discussion Digest, Vol 87, Issue 9
> >>>> ************************************************
> >>>
> >>>
> >>>
> >>> ------------------------------
> >>>
> >>> _______________________________________________
> >>> cellml-discussion mailing list
> >>> cellml-discussion at cellml.org
> >>> http://lists.cellml.org/mailman/listinfo/cellml-discussion
> >>>
> >>>
> >>> End of cellml-discussion Digest, Vol 87, Issue 10
> >>> *************************************************
> >>
> >> _______________________________________________
> >> cellml-discussion mailing list
> >> cellml-discussion at cellml.org
> >> http://lists.cellml.org/mailman/listinfo/cellml-discussion
> >>
> > _______________________________________________
> > cellml-discussion mailing list
> > cellml-discussion at cellml.org
> > http://lists.cellml.org/mailman/listinfo/cellml-discussion
>
> _______________________________________________
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> http://lists.cellml.org/mailman/listinfo/cellml-discussion
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• [cellml-discussion] cellml-discussion Digest, Vol 87, Issue 10, Tommy Yu, 11/24/2011

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