Example cellml/LR2: Luo - Rudy II (1994)

This example solves the Luo & Rudy 1994 model (more commonly known as the LR II or LRd model), defined by a CellML version of the model.

Please note: While this version of the model qualitatively compares well to the LR II paper for the action potential, the intracellular calcium dynamics have not been included correctly - namely there is no calcium-induced calcium-release (CICR) process in this version of the model. The original version of the model simulates CICR via a mechanism whereby CICR is induced if and only if the calcium accumulated in the cell in the 2 ms following (dV/dt)max exceeds a given threshold. This sort of process is a bit tricky to include in the CellML (or at least in a way that will work with the CellML abilitites of CMISS) so has been left out for now. I (Andre) don't see this as too much of a problem as the later LRd based models improve on this mechanism and their CellML implementations should be much better.

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/LR_II_model_1994;
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;LR_II_model_1994 write variables yqs niqslist 1..36 binary;
$Tend = 1500;
$dt = 1.0;
for ($time=0;$time<$Tend;$time+=$dt) {
    fem solve restart to $time;
    fem write history time $time variables yqs binary;
}
fem close history binary;
fem evaluate electrode;LR_II_model_1994 history LR_II_model_1994 from grid yqs iy 1..36 binary;
fem define export;r;$example/LR_II_model_1994;
fem export signal;LR_II_model_1994 electrodes signal LR_II_model_1994 names cell;
# For testing we compare the generated CMISS signal files
if ($TESTING) {
    fem compare signal;LR_II_model_1994 basis both masterfile $example/LR_II_model_1994 comparefile LR_II_model_1994 binary;
}

Files used by this example are:

Name                     Modified     Size

LR2.com 04-Aug-2003 1.3k LR_II_model_1994.binsig 04-Aug-2003 263k LR_II_model_1994.cml 09-Oct-2003 146k LR_II_model_1994.ipcell 04-Aug-2003 16k LR_II_model_1994.ipexpo 04-Aug-2003 658 cellml.ipequa 04-Aug-2003 1.5k cellml.ippara 04-Aug-2003 5.9k rk.ipsolv 04-Aug-2003 907

Download the entire example:

Name                        Modified     Size

examples_cellml_LR2.tar.gz 19-Aug-2006 169k

Testing status by version:

StatusTestedReal time (s)
i686-linux
cmSuccessSun Mar 6 00:04:35 20166
cm-debugSuccessSat Mar 5 00:17:30 20168
mips-irix
cmSuccessSun Aug 19 02:57:31 200783
cm-debugSuccessWed Aug 15 02:30:09 2007134
cm-debug-clear-mallocSuccessSat Aug 18 02:47:52 2007147
cm-debug-clear-malloc7SuccessMon Aug 20 02:46:43 2007140
cm64SuccessSun Aug 19 02:58:57 200784
cm64-debugSuccessTue Aug 21 02:30:51 2007136
cm64-debug-clear-mallocSuccessThu Apr 1 11:41:20 2004126
rs6000-aix
cmSuccessWed Mar 4 01:17:27 200917
cm-debugSuccessMon Mar 2 01:15:37 200928
cm64SuccessWed Mar 4 01:18:35 200914
cm64-debugSuccessTue Mar 3 01:20:02 200925
x86_64-linux
cmSuccessSun Mar 6 00:01:15 20164
cm-debugSuccessSat Mar 5 00:01:59 20165

Testing status by file:


Html last generated: Sun Mar 6 05:51:19 2016

Input last modified: Thu Oct 9 11:36:57 2003


CMISS Help / Examples / cellml / LR2