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 =3; end % There are a total of 9 entries in each of the rate and state variable arrays. % There are a total of 18 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 (second)'); LEGEND_CONSTANTS(:,1) = strpad('NGF in component NGF (dimensionless)'); LEGEND_CONSTANTS(:,2) = strpad('pro_TrkA in component pro_TrkA (dimensionless)'); LEGEND_STATES(:,1) = strpad('TrkA in component TrkA (dimensionless)'); LEGEND_STATES(:,2) = strpad('NGF_TrkA in component NGF_TrkA (dimensionless)'); LEGEND_CONSTANTS(:,3) = strpad('k2_NGF_TrkA in component model_parameters (first_order_rate_constant)'); LEGEND_CONSTANTS(:,4) = strpad('k1_NGF_TrkA in component model_parameters (first_order_rate_constant)'); LEGEND_CONSTANTS(:,5) = strpad('TrkA_turnover in component model_parameters (first_order_rate_constant)'); LEGEND_CONSTANTS(:,6) = strpad('k1_TrkA_phosphorylation in component model_parameters (first_order_rate_constant)'); LEGEND_STATES(:,3) = strpad('pTrkA in component pTrkA (dimensionless)'); LEGEND_STATES(:,4) = strpad('pTrkA_Akt in component pTrkA_Akt (dimensionless)'); LEGEND_STATES(:,5) = strpad('Akt in component Akt (dimensionless)'); LEGEND_CONSTANTS(:,7) = strpad('k1_pTrkA_degradation in component model_parameters (first_order_rate_constant)'); LEGEND_CONSTANTS(:,8) = strpad('k1_Akt_phosphorylation in component model_parameters (first_order_rate_constant)'); LEGEND_CONSTANTS(:,9) = strpad('k1_pTrkA_Akt in component model_parameters (first_order_rate_constant)'); LEGEND_CONSTANTS(:,10) = strpad('k2_pTrkA_Akt in component model_parameters (first_order_rate_constant)'); LEGEND_STATES(:,6) = strpad('pAkt in component pAkt (dimensionless)'); LEGEND_CONSTANTS(:,11) = strpad('k1_pAkt_dephosphorylation in component model_parameters (first_order_rate_constant)'); LEGEND_STATES(:,7) = strpad('S6 in component S6 (dimensionless)'); LEGEND_STATES(:,8) = strpad('pAkt_S6 in component pAkt_S6 (dimensionless)'); LEGEND_CONSTANTS(:,12) = strpad('k1_pAkt_S6 in component model_parameters (first_order_rate_constant)'); LEGEND_CONSTANTS(:,13) = strpad('k2_pAkt_S6 in component model_parameters (first_order_rate_constant)'); LEGEND_CONSTANTS(:,14) = strpad('k1_S6_phosphorylation in component model_parameters (first_order_rate_constant)'); LEGEND_STATES(:,9) = strpad('pS6 in component pS6 (dimensionless)'); LEGEND_CONSTANTS(:,15) = strpad('k1_pS6_dephosphorylation in component model_parameters (first_order_rate_constant)'); LEGEND_ALGEBRAIC(:,1) = strpad('pTrkA_total in component pTrkA_total (dimensionless)'); LEGEND_CONSTANTS(:,16) = strpad('pTrkA_scalefactor in component pTrkA_total (dimensionless)'); LEGEND_ALGEBRAIC(:,2) = strpad('pAkt_total in component pAkt_total (dimensionless)'); LEGEND_CONSTANTS(:,17) = strpad('pAkt_scalefactor in component pAkt_total (dimensionless)'); LEGEND_ALGEBRAIC(:,3) = strpad('pS6_total in component pS6_total (dimensionless)'); LEGEND_CONSTANTS(:,18) = strpad('pS6_scalefactor in component pS6_total (dimensionless)'); LEGEND_RATES(:,1) = strpad('d/dt TrkA in component TrkA (dimensionless)'); LEGEND_RATES(:,2) = strpad('d/dt NGF_TrkA in component NGF_TrkA (dimensionless)'); LEGEND_RATES(:,3) = strpad('d/dt pTrkA in component pTrkA (dimensionless)'); LEGEND_RATES(:,4) = strpad('d/dt pTrkA_Akt in component pTrkA_Akt (dimensionless)'); LEGEND_RATES(:,5) = strpad('d/dt Akt in component Akt (dimensionless)'); LEGEND_RATES(:,6) = strpad('d/dt pAkt in component pAkt (dimensionless)'); LEGEND_RATES(:,8) = strpad('d/dt pAkt_S6 in component pAkt_S6 (dimensionless)'); LEGEND_RATES(:,7) = strpad('d/dt S6 in component S6 (dimensionless)'); LEGEND_RATES(:,9) = strpad('d/dt pS6 in component pS6 (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 = []; CONSTANTS(:,1) = 30.0; CONSTANTS(:,2) = 8.52065e0; STATES(:,1) = 8.52065e0; STATES(:,2) = 0.0; CONSTANTS(:,3) = 1.33747e-2; CONSTANTS(:,4) = 2.69408e-3; CONSTANTS(:,5) = 0.0011032440769796; CONSTANTS(:,6) = 8.33178e-3; STATES(:,3) = 0.0; STATES(:,4) = 0.0; STATES(:,5) = 1.15595e0; CONSTANTS(:,7) = 6.8084e-2; CONSTANTS(:,8) = 2.02517e-2; CONSTANTS(:,9) = 8.82701e-2; CONSTANTS(:,10) = 1.47518e-10; STATES(:,6) = 0.0; CONSTANTS(:,11) = 1.28135e0; STATES(:,7) = 3.55234e0; STATES(:,8) = 0.0; CONSTANTS(:,12) = 6.83666e1; CONSTANTS(:,13) = 5.23519e-00; CONSTANTS(:,14) = 5.65150e-3; STATES(:,9) = 0.0; CONSTANTS(:,15) = 2.93167e-4; CONSTANTS(:,16) = 8.48783e-1; CONSTANTS(:,17) = 2.42381e0; CONSTANTS(:,18) = 5.25843e-1; 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 RATES(:,1) = ( CONSTANTS(:,3).*STATES(:,2)+ CONSTANTS(:,5).*(CONSTANTS(:,2) - STATES(:,1))) - CONSTANTS(:,4).*CONSTANTS(:,1).*STATES(:,1); RATES(:,2) = CONSTANTS(:,4).*CONSTANTS(:,1).*STATES(:,1) - ( CONSTANTS(:,3).*STATES(:,2)+ CONSTANTS(:,6).*STATES(:,2)); RATES(:,3) = ( CONSTANTS(:,6).*STATES(:,2)+ CONSTANTS(:,8).*STATES(:,4)+ CONSTANTS(:,10).*STATES(:,4)) - ( CONSTANTS(:,7).*STATES(:,3)+ CONSTANTS(:,9).*STATES(:,3).*STATES(:,5)); RATES(:,4) = CONSTANTS(:,9).*STATES(:,3).*STATES(:,5) - ( CONSTANTS(:,10).*STATES(:,4)+ CONSTANTS(:,8).*STATES(:,4)); RATES(:,5) = ( CONSTANTS(:,10).*STATES(:,4)+ CONSTANTS(:,11).*STATES(:,6)) - CONSTANTS(:,9).*STATES(:,3).*STATES(:,5); RATES(:,6) = ( CONSTANTS(:,8).*STATES(:,4)+ CONSTANTS(:,13).*STATES(:,8)+ CONSTANTS(:,14).*STATES(:,8)) - ( CONSTANTS(:,11).*STATES(:,6)+ CONSTANTS(:,12).*STATES(:,6).*STATES(:,7)); RATES(:,8) = CONSTANTS(:,12).*STATES(:,6).*STATES(:,7) - ( CONSTANTS(:,13).*STATES(:,8)+ CONSTANTS(:,14).*STATES(:,8)); RATES(:,7) = ( CONSTANTS(:,13).*STATES(:,8)+ CONSTANTS(:,15).*STATES(:,9)) - CONSTANTS(:,12).*STATES(:,6).*STATES(:,7); RATES(:,9) = CONSTANTS(:,14).*STATES(:,8) - CONSTANTS(:,15).*STATES(:,9); 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(:,1) = (STATES(:,3)+STATES(:,4)).*CONSTANTS(:,16); ALGEBRAIC(:,2) = (STATES(:,6)+STATES(:,8)).*CONSTANTS(:,17); ALGEBRAIC(:,3) = STATES(:,9).*CONSTANTS(:,18); 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