- Author:
- Dougal Cowan <devnull@localhost>
- Date:
- 2011-02-23 08:24:01+13:00
- Desc:
- changed note about the session file.
- Permanent Source URI:
- https://staging.physiomeproject.org/workspace/butera_rinzel_smith_II_1999/rawfile/04cd7956502c8e28a39aa308c4a42063db9b7f04/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 outputted file in OpenCell, the one cell model from the
% repository must be in the same folder, and its name should not have been
% changed.
% Ask user how many neurons are to be modelled
disp (' ') ; neuronCount = input ('How many neurons are to be modelled : ') ;
% Prompt user to enter the seed of the random number generation
disp (' ') ; SEED = input ('Please enter the seed of the random number generation: ') ;
% 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
randn ('seed', SEED) ;
g_syn_e = g_syn_e_mean + g_syn_e_stdDev * randn (neuronCount, neuronCount) ;
% Begin XML code, and add imports and connections
f = [
'<?xml version="1.0"?>\n' ...
' <model \n' ...
' xmlns="http://www.cellml.org/cellml/1.1#" \n' ...
' xmlns:cmeta="http://www.cellml.org/metadata/1.0#" \n' ...
' cmeta:id="butera_%d_cell_1999" \n' ...
' name="butera_%d_cell_1999"> \n\n' ...
'\n' ...
'<!-- seed %d -->\n' ...
'<!-- g_syn_e_mean %d -->\n' ...
'<!-- g_syn_e_stdDev %d -->\n' ...
];
xmlCode = sprintf (f , neuronCount, neuronCount, SEED, g_syn_e_mean, g_syn_e_stdDev) ;
for i = 1 : neuronCount
f = [ ...
' <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"/>' ...
' <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' ...
];
importsConnections = sprintf (f, i, i, i,i) ;
xmlCode = [xmlCode importsConnections] ;
end
% Adding g_syn_e units, and initialising the synaptic component code
f = [ ...
' <units name="nanoS">\n' ...
' <unit prefix="nano" units="siemens"/>\n' ...
' </units>\n' ...
'\n' ...
' <units name="millivolt">\n' ...
' <unit prefix="milli" units="volt"/>\n' ...
' </units>\n' ...
'\n' ...
' <units name="millisecond">\n' ...
' <unit prefix="milli" units="second"/>\n' ...
' </units>\n' ...
'\n' ...
' <component cmeta:id="synaptic_coupling" name="synaptic_coupling"> \n' ...
] ;
g_syn_e_misc = sprintf (f) ;
xmlCode = [xmlCode g_syn_e_misc] ;
% Adding sum_g_syn_e_s variables and g_syn_e values
for i = 1 : neuronCount
sum_g_syn_e_s_variables = sprintf (' <variable name="sum_g_syn_e_s_%d" public_interface="out" units="nanoS"/> \n', i) ;
xmlCode = [xmlCode sum_g_syn_e_s_variables] ;
end
formatting = sprintf ('\n') ;
xmlCode = [xmlCode formatting] ;
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
% Adding a variable to represent each neuron and g_syn_e math code
xmlCode = [xmlCode formatting] ;
for i = 1 : neuronCount
neuronVariables = sprintf (' <variable name="s%d" public_interface="in" units="dimensionless"/> \n', i) ;
xmlCode = [xmlCode neuronVariables] ;
end
xmlCode = [xmlCode formatting] ;
initialMath = sprintf (' <math xmlns="http://www.w3.org/1998/Math/MathML"> \n') ;
xmlCode = [xmlCode initialMath] ;
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)
f = [ ...
' <apply>\n' ...
' <times/>\n' ...
' <ci> g_syn_e_%d_%d </ci>\n' ...
' <ci> s%d </ci>\n' ...
' </apply> \n' ...
] ;
g_syn_e_math = sprintf (f, i, j, i) ;
xmlCode = [xmlCode g_syn_e_math] ;
end
end
mathEnd = sprintf (' </apply> \n </apply> \n\n') ;
xmlCode = [xmlCode mathEnd] ;
end
ending = sprintf (' </math> \n </component> \n\n') ;
xmlCode = [xmlCode ending] ;
% Adding code for the component which allows session file creation
initialise = sprintf (' <component name="ModelInterfacing"> \n') ;
xmlCode = [xmlCode initialise] ;
timeDuplicateA = sprintf (' <variable cmeta:id="ModelInterfacing_timeDuplicate" name="timeDuplicate" units="millisecond"/> \n') ;
xmlCode = [xmlCode timeDuplicateA] ;
timeDuplicateB = sprintf (' <variable name="time" public_interface="in" units="millisecond"/> \n\n') ;
xmlCode = [xmlCode timeDuplicateB] ;
for i = 1 : neuronCount
f = [ ...
' <variable name="V%d" public_interface="in" units="millivolt"/>\n' ...
' <variable cmeta:id="ModelInterfacing_V%dDuplicate" name="V%dDuplicate" units="millivolt"/> \n \n' ...
] ;
sessionComponent = sprintf (f, i,i,i) ;
xmlCode = [xmlCode sessionComponent] ;
end
% Adding math for above component
xmlCode = [xmlCode initialMath] ;
timeDuplicateMath = sprintf( ' <apply><eq/><ci>timeDuplicate</ci><ci>time</ci></apply> \n\n') ;
xmlCode = [xmlCode timeDuplicateMath] ;
for i = 1 : neuronCount
sessionMath = sprintf (' <apply><eq/><ci>V%dDuplicate</ci><ci>V%d</ci></apply> \n\n', i,i) ;
xmlCode = [xmlCode sessionMath] ;
end
xmlCode = [xmlCode ending] ;
f = [ ...
' <connection> \n' ...
' <map_components component_1="single_neuron_model1" component_2="ModelInterfacing"/> \n' ...
' <map_variables variable_1="time" variable_2="time"/> \n' ...
' </connection> \n\n' ...
] ;
timeConnection = sprintf (f , i,i,i) ;
xmlCode = [xmlCode timeConnection] ;
% Adding connections for session file creation
for i = 1 : neuronCount
f = [ ...
' <connection> \n' ...
' <map_components component_1="single_neuron_model%d" component_2="ModelInterfacing"/> \n' ...
' <map_variables variable_1="V" variable_2="V%d"/> \n' ...
' </connection> \n\n' ...
] ;
sessionConnections = sprintf (f, i,i) ;
xmlCode = [xmlCode sessionConnections] ;
end
xmlCode = [xmlCode '</model>'] ;
% Create XML file
myfid = fopen ('buteraModelXML.cellml','w') ;
% Write code to file
fprintf (myfid, '%s', xmlCode) ;
% Close file
fclose(myfid) ;
