Chronological Thread 

< Chronological >      < Thread >

---

Hi Alan,


So about the point Interval, can you elaborate more about it? Since what is
the difference of 1-1000ms with 1ms interval and 1-1000ms with 0.01ms
interval? Since some simulation worked at 1ms, and some simulation worked
at 0.01ms. I still need better explanations about this one.

And also, if I convert the file into C++, how can I simulate the point
interval in my code?

Aroli Marcellinus

*Kumoh Institute of Technology**Computational Medicine Laboratory*
61 Daehak-ro (Sinpyeong-dong), Gumi, Gyeongbuk
+82 10 9724 3957
KTalk ID: vondarkness

On Thu, Aug 3, 2017 at 10:06 AM, Alan Garny
<alan.garny AT inria.fr>
wrote:

> Hi Aroli,
>
>
>
> No, “Point interval” is not the same as dt. “Point interval” is used to
> determine how often you want simulation data to be generated (e.g. 1 ms)
> while dt is indeed used to integrate the ODEs (e.g. 0.01 ms when using
> Forward Euler).
>
>
>
> What I meant to say is that you were to download only the file named
> “MainSystemic.cellml” (by clicking on the “Download This File” button under
> the “Downloads” category), then you wouldn’t be able to run that file. On
> the other hand, if you were to download the complete archive (by clicking
> on the “Complete Archive as .tgz” button under the “Downloads” category),
> uncompress the archive and open “MainSystemic.cellml”, then you would be
> able to run that file (since the archive contains a copy of the imported
> CellML files).
>
>
>
> Otheriwse, you can indeed convert a CellML 1.1 model to CellML 1.0. Have a
> look here <http://opencor.ws/user/plugins/tools/CellMLTools.html>.
>
>
>
> HTH, Alan
>
>
>
> On 02/08/2017, 21:42, "Aroli Marcellinus"
> <aroli.marcellinus AT gmail.com>
> wrote:
>
>
>
> Thank you for the reply, Alan,
>
> I just want know, what is POINT INTERVAL actually? Is it same as the dt in
> the ODE?
>
> And also like you said, *CellML file imports other CellML files, so to
> download this CellML file only will clearly not work. You also need the
> other files it imports.*
>
> Let's say I already downloaded all of the file from .tar.gz format, and
> open it in my local PC. How can I make those three dependent files working
> each other? Alternatively, is there any way to convert those dependent
> files into a single file of CellML using any software?
>
>
> Aroli Marcellinus
>
> *Kumoh Institute of TechnologyComputational Medicine Laboratory*
> 61 Daehak-ro (Sinpyeong-dong), Gumi, Gyeongbuk
> +82 10 9724 3957
> KTalk ID: vondarkness
>
>
>
> On Thu, Aug 3, 2017 at 2:00 AM, Alan Garny
> <alan.garny AT inria.fr>
> wrote:
>
> Hi Aroli,
>
>
>
> FWIW, I have just opened the two links you provided and clicked on their
> corresponding “Launch with OpenCOR” link (to the right of the page under
> the “Views Available” header):
>
> · https://models.physiomeproject.org/exposure/
> feccb0f0649425a61526049f35c3b7fb/MainSystemic.cellml/view:
>
> o As expected, this opens a file named “MainSystemic.cellml” using the
> CellML Text view.
>
> o If you then switch to the Simulation Experiment view (and set the
> “Point interval” to, say, 0.001 second), you will be able to run the model.
> Having said that, the only model parameter that you will be able to plot is
> the variable of integration (!).
>
> o Note that this CellML file imports other CellML files, so to download
> this CellML file only will clearly not work. You also need the other files
> it imports.
>
> · https://models.physiomeproject.org/exposure/
> ff8be5f140e68612284488cf9879eb5f/lpc.cellml/view:
>
> o Still as expected, this opens a file named “lpc.cellml” using the
> CellML Text view.
>
> o Again, if you switch to the Simulation Experiment view (and the “Ending
> point” and “Point interval” to, say, 10 s and 0.001 s, respectively), you
> will be able to run the model, as well as plot any of its parameters.
>
>
>
> So, I don’t know whether the models themselves are correct, but they can
> certainly be run.
>
>
>
> HTH, Alan.
>
>
>
> On 02/08/2017, 03:34, "Aroli Marcellinus"
> <aroli.marcellinus AT gmail.com>
> wrote:
>
>
>
> Hello CellML people and Alan,
>
> My research lab has tried to use CellML files to simulate some biological
> phenomenon.
>
> The general way that what we have already done to simulate the CellML is:
>
> - Download CellML files from PMR websites
>
> - Open the CellML file into OpenCOR
>
> - Set the XY axis at the Simulation tab
>
> - Simulate it.
>
> Right now, some of the models, especially in Electrophysiology category,
> are working well and resulted as we expected. However some of the models,
> most of them are in Cardiovascular Circulation model, are not working as we
> expected. What we know the ones that are not working as we expected are:
>
> https://models.physiomeproject.org/exposure/feccb0f0649425a61526049f35c3b7
> fb/MainSystemic.cellml/view
> https://models.physiomeproject.org/exposure/ff8be5f140e68612284488cf9879eb
> 5f/lpc.cellml/view
>
> What we know that since the CellML files are more than one file and
> dependent each other, we don't know how to use the multiple CellML files
> that are dependent each other to simulate them on the OpenCOR.
>
> Maybe you can give us the input or the way to simulate multiple dependent
> CellML files, since this is new thing for us.
>
> That is for now. Sorry for a long message. I hope you know what I'm trying
> to tell in here. Thank you
>
>
>
> Aroli Marcellinus
>
> *Kumoh Institute of TechnologyComputational Medicine Laboratory*
> 61 Daehak-ro (Sinpyeong-dong), Gumi, Gyeongbuk
> +82 10 9724 3957
> KTalk ID: vondarkness
>
>
>

---

• [cellml-discussion] Some of the CellML not working in OpenCOR, Aroli Marcellinus, 08/02/2017
  • Re: [cellml-discussion] Some of the CellML not working in OpenCOR, Alan Garny, 08/03/2017
    • Re: [cellml-discussion] Some of the CellML not working in OpenCOR, Aroli Marcellinus, 08/03/2017
      • Re: [cellml-discussion] Some of the CellML not working in OpenCOR, Alan Garny, 08/03/2017
        • Re: [cellml-discussion] Some of the CellML not working in OpenCOR, Aroli Marcellinus, 08/08/2017
          • Re: [cellml-discussion] Some of the CellML not working in OpenCOR, Alan Garny, 08/09/2017

---

Archive powered by MHonArc 2.6.18.