Example cellml/hodgkin_huxley_1952: Hodgkin-Huxley

This example solves the Hodgkin-Huxley 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

# Will hopefully soon be able to use the example variable in specifying
# the cellml model's URI in the ipcell file.

# 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/hh;

# 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/hh;

# Define the CellML model to use and map the parameters to CMISS and
# specify initial/boundary conditions for the cell model.
# Note: the "save temporary files" question is set to yes for testing
#       of the generated code. You might want to turn this off if you
#       are not running this as a test example.
fem define cell;r;$example/hh;

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

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

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

# Initialise the solve.
fem solve to 0;

# Create a history file to store output variables of interest.
fem open history;hh write variables yqs niqslist 1..8 binary;

# Loop through time integrating the cellular model.
$Tend = 200;
$dt = 1.0;
for ($time=0;$time<$Tend;$time+=$dt) {
    fem solve restart to $time;
    fem write history time $time variables yqs binary;
}

fem close history binary;

# Evaluate signals for the variables from the history file.
fem evaluate electrode;hh history hh from gvariables yqs iy 1,2,3,4,5,6,7,8 electrodes 1 binary;

# Define an export of the CMISS signals to UnEMAP signals..
fem define export;r;$example/hh;

# ..and define names for each of the signals..
fem define leads;r;$example/hh;

# ..and export the signals to a UnEMAP signal file.
fem export signal;hh leads signal hh;

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

Files used by this example are:

Name                     Modified     Size

hodgkin_huxley_1952.com  23-Mar-2003  2.3k
hh.binsig                25-Mar-2003   13k
hh.cml                   21-Jun-2003   37k
hh.ipcell                11-Jun-2003  3.6k
hh.ipequa                26-May-2003  1.5k
hh.ipexpo                23-Mar-2003  658 
hh.ipinit                23-Mar-2003  214 
hh.iplead                23-Mar-2003  2.2k
hh.ipmatc                23-Mar-2003  356 
hh.ipmate                23-Mar-2003  3.2k
hh.ippara                23-Mar-2003  5.9k
hh.ipsolv                23-Mar-2003  1.3k

Download the entire example:

Name                                        Modified     Size

examples_cellml_hodgkin_huxley_1952.tar.gz  19-Aug-2006   16k

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.

  
  
• hh.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 05:51:20 2016

Input last modified: Sat Jun 21 15:11:01 2003