Location: Butera, Rinzel, Smith II 1999 @ 9440efdfc111 / buteraModel.m

Author:

Randall Britten <r.britten@auckland.ac.nz>

Date:

2011-02-16 17:51:41+13:00

Desc:

Fixed problem with indices used for summation: Terms in sum were using same indices as paper, but sum was over j, whereas in paper, sum was over i. Now code sums over i. Pair programmed with Shorojeet Dasgupta.

Permanent Source URI:

https://models.physiomeproject.org/workspace/butera_rinzel_smith_II_1999/rawfile/9440efdfc111145340f96a796f3c288e275daa45/buteraModel.m

% This program creates an XML file in the current directory. The file can
% be run in OpenCell to simulate the neuron model given on p.400 in Butera      
% et. al 1999b. g_syn_e is given pseudo-random values from a normal
% distribution of user specified mean and standard deviation.
%
% Note: To run the file in OpenCell, the one cell model from the repository
% must be in the same folder, and its name should not have been changed.

clc ; clear ;

% Ask user how many neurons are to be modelled
disp (' ') ; neuronCount = input ('How many neurons are to be modelled : ') ;

% Prompt user to enter the mean and standard deviation of the normal dist.
disp (' ') ;
g_syn_e_mean = input ('Please enter the mean of g_syn_e normal distribution : ') ;
g_syn_e_stdDev = input ('Please enter the standard deviation of g_syn_e normal distribution : ') ;

% Create array of pseudo-random g_syn_e values
g_syn_e = g_syn_e_mean + g_syn_e_stdDev * randn (neuronCount, neuronCount) ;

% Begin the XML code
xmlCode = sprintf ('<?xml version="1.0"?> \n<model xmlns="http://www.cellml.org/cellml/1.1#" xmlns:cmeta="http://www.cellml.org/metadata/1.0#" cmeta:id="butera_%d_cell_1999" name="butera_%d_cell_1999"> \n\n', neuronCount, neuronCount) ;

% Adding imports and connections 
for i = 1 : neuronCount
    imports = sprintf ('  <import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="butera_single_cell_1999.cellml"> \n    <component component_ref="single_neuron_model" name="single_neuron_model%d"/> \n  </import> \n\n  <connection> \n    <map_components component_1="single_neuron_model%d" component_2="synaptic_coupling"/> \n    <map_variables variable_1="s" variable_2="s%d"/> \n    <map_variables variable_1="sum_g_syn_e_s" variable_2="sum_g_syn_e_s_%d"/> \n  </connection> \n\n', i, i, i,i) ;
    xmlCode = [xmlCode imports] ;
end

% Adding g_syn_e units and initialising the synaptic_coupling component code
g_syn_e_stuff = sprintf ('  <units name="nanoS"> \n    <unit prefix="nano" units="siemens"/> \n  </units> \n\n  <component cmeta:id="synaptic_coupling" name="synaptic_coupling"> \n') ;
xmlCode = [xmlCode g_syn_e_stuff] ;

% Adding sum_g_syn_e_s variable descriptions
for i = 1 : neuronCount
    sum_g_syn_e_s_descriptors = sprintf ('    <variable name="sum_g_syn_e_s_%d" public_interface="out" units="nanoS"/> \n', i) ;
    xmlCode = [xmlCode sum_g_syn_e_s_descriptors] ;
end

% Formatting
space = sprintf ('\n') ;
xmlCode = [xmlCode space] ;

% Adding g_syn_e values
for i = 1 : neuronCount
    for j = 1 : neuronCount
        if (i ~= j)
            g_syn_e_values = sprintf ('    <variable initial_value="%f" name="g_syn_e_%d_%d" units="nanoS"/> \n', g_syn_e (i, j), i, j) ;
            xmlCode = [xmlCode g_syn_e_values] ;
        end
    end
end

% Formatting
space = sprintf ('\n') ;
xmlCode = [xmlCode space] ;

% Adding g_syn_e components
for i = 1 : neuronCount
    g_syn_e_components = sprintf ('    <variable name="s%d" public_interface="in" units="dimensionless"/> \n', i) ;
    xmlCode = [xmlCode g_syn_e_components] ;
end

% Formatting
space = sprintf ('\n') ;
xmlCode = [xmlCode space] ;

% Initialising the code for g_syn_e math
initialMath = sprintf ('    <math xmlns="http://www.w3.org/1998/Math/MathML"> \n') ;
xmlCode = [xmlCode initialMath] ;

% Adding g_syn_e math code
for j = 1 : neuronCount
    sum_g_syn_e_s_math = sprintf ('      <apply><eq /> \n        <ci> sum_g_syn_e_s_%d </ci> \n        <apply><plus /> \n', j) ;
    xmlCode = [xmlCode sum_g_syn_e_s_math] ;
    for i = 1 : neuronCount
        if (i ~= j)
            g_syn_e_math = sprintf ('		  <apply><times/> \n            <ci> g_syn_e_%d_%d </ci> \n            <ci> s%d </ci> \n          </apply> \n', i, j, i) ;
            xmlCode = [xmlCode g_syn_e_math] ;
        end
    end
    mathEnd = sprintf ('		</apply> \n	  </apply> \n\n') ;
    xmlCode = [xmlCode mathEnd] ;
end

% Ending the g_syn_e component code
g_syn_e_end = sprintf ('	</math> \n  </component> \n\n</model>') ;
xmlCode = [xmlCode g_syn_e_end] ;

% Create XML file
myfid = fopen ('buteraModelXML.xml','w') ;

% Write code to file
fprintf (myfid, '%s', xmlCode) ;

% Close file
fclose(myfid) ;