Re: [cellml-discussion] cellml-discussion Digest, Vol 87, Issue 10
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-boun...@cellml.org [mailto:cellml-discussion- boun...@cellml.org] On Behalf Of Andrew Miller Sent: Tuesday, 25 October 2011 9:41 a.m. To: cellml-discussion@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 There are a few problems with the generated MATLAB that have been found since the final release of OpenCell (which is no longer maintained in Auckland) that have been fixed in the API.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 Nealmn...@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 mn...@uw.edu (206) 543-8769 - On Oct 23, 2011, at 4:00 PM, cellml-discussion-requ...@cellml.org wrote: Send cellml-discussion mailing list submissions to cellml-discussion@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-requ...@cellml.org You can reach the person managing the list at cellml-discussion-ow...@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 Nealmn...@u.washington.edu Subject: Re: [cellml-discussion] cellml-discussion Digest, Vol 87, Issue 9 To: cellml-discussion@cellml.org Message-ID:28198366-57CF-471F-8882- 34e73fc05...@u.washington.edu Content-Type: text/plain; charset=us-ascii Great. Thanks, Lucian and David. M - Maxwell Neal Post-doctoral researcher University of Washington mn...@uw.edu (206) 543-8769 - On Oct 22, 2011, at 4:00 PM, cellml-discussion-requ...@cellml.org wrote: Send cellml-discussion mailing list submissions to cellml-discussion@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-requ...@cellml.org You can reach the person managing the list at cellml-discussion-ow...@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 Nickersondavid.nicker...@gmail.com
Re: [cellml-discussion] cellml-discussion Digest, Vol 87, Issue 10
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. Cheers, David. On Tue, Oct 25, 2011 at 7:58 AM, Maxwell Neal mn...@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 mn...@uw.edu (206) 543-8769 - On Oct 23, 2011, at 4:00 PM, cellml-discussion-requ...@cellml.org wrote: Send cellml-discussion mailing list submissions to cellml-discussion@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-requ...@cellml.org You can reach the person managing the list at cellml-discussion-ow...@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 mn...@u.washington.edu Subject: Re: [cellml-discussion] cellml-discussion Digest, Vol 87, Issue 9 To: cellml-discussion@cellml.org Message-ID: 28198366-57cf-471f-8882-34e73fc05...@u.washington.edu Content-Type: text/plain; charset=us-ascii Great. Thanks, Lucian and David. M - Maxwell Neal Post-doctoral researcher University of Washington mn...@uw.edu (206) 543-8769 - On Oct 22, 2011, at 4:00 PM, cellml-discussion-requ...@cellml.org wrote: Send cellml-discussion mailing list submissions to cellml-discussion@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-requ...@cellml.org You can reach the person managing the list at cellml-discussion-ow...@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.nicker...@gmail.com Subject: Re: [cellml-discussion] nested components in CellML To: CellML Discussion List cellml-discussion@cellml.org Message-ID: CADizRjhqHMOpDDm=8xoZLAD=bcognsm0xdlfma6yeox20k-...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 On Sat, Oct 22, 2011 at 10:10 AM, Lucian Smith lpsm...@spod-central.org wrote: * Maxwell Neal mn...@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@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@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@cellml.org http://lists.cellml.org/mailman/listinfo/cellml-discussion ___
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 Nealmn...@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 mn...@uw.edu (206) 543-8769 - On Oct 23, 2011, at 4:00 PM, cellml-discussion-requ...@cellml.org wrote: Send cellml-discussion mailing list submissions to cellml-discussion@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-requ...@cellml.org You can reach the person managing the list at cellml-discussion-ow...@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 Nealmn...@u.washington.edu Subject: Re: [cellml-discussion] cellml-discussion Digest, Vol 87, Issue 9 To: cellml-discussion@cellml.org Message-ID:28198366-57cf-471f-8882-34e73fc05...@u.washington.edu Content-Type: text/plain; charset=us-ascii Great. Thanks, Lucian and David. M - Maxwell Neal Post-doctoral researcher University of Washington mn...@uw.edu (206) 543-8769 - On Oct 22, 2011, at 4:00 PM, cellml-discussion-requ...@cellml.org wrote: Send cellml-discussion mailing list submissions to cellml-discussion@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-requ...@cellml.org You can reach the person managing the list at cellml-discussion-ow...@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 Nickersondavid.nicker...@gmail.com Subject: Re: [cellml-discussion] nested components in CellML To: CellML Discussion Listcellml-discussion@cellml.org Message-ID: CADizRjhqHMOpDDm=8xoZLAD=bcognsm0xdlfma6yeox20k-...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 On Sat, Oct 22, 2011 at 10:10 AM, Lucian Smithlpsm...@spod-central.org wrote: * Maxwell Nealmn...@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.
