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:

Testing status by file:

• cmiss_test.log
  

  i686-linux
  Success	cm:	cmiss_test.log.retain.
  Success	cm-debug:	cmiss_test.log.retain.
  mips-irix
  Success	cm:	cmiss_test.log.retain.
  Success	cm-debug:	cmiss_test.log.retain.
  Success	cm-debug-clear-malloc:	cmiss_test.log.retain.
  Success	cm-debug-clear-malloc7:	cmiss_test.log.retain.
  Success	cm64:	cmiss_test.log.retain.
  Success	cm64-debug:	cmiss_test.log.retain.
  Success	cm64-debug-clear-malloc:	cmiss_test.log.retain.
  rs6000-aix
  Success	cm:	cmiss_test.log.retain.
  Success	cm-debug:	cmiss_test.log.retain.
  Success	cm64:	cmiss_test.log.retain.
  Success	cm64-debug:	cmiss_test.log.retain.
  x86_64-linux
  Success	cm:	cmiss_test.log.retain.
  Success	cm-debug:	cmiss_test.log.retain.

  
  
• LR_II_model_1994.opcomp
  

  i686-linux
  Success	cm:	ndiff test: no significant differences with generic answer.
  Success	cm-debug:	ndiff test: no significant differences with generic answer.
  mips-irix
  Success	cm:	ndiff test: no significant differences with generic answer.
  Success	cm-debug:	ndiff test: no significant differences with generic answer.
  Success	cm-debug-clear-malloc:	ndiff test: no significant differences with generic answer.
  Success	cm-debug-clear-malloc7:	ndiff test: no significant differences with generic answer.
  Success	cm64:	ndiff test: no significant differences with generic answer.
  Success	cm64-debug:	ndiff test: no significant differences with generic answer.
  Success	cm64-debug-clear-malloc:	ndiff test: no significant differences with generic answer.
  rs6000-aix
  Success	cm:	ndiff test: no significant differences with generic answer.
  Success	cm-debug:	ndiff test: no significant differences with generic answer.
  Success	cm64:	ndiff test: no significant differences with generic answer.
  Success	cm64-debug:	ndiff test: no significant differences with generic answer.
  x86_64-linux
  Success	cm:	ndiff test: no significant differences with generic answer.
  Success	cm-debug:	ndiff test: no significant differences with generic answer.

  
  

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

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