Generated Code
The following is matlab code generated by the CellML API from this CellML file. (Back to language selection)
The raw code is available.
function [VOI, STATES, ALGEBRAIC, CONSTANTS] = mainFunction()
% This is the "main function". In Matlab, things work best if you rename this function to match the filename.
[VOI, STATES, ALGEBRAIC, CONSTANTS] = solveModel();
end
function [algebraicVariableCount] = getAlgebraicVariableCount()
% Used later when setting a global variable with the number of algebraic variables.
% Note: This is not the "main method".
algebraicVariableCount =13;
end
% There are a total of 4 entries in each of the rate and state variable arrays.
% There are a total of 29 entries in the constant variable array.
%
function [VOI, STATES, ALGEBRAIC, CONSTANTS] = solveModel()
% Create ALGEBRAIC of correct size
global algebraicVariableCount; algebraicVariableCount = getAlgebraicVariableCount();
% Initialise constants and state variables
[INIT_STATES, CONSTANTS] = initConsts;
% Set timespan to solve over
tspan = [0, 10];
% Set numerical accuracy options for ODE solver
options = odeset('RelTol', 1e-06, 'AbsTol', 1e-06, 'MaxStep', 1);
% Solve model with ODE solver
[VOI, STATES] = ode15s(@(VOI, STATES)computeRates(VOI, STATES, CONSTANTS), tspan, INIT_STATES, options);
% Compute algebraic variables
[RATES, ALGEBRAIC] = computeRates(VOI, STATES, CONSTANTS);
ALGEBRAIC = computeAlgebraic(ALGEBRAIC, CONSTANTS, STATES, VOI);
% Plot state variables against variable of integration
[LEGEND_STATES, LEGEND_ALGEBRAIC, LEGEND_VOI, LEGEND_CONSTANTS] = createLegends();
figure();
plot(VOI, STATES);
xlabel(LEGEND_VOI);
l = legend(LEGEND_STATES);
set(l,'Interpreter','none');
end
function [LEGEND_STATES, LEGEND_ALGEBRAIC, LEGEND_VOI, LEGEND_CONSTANTS] = createLegends()
LEGEND_STATES = ''; LEGEND_ALGEBRAIC = ''; LEGEND_VOI = ''; LEGEND_CONSTANTS = '';
LEGEND_STATES(:,1) = strpad('P_Open in component kinetics (dimensionless)');
LEGEND_STATES(:,2) = strpad('P_Closed in component kinetics (dimensionless)');
LEGEND_STATES(:,3) = strpad('P_I1 in component kinetics (dimensionless)');
LEGEND_STATES(:,4) = strpad('P_I2 in component kinetics (dimensionless)');
LEGEND_VOI = strpad('time in component environment (ms)');
LEGEND_ALGEBRAIC(:,3) = strpad('current in component stimulus_protocol (nA_per_nF)');
LEGEND_ALGEBRAIC(:,4) = strpad('voltage_out in component environment (mV)');
LEGEND_ALGEBRAIC(:,5) = strpad('transmembranevoltage in component environment (mV)');
LEGEND_ALGEBRAIC(:,2) = strpad('pressure in component environment (mmHg)');
LEGEND_ALGEBRAIC(:,1) = strpad('stretch in component stimulus_protocol (dimensionless)');
LEGEND_CONSTANTS(:,1) = strpad('pressure_stim_offset in component environment (ms)');
LEGEND_CONSTANTS(:,2) = strpad('pressure_stim_period in component environment (ms)');
LEGEND_CONSTANTS(:,3) = strpad('pressure_stim_duration in component environment (ms)');
LEGEND_CONSTANTS(:,4) = strpad('pressure_stim_amplitude in component environment (dimensionless)');
LEGEND_CONSTANTS(:,5) = strpad('current_stim_offset in component environment (ms)');
LEGEND_CONSTANTS(:,6) = strpad('current_stim_period in component environment (ms)');
LEGEND_CONSTANTS(:,7) = strpad('current_stim_duration in component environment (ms)');
LEGEND_CONSTANTS(:,8) = strpad('current_stim_amplitude in component environment (nA_per_nF)');
LEGEND_CONSTANTS(:,9) = strpad('current_stim_end in component environment (ms)');
LEGEND_CONSTANTS(:,10) = strpad('current_N_period_total in component environment (dimensionless)');
LEGEND_CONSTANTS(:,11) = strpad('current_N_period_applied in component environment (dimensionless)');
LEGEND_CONSTANTS(:,12) = strpad('r1 in component kinetics (per_ms)');
LEGEND_CONSTANTS(:,13) = strpad('r3 in component kinetics (per_ms)');
LEGEND_CONSTANTS(:,14) = strpad('r4 in component kinetics (per_ms)');
LEGEND_CONSTANTS(:,15) = strpad('r5 in component kinetics (per_ms)');
LEGEND_CONSTANTS(:,16) = strpad('r6 in component kinetics (per_ms)');
LEGEND_CONSTANTS(:,17) = strpad('r7 in component kinetics (per_ms)');
LEGEND_CONSTANTS(:,18) = strpad('r8 in component kinetics (per_ms)');
LEGEND_CONSTANTS(:,19) = strpad('ce1 in component kinetics (dimensionless)');
LEGEND_CONSTANTS(:,20) = strpad('ce3 in component kinetics (dimensionless)');
LEGEND_CONSTANTS(:,21) = strpad('ce4 in component kinetics (dimensionless)');
LEGEND_CONSTANTS(:,22) = strpad('cm4 in component kinetics (dimensionless)');
LEGEND_CONSTANTS(:,23) = strpad('ce5 in component kinetics (dimensionless)');
LEGEND_CONSTANTS(:,24) = strpad('ce6 in component kinetics (dimensionless)');
LEGEND_CONSTANTS(:,25) = strpad('ce7 in component kinetics (dimensionless)');
LEGEND_CONSTANTS(:,26) = strpad('ce8 in component kinetics (dimensionless)');
LEGEND_CONSTANTS(:,27) = strpad('r2 in component kinetics (per_ms)');
LEGEND_CONSTANTS(:,28) = strpad('ce2 in component kinetics (dimensionless)');
LEGEND_CONSTANTS(:,29) = strpad('cm2 in component kinetics (dimensionless)');
LEGEND_ALGEBRAIC(:,6) = strpad('p_O_I1 in component kinetics (per_ms)');
LEGEND_ALGEBRAIC(:,7) = strpad('p_I1_O in component kinetics (per_ms)');
LEGEND_ALGEBRAIC(:,8) = strpad('p_I1_C in component kinetics (per_ms)');
LEGEND_ALGEBRAIC(:,9) = strpad('p_C_I1 in component kinetics (per_ms)');
LEGEND_ALGEBRAIC(:,10) = strpad('p_C_O in component kinetics (per_ms)');
LEGEND_ALGEBRAIC(:,11) = strpad('p_O_C in component kinetics (per_ms)');
LEGEND_ALGEBRAIC(:,12) = strpad('p_I2_O in component kinetics (per_ms)');
LEGEND_ALGEBRAIC(:,13) = strpad('p_O_I2 in component kinetics (per_ms)');
LEGEND_RATES(:,1) = strpad('d/dt P_Open in component kinetics (dimensionless)');
LEGEND_RATES(:,2) = strpad('d/dt P_Closed in component kinetics (dimensionless)');
LEGEND_RATES(:,3) = strpad('d/dt P_I1 in component kinetics (dimensionless)');
LEGEND_RATES(:,4) = strpad('d/dt P_I2 in component kinetics (dimensionless)');
LEGEND_STATES = LEGEND_STATES';
LEGEND_ALGEBRAIC = LEGEND_ALGEBRAIC';
LEGEND_RATES = LEGEND_RATES';
LEGEND_CONSTANTS = LEGEND_CONSTANTS';
end
function [STATES, CONSTANTS] = initConsts()
VOI = 0; CONSTANTS = []; STATES = []; ALGEBRAIC = [];
STATES(:,1) = 0.0;
STATES(:,2) = 0.3;
STATES(:,3) = 0.1;
STATES(:,4) = 0.6;
CONSTANTS(:,1) = 100;
CONSTANTS(:,2) = 2000;
CONSTANTS(:,3) = 5;
CONSTANTS(:,4) = 1.1;
CONSTANTS(:,5) = 100;
CONSTANTS(:,6) = 1000;
CONSTANTS(:,7) = 500;
CONSTANTS(:,8) = 80;
CONSTANTS(:,9) = 999999999999999;
CONSTANTS(:,10) = 1;
CONSTANTS(:,11) = 1;
CONSTANTS(:,12) = 0.02634342;
CONSTANTS(:,13) = 0.0008000712;
CONSTANTS(:,14) = 0.008945307;
CONSTANTS(:,15) = 1.3529515e-5;
CONSTANTS(:,16) = 6.206403e-5;
CONSTANTS(:,17) = 6.603723e-6;
CONSTANTS(:,18) = 0.00079357607;
CONSTANTS(:,19) = -2.3753126;
CONSTANTS(:,20) = -5.6010337;
CONSTANTS(:,21) = 0.70629007;
CONSTANTS(:,22) = -12.101605;
CONSTANTS(:,23) = 6.46389;
CONSTANTS(:,24) = -1.2173947;
CONSTANTS(:,25) = 8.739162;
CONSTANTS(:,26) = -3.364573;
CONSTANTS(:,27) = ( CONSTANTS(:,12).*CONSTANTS(:,13).*CONSTANTS(:,15))./( CONSTANTS(:,14).*CONSTANTS(:,16));
CONSTANTS(:,28) = ((CONSTANTS(:,19)+CONSTANTS(:,20)+CONSTANTS(:,23)) - CONSTANTS(:,21)) - CONSTANTS(:,24);
CONSTANTS(:,29) = - CONSTANTS(:,22);
if (isempty(STATES)), warning('Initial values for states not set');, end
end
function [RATES, ALGEBRAIC] = computeRates(VOI, STATES, CONSTANTS)
global algebraicVariableCount;
statesSize = size(STATES);
statesColumnCount = statesSize(2);
if ( statesColumnCount == 1)
STATES = STATES';
ALGEBRAIC = zeros(1, algebraicVariableCount);
utilOnes = 1;
else
statesRowCount = statesSize(1);
ALGEBRAIC = zeros(statesRowCount, algebraicVariableCount);
RATES = zeros(statesRowCount, statesColumnCount);
utilOnes = ones(statesRowCount, 1);
end
ALGEBRAIC(:,3) = piecewise({VOI>=CONSTANTS(:,5)&VOI<CONSTANTS(:,9)& rem(VOI - CONSTANTS(:,5), CONSTANTS(:,6))<=CONSTANTS(:,7)& rem(VOI - CONSTANTS(:,5), CONSTANTS(:,10).*CONSTANTS(:,6))< CONSTANTS(:,11).*CONSTANTS(:,6), CONSTANTS(:,8) }, 0.00000);
ALGEBRAIC(:,4) = (ALGEBRAIC(:,3)./1.00000).*1.00000;
ALGEBRAIC(:,6) = CONSTANTS(:,12).*exp(( CONSTANTS(:,19).*ALGEBRAIC(:,4))./140.000);
ALGEBRAIC(:,1) = piecewise({VOI>=CONSTANTS(:,1)& rem(VOI - CONSTANTS(:,1), CONSTANTS(:,2))<=CONSTANTS(:,3), CONSTANTS(:,4) }, 1.00000);
ALGEBRAIC(:,2) = 350.000.*max([utilOnes.*(0.00000), utilOnes.*( ALGEBRAIC(:,1) - 1.00000)],[],2);
ALGEBRAIC(:,7) = CONSTANTS(:,27).*exp(( CONSTANTS(:,28).*ALGEBRAIC(:,4))./140.000+( CONSTANTS(:,29).*ALGEBRAIC(:,2))./70.0000);
ALGEBRAIC(:,8) = CONSTANTS(:,13).*exp(( CONSTANTS(:,20).*ALGEBRAIC(:,4))./140.000);
ALGEBRAIC(:,9) = CONSTANTS(:,14).*exp(( CONSTANTS(:,21).*ALGEBRAIC(:,4))./140.000+( CONSTANTS(:,22).*ALGEBRAIC(:,2))./70.0000);
RATES(:,3) = - (ALGEBRAIC(:,7)+ALGEBRAIC(:,8)).*STATES(:,3)+ ALGEBRAIC(:,9).*STATES(:,2)+ ALGEBRAIC(:,6).*STATES(:,1);
ALGEBRAIC(:,10) = CONSTANTS(:,15).*exp(( CONSTANTS(:,23).*ALGEBRAIC(:,4))./140.000);
ALGEBRAIC(:,11) = CONSTANTS(:,16).*exp(( CONSTANTS(:,24).*ALGEBRAIC(:,4))./140.000);
RATES(:,2) = - (ALGEBRAIC(:,9)+ALGEBRAIC(:,10)).*STATES(:,2)+ ALGEBRAIC(:,11).*STATES(:,1)+ ALGEBRAIC(:,8).*STATES(:,3);
ALGEBRAIC(:,12) = CONSTANTS(:,17).*exp(( (( CONSTANTS(:,25).*ALGEBRAIC(:,4))./140.000).*ALGEBRAIC(:,2))./70.0000);
ALGEBRAIC(:,13) = CONSTANTS(:,18).*exp(( CONSTANTS(:,26).*ALGEBRAIC(:,4))./140.000);
RATES(:,1) = - (ALGEBRAIC(:,6)+ALGEBRAIC(:,13)+ALGEBRAIC(:,11)).*STATES(:,1)+ ALGEBRAIC(:,10).*STATES(:,2)+ ALGEBRAIC(:,7).*STATES(:,3)+ ALGEBRAIC(:,12).*STATES(:,4);
RATES(:,4) = - ALGEBRAIC(:,12).*STATES(:,4)+ ALGEBRAIC(:,13).*STATES(:,1);
RATES = RATES';
end
% Calculate algebraic variables
function ALGEBRAIC = computeAlgebraic(ALGEBRAIC, CONSTANTS, STATES, VOI)
statesSize = size(STATES);
statesColumnCount = statesSize(2);
if ( statesColumnCount == 1)
STATES = STATES';
utilOnes = 1;
else
statesRowCount = statesSize(1);
utilOnes = ones(statesRowCount, 1);
end
ALGEBRAIC(:,3) = piecewise({VOI>=CONSTANTS(:,5)&VOI<CONSTANTS(:,9)& rem(VOI - CONSTANTS(:,5), CONSTANTS(:,6))<=CONSTANTS(:,7)& rem(VOI - CONSTANTS(:,5), CONSTANTS(:,10).*CONSTANTS(:,6))< CONSTANTS(:,11).*CONSTANTS(:,6), CONSTANTS(:,8) }, 0.00000);
ALGEBRAIC(:,4) = (ALGEBRAIC(:,3)./1.00000).*1.00000;
ALGEBRAIC(:,6) = CONSTANTS(:,12).*exp(( CONSTANTS(:,19).*ALGEBRAIC(:,4))./140.000);
ALGEBRAIC(:,1) = piecewise({VOI>=CONSTANTS(:,1)& rem(VOI - CONSTANTS(:,1), CONSTANTS(:,2))<=CONSTANTS(:,3), CONSTANTS(:,4) }, 1.00000);
ALGEBRAIC(:,2) = 350.000.*max([utilOnes.*(0.00000), utilOnes.*( ALGEBRAIC(:,1) - 1.00000)],[],2);
ALGEBRAIC(:,7) = CONSTANTS(:,27).*exp(( CONSTANTS(:,28).*ALGEBRAIC(:,4))./140.000+( CONSTANTS(:,29).*ALGEBRAIC(:,2))./70.0000);
ALGEBRAIC(:,8) = CONSTANTS(:,13).*exp(( CONSTANTS(:,20).*ALGEBRAIC(:,4))./140.000);
ALGEBRAIC(:,9) = CONSTANTS(:,14).*exp(( CONSTANTS(:,21).*ALGEBRAIC(:,4))./140.000+( CONSTANTS(:,22).*ALGEBRAIC(:,2))./70.0000);
ALGEBRAIC(:,10) = CONSTANTS(:,15).*exp(( CONSTANTS(:,23).*ALGEBRAIC(:,4))./140.000);
ALGEBRAIC(:,11) = CONSTANTS(:,16).*exp(( CONSTANTS(:,24).*ALGEBRAIC(:,4))./140.000);
ALGEBRAIC(:,12) = CONSTANTS(:,17).*exp(( (( CONSTANTS(:,25).*ALGEBRAIC(:,4))./140.000).*ALGEBRAIC(:,2))./70.0000);
ALGEBRAIC(:,13) = CONSTANTS(:,18).*exp(( CONSTANTS(:,26).*ALGEBRAIC(:,4))./140.000);
ALGEBRAIC(:,5) = (ALGEBRAIC(:,4) - 5.00000).*STATES(:,1);
end
% Compute result of a piecewise function
function x = piecewise(cases, default)
set = [0];
for i = 1:2:length(cases)
if (length(cases{i+1}) == 1)
x(cases{i} & ~set,:) = cases{i+1};
else
x(cases{i} & ~set,:) = cases{i+1}(cases{i} & ~set);
end
set = set | cases{i};
if(set), break, end
end
if (length(default) == 1)
x(~set,:) = default;
else
x(~set,:) = default(~set);
end
end
% Pad out or shorten strings to a set length
function strout = strpad(strin)
req_length = 160;
insize = size(strin,2);
if insize > req_length
strout = strin(1:req_length);
else
strout = [strin, blanks(req_length - insize)];
end
end