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 =25;
end
% There are a total of 7 entries in each of the rate and state variable arrays.
% There are a total of 30 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_CONSTANTS(:,1) = strpad('concentration in component Subtilin (nM)');
LEGEND_CONSTANTS(:,2) = strpad('RNA1 in component SpeciesInitialConcentrations (nM)');
LEGEND_CONSTANTS(:,3) = strpad('RNA2 in component SpeciesInitialConcentrations (nM)');
LEGEND_CONSTANTS(:,4) = strpad('spaK in component SpeciesInitialConcentrations (nM)');
LEGEND_CONSTANTS(:,5) = strpad('spaR in component SpeciesInitialConcentrations (nM)');
LEGEND_CONSTANTS(:,6) = strpad('spaKactive in component SpeciesInitialConcentrations (nM)');
LEGEND_CONSTANTS(:,7) = strpad('spaRactive in component SpeciesInitialConcentrations (nM)');
LEGEND_CONSTANTS(:,8) = strpad('GFP in component SpeciesInitialConcentrations (nM)');
LEGEND_CONSTANTS(:,30) = strpad('JRNA in component Template_Promoter_Constitutive (nM_per_s)');
LEGEND_ALGEBRAIC(:,5) = strpad('JGain in component RNA1_interface (nM_per_s)');
LEGEND_ALGEBRAIC(:,1) = strpad('J in component Template_RxR1P1 (nM_per_s)');
LEGEND_ALGEBRAIC(:,12) = strpad('J in component Template_ProteinCDS (nM_per_s)');
LEGEND_ALGEBRAIC(:,19) = strpad('J in component Template_RxR2P1 (nM_per_s)');
LEGEND_ALGEBRAIC(:,16) = strpad('J in component Template_RxR1P1 (nM_per_s)');
LEGEND_ALGEBRAIC(:,14) = strpad('J in component Template_RxR1P1 (nM_per_s)');
LEGEND_ALGEBRAIC(:,15) = strpad('J in component Template_RxR2P1 (nM_per_s)');
LEGEND_ALGEBRAIC(:,20) = strpad('JGain in component spaK_interface (nM_per_s)');
LEGEND_ALGEBRAIC(:,17) = strpad('J in component Template_RxR1P1 (nM_per_s)');
LEGEND_ALGEBRAIC(:,21) = strpad('JGain in component spaKactive_interface (nM_per_s)');
LEGEND_ALGEBRAIC(:,6) = strpad('J in component Template_ProteinCDS (nM_per_s)');
LEGEND_ALGEBRAIC(:,18) = strpad('J in component Template_RxR1P1 (nM_per_s)');
LEGEND_ALGEBRAIC(:,22) = strpad('J in component Template_RxR1P1 (nM_per_s)');
LEGEND_ALGEBRAIC(:,23) = strpad('JGain in component spaR_interface (nM_per_s)');
LEGEND_ALGEBRAIC(:,24) = strpad('J in component Template_RxR1P1 (nM_per_s)');
LEGEND_ALGEBRAIC(:,25) = strpad('JGain in component spaRactive_interface (nM_per_s)');
LEGEND_ALGEBRAIC(:,3) = strpad('JRNA in component Template_Promoter_Inductive (nM_per_s)');
LEGEND_ALGEBRAIC(:,10) = strpad('JGain in component RNA2_interface (nM_per_s)');
LEGEND_ALGEBRAIC(:,7) = strpad('J in component Template_RxR1P1 (nM_per_s)');
LEGEND_ALGEBRAIC(:,8) = strpad('J in component Template_ProteinCDS (nM_per_s)');
LEGEND_ALGEBRAIC(:,13) = strpad('JGain in component GFP_interface (nM_per_s)');
LEGEND_ALGEBRAIC(:,11) = strpad('J in component Template_RxR1P1 (nM_per_s)');
LEGEND_CONSTANTS(:,9) = strpad('cellVolume in component Chassis_Bacillus (femtoliter)');
LEGEND_VOI = strpad('time in component Time (second)');
LEGEND_CONSTANTS(:,10) = strpad('k in component Bugbuster_Promoter1 (PoPs)');
LEGEND_STATES(:,1) = strpad('concentration in component Template_Species (nM)');
LEGEND_CONSTANTS(:,11) = strpad('kDecay in component Bioenvironment_Degradation_BugbusterRNA1 (per_s)');
LEGEND_ALGEBRAIC(:,2) = strpad('RNARiPs in component Template_RBS (RiPsInAttoMoles)');
LEGEND_CONSTANTS(:,12) = strpad('k in component Bugbuster_RBS_spaR (RiPs)');
LEGEND_ALGEBRAIC(:,9) = strpad('RNARiPs in component Template_RBS (RiPsInAttoMoles)');
LEGEND_CONSTANTS(:,13) = strpad('k in component Bugbuster_RBS_spaK (RiPs)');
LEGEND_STATES(:,2) = strpad('concentration in component Template_Species (nM)');
LEGEND_CONSTANTS(:,14) = strpad('kDecay in component Bioenvironment_Degradation_spaK (per_s)');
LEGEND_CONSTANTS(:,15) = strpad('k in component Bioenvironment_RxR2P1_spaKActivation (per_nM_per_s)');
LEGEND_STATES(:,3) = strpad('concentration in component Template_Species (nM)');
LEGEND_CONSTANTS(:,16) = strpad('k in component Bioenvironment_Dephosphorylation_spaKactive (per_s)');
LEGEND_CONSTANTS(:,17) = strpad('kDecay in component Bioenvironment_Degradation_spaKactive (per_s)');
LEGEND_STATES(:,4) = strpad('concentration in component Template_Species (nM)');
LEGEND_CONSTANTS(:,18) = strpad('kDecay in component Bioenvironment_Degradation_spaR (per_s)');
LEGEND_CONSTANTS(:,19) = strpad('k in component Bioenvironment_RxR2P1_spaRActivation (per_nM_per_s)');
LEGEND_STATES(:,5) = strpad('concentration in component Template_Species (nM)');
LEGEND_CONSTANTS(:,20) = strpad('k in component Bioenvironment_Dephosphorylation_spaRactive (per_s)');
LEGEND_CONSTANTS(:,21) = strpad('kDecay in component Bioenvironment_Degradation_spaRactive (per_s)');
LEGEND_CONSTANTS(:,22) = strpad('k in component Bugbuster_Promoter2 (PoPs)');
LEGEND_CONSTANTS(:,23) = strpad('n in component Bugbuster_Promoter2 (dimensionless)');
LEGEND_CONSTANTS(:,24) = strpad('Km in component Bugbuster_Promoter2 (nM)');
LEGEND_STATES(:,6) = strpad('concentration in component Template_Species (nM)');
LEGEND_CONSTANTS(:,25) = strpad('kDecay in component Bioenvironment_Degradation_BugbusterRNA2 (per_s)');
LEGEND_ALGEBRAIC(:,4) = strpad('RNARiPs in component Template_RBS (RiPsInAttoMoles)');
LEGEND_CONSTANTS(:,26) = strpad('k in component Bugbuster_RBS_GFP (RiPs)');
LEGEND_STATES(:,7) = strpad('concentration in component Template_Species (nM)');
LEGEND_CONSTANTS(:,27) = strpad('kDecay in component Bioenvironment_Degradation_GFP (per_s)');
LEGEND_CONSTANTS(:,28) = strpad('avogadrosConstant in component Template_Promoter_Constitutive (per_mole)');
LEGEND_CONSTANTS(:,29) = strpad('avogadrosConstant in component Template_Promoter_Inductive (per_mole)');
LEGEND_RATES(:,1) = strpad('d/dt concentration in component Template_Species (nM)');
LEGEND_RATES(:,2) = strpad('d/dt concentration in component Template_Species (nM)');
LEGEND_RATES(:,3) = strpad('d/dt concentration in component Template_Species (nM)');
LEGEND_RATES(:,4) = strpad('d/dt concentration in component Template_Species (nM)');
LEGEND_RATES(:,5) = strpad('d/dt concentration in component Template_Species (nM)');
LEGEND_RATES(:,6) = strpad('d/dt concentration in component Template_Species (nM)');
LEGEND_RATES(:,7) = strpad('d/dt concentration in component Template_Species (nM)');
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) = 1000;
CONSTANTS(:,2) = 0;
CONSTANTS(:,3) = 0;
CONSTANTS(:,4) = 0;
CONSTANTS(:,5) = 0;
CONSTANTS(:,6) = 0;
CONSTANTS(:,7) = 0;
CONSTANTS(:,8) = 0;
CONSTANTS(:,9) = 1;
CONSTANTS(:,10) = 0.04;
CONSTANTS(:,11) = 0.0058;
CONSTANTS(:,12) = 0.1;
CONSTANTS(:,13) = 0.1818;
CONSTANTS(:,14) = 0.0012;
CONSTANTS(:,15) = 1e-4;
CONSTANTS(:,16) = 0.1;
CONSTANTS(:,17) = 0.0012;
CONSTANTS(:,18) = 0.0012;
CONSTANTS(:,19) = 1e-4;
CONSTANTS(:,20) = 0.1;
CONSTANTS(:,21) = 0.0012;
CONSTANTS(:,22) = 0.04;
CONSTANTS(:,23) = 2;
CONSTANTS(:,24) = 320;
CONSTANTS(:,25) = 0.0058;
CONSTANTS(:,26) = 0.145;
CONSTANTS(:,27) = 0.0012;
CONSTANTS(:,28) = 6.0221415e23;
CONSTANTS(:,29) = 6.0221415e23;
CONSTANTS(:,30) = CONSTANTS(:,10).*1.00000e+09./( CONSTANTS(:,9).*1.00000e-15.*CONSTANTS(:,28));
STATES(:,1) = CONSTANTS(:,2);
STATES(:,2) = CONSTANTS(:,4);
STATES(:,3) = CONSTANTS(:,6);
STATES(:,4) = CONSTANTS(:,5);
STATES(:,5) = CONSTANTS(:,7);
STATES(:,6) = CONSTANTS(:,3);
STATES(:,7) = CONSTANTS(:,8);
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);
else
statesRowCount = statesSize(1);
ALGEBRAIC = zeros(statesRowCount, algebraicVariableCount);
RATES = zeros(statesRowCount, statesColumnCount);
end
ALGEBRAIC(:,1) = CONSTANTS(:,11).*STATES(:,1);
ALGEBRAIC(:,5) = CONSTANTS(:,30) - ALGEBRAIC(:,1);
RATES(:,1) = ALGEBRAIC(:,5);
ALGEBRAIC(:,3) = CONSTANTS(:,22).*STATES(:,5) .^ CONSTANTS(:,23)./(CONSTANTS(:,24) .^ CONSTANTS(:,23)+STATES(:,5) .^ CONSTANTS(:,23)).*1.00000e+09./( CONSTANTS(:,9).*1.00000e-15.*CONSTANTS(:,29));
ALGEBRAIC(:,7) = CONSTANTS(:,25).*STATES(:,6);
ALGEBRAIC(:,10) = ALGEBRAIC(:,3) - ALGEBRAIC(:,7);
RATES(:,6) = ALGEBRAIC(:,10);
ALGEBRAIC(:,4) = 1.00000e+09.*CONSTANTS(:,26).*STATES(:,6).*CONSTANTS(:,9).*1.00000e-15;
ALGEBRAIC(:,8) = 1.00000e+06.*ALGEBRAIC(:,4)./CONSTANTS(:,9);
ALGEBRAIC(:,11) = CONSTANTS(:,27).*STATES(:,7);
ALGEBRAIC(:,13) = ALGEBRAIC(:,8) - ALGEBRAIC(:,11);
RATES(:,7) = ALGEBRAIC(:,13);
ALGEBRAIC(:,9) = 1.00000e+09.*CONSTANTS(:,13).*STATES(:,1).*CONSTANTS(:,9).*1.00000e-15;
ALGEBRAIC(:,12) = 1.00000e+06.*ALGEBRAIC(:,9)./CONSTANTS(:,9);
ALGEBRAIC(:,19) = STATES(:,3).*STATES(:,4).*CONSTANTS(:,19);
ALGEBRAIC(:,16) = CONSTANTS(:,16).*STATES(:,3);
ALGEBRAIC(:,14) = CONSTANTS(:,14).*STATES(:,2);
ALGEBRAIC(:,15) = CONSTANTS(:,1).*STATES(:,2).*CONSTANTS(:,15);
ALGEBRAIC(:,20) = ALGEBRAIC(:,12)+ALGEBRAIC(:,19)+ALGEBRAIC(:,16) - (ALGEBRAIC(:,15)+ALGEBRAIC(:,14));
RATES(:,2) = ALGEBRAIC(:,20);
ALGEBRAIC(:,17) = CONSTANTS(:,17).*STATES(:,3);
ALGEBRAIC(:,21) = ALGEBRAIC(:,15) - ALGEBRAIC(:,17)+ALGEBRAIC(:,16)+ALGEBRAIC(:,19);
RATES(:,3) = ALGEBRAIC(:,21);
ALGEBRAIC(:,2) = 1.00000e+09.*CONSTANTS(:,12).*STATES(:,1).*CONSTANTS(:,9).*1.00000e-15;
ALGEBRAIC(:,6) = 1.00000e+06.*ALGEBRAIC(:,2)./CONSTANTS(:,9);
ALGEBRAIC(:,18) = CONSTANTS(:,18).*STATES(:,4);
ALGEBRAIC(:,22) = CONSTANTS(:,20).*STATES(:,5);
ALGEBRAIC(:,23) = ALGEBRAIC(:,6)+ALGEBRAIC(:,22) - (ALGEBRAIC(:,18)+ALGEBRAIC(:,19));
RATES(:,4) = ALGEBRAIC(:,23);
ALGEBRAIC(:,24) = CONSTANTS(:,21).*STATES(:,5);
ALGEBRAIC(:,25) = ALGEBRAIC(:,19) - ALGEBRAIC(:,24)+ALGEBRAIC(:,22);
RATES(:,5) = ALGEBRAIC(:,25);
RATES = RATES';
end
% Calculate algebraic variables
function ALGEBRAIC = computeAlgebraic(ALGEBRAIC, CONSTANTS, STATES, VOI)
ALGEBRAIC(:,1) = CONSTANTS(:,11).*STATES(:,1);
ALGEBRAIC(:,5) = CONSTANTS(:,30) - ALGEBRAIC(:,1);
ALGEBRAIC(:,3) = CONSTANTS(:,22).*STATES(:,5) .^ CONSTANTS(:,23)./(CONSTANTS(:,24) .^ CONSTANTS(:,23)+STATES(:,5) .^ CONSTANTS(:,23)).*1.00000e+09./( CONSTANTS(:,9).*1.00000e-15.*CONSTANTS(:,29));
ALGEBRAIC(:,7) = CONSTANTS(:,25).*STATES(:,6);
ALGEBRAIC(:,10) = ALGEBRAIC(:,3) - ALGEBRAIC(:,7);
ALGEBRAIC(:,4) = 1.00000e+09.*CONSTANTS(:,26).*STATES(:,6).*CONSTANTS(:,9).*1.00000e-15;
ALGEBRAIC(:,8) = 1.00000e+06.*ALGEBRAIC(:,4)./CONSTANTS(:,9);
ALGEBRAIC(:,11) = CONSTANTS(:,27).*STATES(:,7);
ALGEBRAIC(:,13) = ALGEBRAIC(:,8) - ALGEBRAIC(:,11);
ALGEBRAIC(:,9) = 1.00000e+09.*CONSTANTS(:,13).*STATES(:,1).*CONSTANTS(:,9).*1.00000e-15;
ALGEBRAIC(:,12) = 1.00000e+06.*ALGEBRAIC(:,9)./CONSTANTS(:,9);
ALGEBRAIC(:,19) = STATES(:,3).*STATES(:,4).*CONSTANTS(:,19);
ALGEBRAIC(:,16) = CONSTANTS(:,16).*STATES(:,3);
ALGEBRAIC(:,14) = CONSTANTS(:,14).*STATES(:,2);
ALGEBRAIC(:,15) = CONSTANTS(:,1).*STATES(:,2).*CONSTANTS(:,15);
ALGEBRAIC(:,20) = ALGEBRAIC(:,12)+ALGEBRAIC(:,19)+ALGEBRAIC(:,16) - (ALGEBRAIC(:,15)+ALGEBRAIC(:,14));
ALGEBRAIC(:,17) = CONSTANTS(:,17).*STATES(:,3);
ALGEBRAIC(:,21) = ALGEBRAIC(:,15) - ALGEBRAIC(:,17)+ALGEBRAIC(:,16)+ALGEBRAIC(:,19);
ALGEBRAIC(:,2) = 1.00000e+09.*CONSTANTS(:,12).*STATES(:,1).*CONSTANTS(:,9).*1.00000e-15;
ALGEBRAIC(:,6) = 1.00000e+06.*ALGEBRAIC(:,2)./CONSTANTS(:,9);
ALGEBRAIC(:,18) = CONSTANTS(:,18).*STATES(:,4);
ALGEBRAIC(:,22) = CONSTANTS(:,20).*STATES(:,5);
ALGEBRAIC(:,23) = ALGEBRAIC(:,6)+ALGEBRAIC(:,22) - (ALGEBRAIC(:,18)+ALGEBRAIC(:,19));
ALGEBRAIC(:,24) = CONSTANTS(:,21).*STATES(:,5);
ALGEBRAIC(:,25) = ALGEBRAIC(:,19) - ALGEBRAIC(:,24)+ALGEBRAIC(:,22);
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