Example cellml/noble_1998: Noble 1998 single cell

This example solves the Noble 1998 ionic current model defined by a CellML version of the model.

NOTE: This example requires a CellML 1.0 enabled version of CMISS to run.


The comfile run by this example is as follows:

# Example showing how to use a cellml model

# If the example path is not set, default to current directory
if (! defined $example) {
    $example = "./";
}
# Drop off the trailing / in the example path
$chopped = chop $example;
if ($chopped ne "/") {
    $example .= $chopped;
}

$format = "binary";

fem define parameters;r;$example/n98;

# default nodes, elements and grids to get a single grid point
fem define node;d;
fem define bas;d;
fem define elem;d;
fem define grid;d;
fem update grid geometry;
fem update grid metric;

# Define the a user defined CellML electrophysiological model
fem define equation;r;$example/n98;

# Define the CellML model to use and map the parameters to CMISS and
# specify initial/boundary conditions for the cell model.
fem define cell;r;$example/n98;

# Initialise the spatial properties of the model (there are none).
fem define material;r;$example/n98 cell;
fem define material;r;$example/n98;
fem update grid material;

# Define the zero transmembrane flux boundary condition.
fem define initial;r;$example/n98;

# Define an explicit Adams integrator.
fem define solve;r;$example/n98;

# Initialise the solve.
fem solve to 0;

# Create a history file to store output variables of interest.
fem open history;n98 write variables yqs niqslist 1..57 $format;
fem write history time 0 variables yqs $format;

# Loop through time integrating the cellular model.
$Tend = 500;
$dt = 1.0;
for ($time=$dt;$time<$Tend;$time+=$dt) {
    fem solve restart to $time;
    fem write history time $time variables yqs $format;
}

fem close history $format;

# Evaluate signals for the variables from the history file.
fem evaluate electrode;n98 history n98 from grid yqs iy 1..57 $format;

# Define an export of the CMISS signals to UnEMAP signals..
fem define export;r;$example/n98;
# ..and export the signals to a UnEMAP signal file.
fem export signal;n98 electrodes signal n98 names cell;

# For testing we compare the generated CMISS signal files
if ($TESTING) {
    fem compare signal;n98 basis both masterfile $example/n98 comparefile n98 $format;
}

Files used by this example are:

Name            Modified     Size

noble_1998.com 07-Apr-2003 2.0k n98.binsig 08-Apr-2003 129k n98.cml 04-Oct-2003 204k n98.ipcell 05-Apr-2003 23k n98.ipequa 26-May-2003 1.5k n98.ipexpo 05-Apr-2003 659 n98.ipinit 05-Apr-2003 214 n98.ipmatc 05-Apr-2003 356 n98.ipmate 05-Apr-2003 3.2k n98.ippara 05-Apr-2003 5.9k n98.ipsolv 05-Apr-2003 1.3k

Download the entire example:

Name                               Modified     Size

examples_cellml_noble_1998.tar.gz 19-Aug-2006 122k

Testing status by version:

StatusTestedReal time (s)
i686-linux
cmSuccessSun Mar 6 00:04:21 20165
cm-debugSuccessSat Mar 5 00:19:16 20169
mips-irix
cmSuccessSun Aug 19 02:35:49 200761
cm-debugSuccessWed Aug 15 02:23:28 2007127
cm-debug-clear-mallocSuccessSat Aug 18 02:40:59 2007145
cm-debug-clear-malloc7SuccessMon Aug 20 02:48:57 2007132
cm64SuccessSun Aug 19 02:36:06 200764
cm64-debugSuccessTue Aug 21 02:23:52 2007133
cm64-debug-clear-mallocSuccessThu Apr 1 11:52:07 2004202
rs6000-aix
cmSuccessWed Mar 4 01:13:08 20098
cm-debugSuccessMon Mar 2 01:15:48 200926
cm64SuccessWed Mar 4 01:13:09 20097
cm64-debugSuccessTue Mar 3 01:20:43 200925
x86_64-linux
cmSuccessSun Mar 6 00:01:15 20163
cm-debugSuccessSat Mar 5 00:02:07 20166

Testing status by file:


Html last generated: Sun Mar 6 05:51:21 2016

Input last modified: Sat Oct 4 14:34:49 2003


CMISS Help / Examples / cellml / noble_1998