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 =7; end % There are a total of 3 entries in each of the rate and state variable arrays. % There are a total of 14 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_VOI = strpad('time in component environment (millisecond)'); LEGEND_STATES(:,1) = strpad('V in component V (millivolt)'); LEGEND_CONSTANTS(:,1) = strpad('C in component V (microF_per_cm2)'); LEGEND_CONSTANTS(:,2) = strpad('i_app in component V (microA_per_cm2)'); LEGEND_ALGEBRAIC(:,1) = strpad('i_L in component i_L (microA_per_cm2)'); LEGEND_ALGEBRAIC(:,4) = strpad('i_Ca in component i_Ca (microA_per_cm2)'); LEGEND_ALGEBRAIC(:,7) = strpad('i_K in component i_K (microA_per_cm2)'); LEGEND_CONSTANTS(:,3) = strpad('g_L in component i_L (milliS_per_cm2)'); LEGEND_CONSTANTS(:,4) = strpad('E_L in component i_L (millivolt)'); LEGEND_CONSTANTS(:,5) = strpad('E_Ca in component i_Ca (millivolt)'); LEGEND_CONSTANTS(:,6) = strpad('g_Ca in component i_Ca (milliS_per_cm2)'); LEGEND_STATES(:,2) = strpad('m in component i_Ca_m_gate (dimensionless)'); LEGEND_ALGEBRAIC(:,2) = strpad('m_infinity in component i_Ca_m_gate (dimensionless)'); LEGEND_ALGEBRAIC(:,5) = strpad('lambda_m in component i_Ca_m_gate (per_millisecond)'); LEGEND_CONSTANTS(:,7) = strpad('lambda_m_bar in component i_Ca_m_gate (per_millisecond)'); LEGEND_CONSTANTS(:,8) = strpad('V1 in component i_Ca_m_gate (millivolt)'); LEGEND_CONSTANTS(:,9) = strpad('V2 in component i_Ca_m_gate (millivolt)'); LEGEND_CONSTANTS(:,10) = strpad('E_K in component i_K (millivolt)'); LEGEND_CONSTANTS(:,11) = strpad('g_K in component i_K (milliS_per_cm2)'); LEGEND_STATES(:,3) = strpad('n in component i_K_n_gate (dimensionless)'); LEGEND_ALGEBRAIC(:,3) = strpad('n_infinity in component i_K_n_gate (dimensionless)'); LEGEND_ALGEBRAIC(:,6) = strpad('lambda_n in component i_K_n_gate (per_millisecond)'); LEGEND_CONSTANTS(:,12) = strpad('lambda_n_bar in component i_K_n_gate (per_millisecond)'); LEGEND_CONSTANTS(:,13) = strpad('V3 in component i_K_n_gate (millivolt)'); LEGEND_CONSTANTS(:,14) = strpad('V4 in component i_K_n_gate (millivolt)'); LEGEND_RATES(:,1) = strpad('d/dt V in component V (millivolt)'); LEGEND_RATES(:,2) = strpad('d/dt m in component i_Ca_m_gate (dimensionless)'); LEGEND_RATES(:,3) = strpad('d/dt n in component i_K_n_gate (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) = -50; CONSTANTS(:,1) = 20.0; CONSTANTS(:,2) = 540.0; CONSTANTS(:,3) = 2.0; CONSTANTS(:,4) = -50.00; CONSTANTS(:,5) = 100.0; CONSTANTS(:,6) = 4.0; STATES(:,2) = 0.1; CONSTANTS(:,7) = 1.0; CONSTANTS(:,8) = 0.0; CONSTANTS(:,9) = 15.0; CONSTANTS(:,10) = -70.0; CONSTANTS(:,11) = 8.0; STATES(:,3) = 0.1; CONSTANTS(:,12) = 0.1; CONSTANTS(:,13) = 10.0; CONSTANTS(:,14) = 10.0; 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(:,2) = 0.500000.*(1.00000+ tanh((STATES(:,1) - CONSTANTS(:,8))./CONSTANTS(:,9))); ALGEBRAIC(:,5) = CONSTANTS(:,7).*cosh((STATES(:,1) - CONSTANTS(:,8))./( 2.00000.*CONSTANTS(:,9))); RATES(:,2) = ALGEBRAIC(:,5).*(ALGEBRAIC(:,2) - STATES(:,2)); ALGEBRAIC(:,3) = 0.500000.*(1.00000+ tanh((STATES(:,1) - CONSTANTS(:,13))./CONSTANTS(:,14))); ALGEBRAIC(:,6) = CONSTANTS(:,12).*cosh((STATES(:,1) - CONSTANTS(:,13))./( 2.00000.*CONSTANTS(:,14))); RATES(:,3) = ALGEBRAIC(:,6).*(ALGEBRAIC(:,3) - STATES(:,3)); ALGEBRAIC(:,1) = CONSTANTS(:,3).*(STATES(:,1) - CONSTANTS(:,4)); ALGEBRAIC(:,4) = CONSTANTS(:,6).*STATES(:,2).*(STATES(:,1) - CONSTANTS(:,5)); ALGEBRAIC(:,7) = CONSTANTS(:,11).*STATES(:,3).*(STATES(:,1) - CONSTANTS(:,10)); RATES(:,1) = (CONSTANTS(:,2) - (ALGEBRAIC(:,1)+ALGEBRAIC(:,4)+ALGEBRAIC(:,7)))./CONSTANTS(:,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(:,2) = 0.500000.*(1.00000+ tanh((STATES(:,1) - CONSTANTS(:,8))./CONSTANTS(:,9))); ALGEBRAIC(:,5) = CONSTANTS(:,7).*cosh((STATES(:,1) - CONSTANTS(:,8))./( 2.00000.*CONSTANTS(:,9))); ALGEBRAIC(:,3) = 0.500000.*(1.00000+ tanh((STATES(:,1) - CONSTANTS(:,13))./CONSTANTS(:,14))); ALGEBRAIC(:,6) = CONSTANTS(:,12).*cosh((STATES(:,1) - CONSTANTS(:,13))./( 2.00000.*CONSTANTS(:,14))); ALGEBRAIC(:,1) = CONSTANTS(:,3).*(STATES(:,1) - CONSTANTS(:,4)); ALGEBRAIC(:,4) = CONSTANTS(:,6).*STATES(:,2).*(STATES(:,1) - CONSTANTS(:,5)); ALGEBRAIC(:,7) = CONSTANTS(:,11).*STATES(:,3).*(STATES(:,1) - CONSTANTS(:,10)); 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