Chronological Thread 

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Hi Aroli,

You can see another example in here for a pure CellML S1S2 protocol
definition:
https://models.physiomeproject.org/w/andre/nickerson-2008/file/d6328d18c94e9dad70f4d0e4b250e89429773b62/cellml/protocols;
in particular
https://models.physiomeproject.org/w/andre/nickerson-2008/rawfile/d6328d18c94e9dad70f4d0e4b250e89429773b62/cellml/protocols/S1S2-restitution.xml
defines the switch from a periodic stimulus protocol to a single pulse
at the appropriate interval. Note these files won't simulate in
OpenCOR on their own, but maybe give an idea how to implement your own
S1S2 in CellML if you are after a pure CellML solution.

The protocol language used in the WebLab is a lot more capable in
terms of specifying arbitrary stimulus protocols, as well as being
able to pull out restitution/APD properties - which can't be done in
pure CellML.

Cheers,
Andre.

On 12 April 2018 at 03:47, Cooper, Jonathan
<j.p.cooper AT ucl.ac.uk>
wrote:
> Hi Aroli,
>
>
>
> I’m not sure I quite understand your question. The plot you link shows both
> the AP arising from the last S1 stimulus and the AP from the S2 stimulus. In
> the version of S1-S2 restitution there, we do many S1 paces to get the model
> to quasi-steady-state. However, it’s possible to write a different version
> of the protocol if you want it to do something different. There’s a link to
> the protocol at the top of the results page, so you can see how it’s
> implemented.
>
>
>
> Best wishes,
>
> Jonathan
>
>
>
> From:
> <cellml-discussion-request AT lists.cellml.org>
> on behalf of Aroli
> Marcellinus
> <aroli.marcellinus AT gmail.com>
> Reply-To:
> "cellml-discussion AT cellml.org"
>
> <cellml-discussion AT cellml.org>
> Date: Thursday, 12 April 2018 at 05:05
> To:
> "cellml-discussion AT cellml.org"
>
> <cellml-discussion AT cellml.org>
>
>
> Subject: Re: [cellml-discussion] S1S2 Stimulus Protocol in CellML cell model
>
>
>
> Hi Cooper,
>
> Thank you for the recommendation. I have looked at the simulator, but can
> you explain to me about the simulator? Since I just only found S2 result,
> but no S1. How can I simulate both S1 and S2 simulation on this platform?
>
>
> Aroli Marcellinus
> Kumoh Institute of Technology
> Computational Medicine Laboratory
> 61 Daehak-ro (Sinpyeong-dong), Gumi, Gyeongbuk
> +82 10 9724 3957
> KTalk ID: vondarkness
>
>
>
> On Wed, Apr 11, 2018 at 6:41 PM, Cooper, Jonathan
> <j.p.cooper AT ucl.ac.uk>
> wrote:
>
> Hi Aroli,
>
>
>
> You might also want to look at our Web Lab, which has a S1-S2 restitution
> protocol - https://chaste.cs.ox.ac.uk/WebLab/db/protocols/7 - run on a range
> of models, including post-processing of the raw results. We can give you an
> account if you want to add your own CellML files to the collection.
>
>
>
> Best wishes,
>
> Jonathan
>
>
>
> From:
> <cellml-discussion-request AT lists.cellml.org>
> on behalf of Alan Garny
> <a.garny AT auckland.ac.nz>
> Reply-To:
> "cellml-discussion AT cellml.org"
>
> <cellml-discussion AT cellml.org>
> Date: Wednesday, 11 April 2018 at 02:15
> To: cellml-discussion Mailing List
> <cellml-discussion AT lists.cellml.org>
> Subject: Re: [cellml-discussion] S1S2 Stimulus Protocol in CellML cell model
>
>
>
> Hi Aroli,
>
>
>
> Yes, an S1S2 stimulus protocol can be applied to a CellML file. Just replace
> the existing stimulus protocol (if any) in the CellML file with your S1S2
> stimulus protocol.
>
>
>
> Alan
>
>
>
> From:
> <cellml-discussion-request AT lists.cellml.org>
> on behalf of Aroli
> Marcellinus
> <aroli.marcellinus AT gmail.com>
> Reply-To: cellml-discussion Mailing List
> <cellml-discussion AT lists.cellml.org>
> Date: Wednesday, 11 April 2018 at 1:03 PM
> To: cellml-discussion Mailing List
> <cellml-discussion AT lists.cellml.org>
> Subject: [cellml-discussion] S1S2 Stimulus Protocol in CellML cell model
>
>
>
> Hello everyone,
>
> I just want to know if the S1S2 stimulus can be applied to CellML cell
> models. Is there any reference or method to replace the common stimulus
> protocol into S1S2 stimulus protocol?
>
> Thank you
>
>
>
>
> Aroli Marcellinus
> Kumoh Institute of Technology
> Computational Medicine Laboratory
> 61 Daehak-ro (Sinpyeong-dong), Gumi, Gyeongbuk
> +82 10 9724 3957
> KTalk ID: vondarkness
>
>



--


David Nickerson
about.me/david.nickerson

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• [cellml-discussion] S1S2 Stimulus Protocol in CellML cell model, Aroli Marcellinus, 04/11/2018
  • Re: [cellml-discussion] S1S2 Stimulus Protocol in CellML cell model, Alan Garny, 04/11/2018
    • Re: [cellml-discussion] S1S2 Stimulus Protocol in CellML cell model, Cooper, Jonathan, 04/11/2018
      • Re: [cellml-discussion] S1S2 Stimulus Protocol in CellML cell model, Aroli Marcellinus, 04/12/2018
        • Re: [cellml-discussion] S1S2 Stimulus Protocol in CellML cell model, Cooper, Jonathan, 04/12/2018
          • Re: [cellml-discussion] S1S2 Stimulus Protocol in CellML cell model, David Nickerson, 04/13/2018
            • Re: [cellml-discussion] S1S2 Stimulus Protocol in CellML cell model, Aroli Marcellinus, 04/13/2018
              • Re: [cellml-discussion] S1S2 Stimulus Protocol in CellML cell model, Aroli Marcellinus, 04/13/2018

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