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:

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.

  
  
• n98.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 05:51:21 2016

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