- From: Aroli Marcellinus <aroli.marcellinus AT gmail.com>
- To: cellml-discussion AT cellml.org, Alan Garny <alan.garny AT inria.fr>
- Subject: Re: [cellml-discussion] Some of the CellML not working in OpenCOR
- Date: Thu, 3 Aug 2017 09:42:42 +0900
- Authentication-results: mx3.auckland.ac.nz; spf=Pass smtp.mailfrom=aroli.marcellinus AT gmail.com; dkim=pass (signature verified) header.i=@gmail.com; dmarc=pass (p=none dis=none) d=gmail.com
- Ironport-phdr: 9a23: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
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 Technology**Computational 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
>
>
<https://models.physiomeproject.org/exposure/feccb0f0649425a61526049f35c3b7fb/MainSystemic.cellml/view>
>
:
>
- As expected, this opens a file named “MainSystemic.cellml” using
>
the CellML Text view.
>
- 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 (!).
>
- 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
>
>
<https://models.physiomeproject.org/exposure/ff8be5f140e68612284488cf9879eb5f/lpc.cellml/view>
>
:
>
- Still as expected, this opens a file named “lpc.cellml” using the
>
CellML Text view.
>
- 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
>
Archive powered by MHonArc 2.6.18.