Example cellml/ebihara_johnson_1980: EJ modified BR

This example solves the Beeler Reuter model with the substitution of the Ebihara & Johnson (1980) sodium channel in place of the original formulation, 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:

# 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 .= $chopped;
}
fem define parameters;r;$example/cellml;
fem define node;d;
fem define bas;d;
fem define elem;d;
fem define grid;d;
fem update grid geometry;
fem update grid metric;
fem define equation;r;$example/cellml;
fem define cell;r;$example/ebihara_johnson_model_1980;
fem define material;d cell;
fem define material;d;
fem update grid material;
fem define initial;d;
fem define solve;r;$example/rk;
fem solve to 0;
fem open history;ebihara_johnson_model_1980 write variables yqs niqslist 1..13 binary;
$Tend = 1500;
$dt = 1.0;
for ($time=0;$time<$Tend;$time+=$dt) {
    fem solve restart to $time;
    fem write history time $time variables yqs binary;
}
fem close history binary;
fem evaluate electrode;ebihara_johnson_model_1980 history ebihara_johnson_model_1980 from grid yqs iy 1..13 binary;
fem define export;r;$example/ebihara_johnson_model_1980;
fem export signal;ebihara_johnson_model_1980 electrodes signal ebihara_johnson_model_1980 names cell;
# For testing we compare the generated CMISS signal files
if ($TESTING) {
    fem compare signal;ebihara_johnson_model_1980 basis both masterfile $example/ebihara_johnson_model_1980 comparefile ebihara_johnson_model_1980 binary;
}

Files used by this example are:

Name                               Modified     Size

ebihara_johnson_1980.com 26-Jul-2003 1.4k cellml.ipequa 26-Jul-2003 1.5k cellml.ippara 26-Jul-2003 5.9k ebihara_johnson_model_1980.binsig 28-Jul-2003 127k ebihara_johnson_model_1980.cml 04-Oct-2003 49k ebihara_johnson_model_1980.ipcell 26-Jul-2003 3.8k ebihara_johnson_model_1980.ipexpo 26-Jul-2003 658 rk.ipsolv 26-Jul-2003 897

Download the entire example:

Name                                         Modified     Size

examples_cellml_ebihara_johnson_1980.tar.gz 19-Aug-2006 72k

Testing status by version:

StatusTestedReal time (s)
i686-linux
cmSuccessSun Mar 6 00:04:10 20164
cm-debugSuccessSat Mar 5 00:15:39 20166
mips-irix
cmSuccessSun Aug 19 02:37:12 200764
cm-debugSuccessWed Aug 15 02:09:26 2007106
cm-debug-clear-mallocSuccessSat Aug 18 02:25:12 2007110
cm-debug-clear-malloc7SuccessMon Aug 20 02:25:35 2007114
cm64SuccessSun Aug 19 02:38:18 200765
cm64-debugSuccessTue Aug 21 02:13:35 2007106
cm64-debug-clear-mallocSuccessThu Apr 1 11:45:00 200452
rs6000-aix
cmSuccessWed Mar 4 01:16:14 200910
cm-debugSuccessMon Mar 2 01:11:58 200917
cm64SuccessWed Mar 4 01:14:28 200912
cm64-debugSuccessTue Mar 3 01:18:00 200917
x86_64-linux
cmSuccessSun Mar 6 00:01:11 20162
cm-debugSuccessSat Mar 5 00:01:54 20163

Testing status by file:


Html last generated: Sun Mar 6 05:51:20 2016

Input last modified: Sat Oct 4 22:06:37 2003


CMISS Help / Examples / cellml / ebihara_johnson_1980