% This file works with OCTAVE and is automatically generated with % the System Biology Format Converter (http://sbfc.sourceforge.net/) % from an SBML file. % To run this file with Matlab you must edit the comments providing % the definition of the ode solver and the signature for the % xdot function. % % The conversion system has the following limitations: % - You may have to re order some reactions and Assignment Rules definition % - Delays are not taken into account % - You should change the lsode parameters (start, end, steps) to get better results % % % Model name = SABIOmdl26Dec2024404 % % function main() %Initial conditions vector x0=zeros(98,1); x0(1) = 1.0; x0(2) = 1.0; x0(3) = 1.0; x0(4) = 1.0; x0(5) = 1.0; x0(6) = 1.0; x0(7) = 1.0; x0(8) = 1.0; x0(9) = 1.0; x0(10) = 1.0; x0(11) = 1.0; x0(12) = 1.0; x0(13) = 1.0; x0(14) = 1.0; x0(15) = 1.0; x0(16) = 1.0; x0(17) = 1.0; x0(18) = 1.0; x0(19) = 1.0; x0(20) = 1.0; x0(21) = 1.0; x0(22) = 1.0; x0(23) = 1.0; x0(24) = 1.0; x0(25) = 1.0; x0(26) = 1.0; x0(27) = 1.0; x0(28) = 1.0; x0(29) = 1.0; x0(30) = 1.0; x0(31) = 1.0; x0(32) = 1.0; x0(33) = 1.0; x0(34) = 1.0; x0(35) = 1.0; x0(36) = 1.0; x0(37) = 1.0; x0(38) = 1.0; x0(39) = 1.0; x0(40) = 1.0; x0(41) = 1.0; x0(42) = 1.0; x0(43) = 1.0; x0(44) = 1.0; x0(45) = 1.0; x0(46) = 1.0; x0(47) = 1.0; x0(48) = 1.0; x0(49) = 1.0; x0(50) = 1.0; x0(51) = 1.0; x0(52) = 1.0; x0(53) = 1.0; x0(54) = 1.0; x0(55) = 1.0; x0(56) = 1.0; x0(57) = 1.0; x0(58) = 1.0; x0(59) = 1.0; x0(60) = 1.0; x0(61) = 1.0; x0(62) = 1.0; x0(63) = 1.0; x0(64) = 1.0; x0(65) = 1.0; x0(66) = 1.0; x0(67) = 1.0; x0(68) = 1.0; x0(69) = 1.0; x0(70) = 1.0; x0(71) = 1.0; x0(72) = 1.0; x0(73) = 1.0; x0(74) = 1.0; x0(75) = 1.0; x0(76) = 1.0; x0(77) = 1.0; x0(78) = 1.0; x0(79) = 1.0; x0(80) = 1.0; x0(81) = 1.0; x0(82) = 1.0; x0(83) = 1.0; x0(84) = 1.0; x0(85) = 1.0; x0(86) = 1.0; x0(87) = 1.0; x0(88) = 1.0; x0(89) = 1.0; x0(90) = 1.0; x0(91) = 1.0; x0(92) = 1.0; x0(93) = 1.0; x0(94) = 1.0; x0(95) = 1.0; x0(96) = 1.0; x0(97) = 1.0; x0(98) = 1.0; % Depending on whether you are using Octave or Matlab, % you should comment / uncomment one of the following blocks. % This should also be done for the definition of the function f below. % Start Matlab code % tspan=[0:0.01:100]; % opts = odeset('AbsTol',1e-3); % [t,x]=ode23tb(@f,tspan,x0,opts); % End Matlab code % Start Octave code t=linspace(0,100,100); x=lsode('f',x0,t); % End Octave code plot(t,x); end % Depending on whether you are using Octave or Matlab, % you should comment / uncomment one of the following blocks. % This should also be done for the definition of the function f below. % Start Matlab code %function xdot=f(t,x) % End Matlab code % Start Octave code function xdot=f(x,t) % End Octave code % Compartment: id = compart_cytosol, name = cytosol, constant compartment_compart_cytosol=NaN; % Compartment: id = compart_membrane, name = membrane, constant compartment_compart_membrane=NaN; % Compartment: id = compart_lysosome, name = lysosome, constant compartment_compart_lysosome=NaN; % Compartment: id = compart_mitochondrion, name = mitochondrion, constant compartment_compart_mitochondrion=NaN; % Compartment: id = compart_Cell, name = Cell, constant compartment_compart_Cell=NaN; % Reaction: id = REAC_2 % Local Parameter: id = Km_SPC_28371_lysosome, name = Km_4MethylumbelliferylalphaDgalactoside reaction_REAC_2_Km_SPC_28371_lysosome=0.003; reaction_REAC_2=KL_50493(reaction_REAC_2_Vmax, x(12), reaction_REAC_2_Km_SPC_28371_lysosome); % Reaction: id = REAC_3 % Local Parameter: id = Ki_SPC_27857_mitochondrion, name = Ki_two3Didehydrotwo3dideoxythymidine reaction_REAC_3_Ki_SPC_27857_mitochondrion=7.8E-5; reaction_REAC_3=KL_41756(reaction_REAC_3_Ki_SPC_27857_mitochondrion, x(17), x(16)); % Reaction: id = REAC_4 % Local Parameter: id = Ki_SPC_13796_mitochondrion, name = Ki_5Fluorodeoxyuridine reaction_REAC_4_Ki_SPC_13796_mitochondrion=1.3E-5; reaction_REAC_4=KL_41757(reaction_REAC_4_Ki_SPC_13796_mitochondrion, x(17), x(16)); % Reaction: id = REAC_5 % Local Parameter: id = Ki_SPC_27854_mitochondrion, name = Ki_3Azidotwo3dideoxythymidine reaction_REAC_5_Ki_SPC_27854_mitochondrion=2.0E-6; reaction_REAC_5=KL_41754(x(16), x(17), reaction_REAC_5_Ki_SPC_27854_mitochondrion); % Reaction: id = REAC_6 % Local Parameter: id = Ki_SPC_27856_mitochondrion, name = Ki_3Fluorotwo3dideoxythymidine reaction_REAC_6_Ki_SPC_27856_mitochondrion=1.0E-5; reaction_REAC_6=KL_41755(x(17), reaction_REAC_6_Ki_SPC_27856_mitochondrion, x(16)); % Reaction: id = REAC_7 % Local Parameter: id = Km_SPC_34_mitochondrion, name = Km_ATP reaction_REAC_7_Km_SPC_34_mitochondrion=2.0E-6; reaction_REAC_7=KL_41750(reaction_REAC_7_Km_SPC_34_mitochondrion, x(16), reaction_REAC_7_Vmax, x(17)); % Reaction: id = REAC_8 % Local Parameter: id = Km_SPC_34_mitochondrion, name = Km_ATP reaction_REAC_8_Km_SPC_34_mitochondrion=3.0E-6; reaction_REAC_8=KL_41752(x(17), x(29), reaction_REAC_8_Km_SPC_34_mitochondrion, reaction_REAC_8_Vmax); % Reaction: id = REAC_9 % Local Parameter: id = Km_SPC_1286_mitochondrion, name = Km_CTP reaction_REAC_9_Km_SPC_1286_mitochondrion=6.0E-6; reaction_REAC_9=KL_41751(x(32), reaction_REAC_9_Vmax, reaction_REAC_9_Km_SPC_1286_mitochondrion, x(16)); % Reaction: id = REAC_10 % Local Parameter: id = n_SPC_27854_mitochondrion, name = n_3Azidotwo3dideoxythymidine reaction_REAC_10_n_SPC_27854_mitochondrion=0.4; % Local Parameter: id = Vmax_Km_SPC_27854_mitochondrion, name = Vmax_Km_3Azidotwo3dideoxythymidine reaction_REAC_10_Vmax_Km_SPC_27854_mitochondrion=2.666667; % Local Parameter: id = Km2_SPC_27854_mitochondrion, name = Km2_3Azidotwo3dideoxythymidine reaction_REAC_10_Km2_SPC_27854_mitochondrion=9.0E-5; % Local Parameter: id = Km1_SPC_27854_mitochondrion, name = Km1_3Azidotwo3dideoxythymidine reaction_REAC_10_Km1_SPC_27854_mitochondrion=2.0E-7; % Local Parameter: id = Vmax, name = Vmax reaction_REAC_10_Vmax=5.333333E-7; reaction_REAC_10=KL_41749(reaction_REAC_10_n_SPC_27854_mitochondrion, reaction_REAC_10_Vmax_Km_SPC_27854_mitochondrion, reaction_REAC_10_Km2_SPC_27854_mitochondrion, reaction_REAC_10_Km1_SPC_27854_mitochondrion, x(17), reaction_REAC_10_Vmax); % Reaction: id = REAC_11 % Local Parameter: id = Km_SPC_1286_mitochondrion, name = Km_CTP reaction_REAC_11_Km_SPC_1286_mitochondrion=9.0E-6; reaction_REAC_11=KL_41753(x(32), reaction_REAC_11_Vmax, reaction_REAC_11_Km_SPC_1286_mitochondrion, x(29)); % Reaction: id = REAC_12 % Local Parameter: id = Ki_SPC_2074_mitochondrion, name = Ki_twoDeoxyuridine reaction_REAC_12_Ki_SPC_2074_mitochondrion=7.5E-5; reaction_REAC_12=KL_41758(x(16), x(17), reaction_REAC_12_Ki_SPC_2074_mitochondrion); % Reaction: id = REAC_13 % Local Parameter: id = Ki_SPC_2178_mitochondrion, name = Ki_twoDeoxycytidine reaction_REAC_13_Ki_SPC_2178_mitochondrion=6.3E-4; reaction_REAC_13=KL_41759(x(16), reaction_REAC_13_Ki_SPC_2178_mitochondrion, x(17)); % Reaction: id = REAC_14 % Local Parameter: id = Ki_SPC_2074_mitochondrion, name = Ki_twoDeoxyuridine reaction_REAC_14_Ki_SPC_2074_mitochondrion=6.9E-4; reaction_REAC_14=KL_41766(x(17), x(29), reaction_REAC_14_Ki_SPC_2074_mitochondrion); % Reaction: id = REAC_15 % Local Parameter: id = Ki_SPC_1315_mitochondrion, name = Ki_Thymidine reaction_REAC_15_Ki_SPC_1315_mitochondrion=6.0E-6; reaction_REAC_15=KL_41765(reaction_REAC_15_Ki_SPC_1315_mitochondrion, x(29), x(17)); % Reaction: id = REAC_16 % Local Parameter: id = Ki_SPC_27854_mitochondrion, name = Ki_3Azidotwo3dideoxythymidine reaction_REAC_16_Ki_SPC_27854_mitochondrion=1.3E-4; reaction_REAC_16=KL_41764(x(29), x(17), reaction_REAC_16_Ki_SPC_27854_mitochondrion); % Reaction: id = REAC_17 % Local Parameter: id = Ki_SPC_2178_mitochondrion, name = Ki_twoDeoxycytidine reaction_REAC_17_Ki_SPC_2178_mitochondrion=6.7E-5; reaction_REAC_17=KL_41763(reaction_REAC_17_Ki_SPC_2178_mitochondrion, x(17), x(38)); % Reaction: id = REAC_18 % Local Parameter: id = Ki_SPC_1315_mitochondrion, name = Ki_Thymidine reaction_REAC_18_Ki_SPC_1315_mitochondrion=2.0E-7; reaction_REAC_18=KL_41762(reaction_REAC_18_Ki_SPC_1315_mitochondrion, x(17), x(38)); % Reaction: id = REAC_19 % Local Parameter: id = Ki_SPC_13796_mitochondrion, name = Ki_5Fluorodeoxyuridine reaction_REAC_19_Ki_SPC_13796_mitochondrion=2.0E-6; reaction_REAC_19=KL_41760(x(38), x(17), reaction_REAC_19_Ki_SPC_13796_mitochondrion); % Reaction: id = REAC_20 % Local Parameter: id = Ki_SPC_27854_mitochondrion, name = Ki_3Azidotwo3dideoxythymidine reaction_REAC_20_Ki_SPC_27854_mitochondrion=1.0E-6; reaction_REAC_20=KL_41761(x(38), x(17), reaction_REAC_20_Ki_SPC_27854_mitochondrion); % Reaction: id = REAC_21 % Local Parameter: id = Km1_SPC_1315_mitochondrion, name = Km1_Thymidine reaction_REAC_21_Km1_SPC_1315_mitochondrion=3.0E-7; % Local Parameter: id = Km2_SPC_1315_mitochondrion, name = Km2_Thymidine reaction_REAC_21_Km2_SPC_1315_mitochondrion=1.6E-5; % Local Parameter: id = Vmax, name = Vmax reaction_REAC_21_Vmax=9.333333E-6; % Local Parameter: id = n_SPC_1315_mitochondrion, name = n_Thymidine reaction_REAC_21_n_SPC_1315_mitochondrion=0.5; % Local Parameter: id = Vmax_Km_SPC_1315_mitochondrion, name = Vmax_Km_Thymidine reaction_REAC_21_Vmax_Km_SPC_1315_mitochondrion=31.1; reaction_REAC_21=KL_41745(reaction_REAC_21_Km1_SPC_1315_mitochondrion, x(17), reaction_REAC_21_Km2_SPC_1315_mitochondrion, reaction_REAC_21_Vmax, reaction_REAC_21_n_SPC_1315_mitochondrion, reaction_REAC_21_Vmax_Km_SPC_1315_mitochondrion); % Reaction: id = REAC_22 % Local Parameter: id = Vmax_Km_SPC_2178_mitochondrion, name = Vmax_Km_twoDeoxycytidine reaction_REAC_22_Vmax_Km_SPC_2178_mitochondrion=0.4166667; % Local Parameter: id = Vmax, name = Vmax reaction_REAC_22_Vmax=1.5E-5; % Local Parameter: id = Km_SPC_2178_mitochondrion, name = Km_twoDeoxycytidine reaction_REAC_22_Km_SPC_2178_mitochondrion=3.6E-5; reaction_REAC_22=KL_41746(reaction_REAC_22_Vmax_Km_SPC_2178_mitochondrion, x(29), reaction_REAC_22_Vmax, reaction_REAC_22_Km_SPC_2178_mitochondrion, x(17)); % Reaction: id = REAC_23 % Local Parameter: id = Vmax_Km_SPC_2074_mitochondrion, name = Vmax_Km_twoDeoxyuridine reaction_REAC_23_Vmax_Km_SPC_2074_mitochondrion=1.916667; % Local Parameter: id = Vmax, name = Vmax reaction_REAC_23_Vmax=1.15E-5; % Local Parameter: id = Km_SPC_2074_mitochondrion, name = Km_twoDeoxyuridine reaction_REAC_23_Km_SPC_2074_mitochondrion=6.0E-6; reaction_REAC_23=KL_41747(x(17), reaction_REAC_23_Vmax_Km_SPC_2074_mitochondrion, reaction_REAC_23_Vmax, reaction_REAC_23_Km_SPC_2074_mitochondrion, x(38)); % Reaction: id = REAC_24 % Local Parameter: id = Km_SPC_13796_mitochondrion, name = Km_5Fluorodeoxyuridine reaction_REAC_24_Km_SPC_13796_mitochondrion=7.0E-7; % Local Parameter: id = Vmax_Km_SPC_13796_mitochondrion, name = Vmax_Km_5Fluorodeoxyuridine reaction_REAC_24_Vmax_Km_SPC_13796_mitochondrion=10.23333; % Local Parameter: id = Vmax, name = Vmax reaction_REAC_24_Vmax=7.166667E-6; reaction_REAC_24=KL_41748(reaction_REAC_24_Km_SPC_13796_mitochondrion, x(22), reaction_REAC_24_Vmax_Km_SPC_13796_mitochondrion, x(17), reaction_REAC_24_Vmax); % Reaction: id = REAC_25 % Local Parameter: id = Ki_SPC_1678_mitochondrion, name = Ki_dCTP reaction_REAC_25_Ki_SPC_1678_mitochondrion=2.0E-4; % Local Parameter: id = n_SPC_1678_mitochondrion, name = n_dCTP reaction_REAC_25_n_SPC_1678_mitochondrion=0.6; reaction_REAC_25=KL_41768(x(54), reaction_REAC_25_Ki_SPC_1678_mitochondrion, x(16), reaction_REAC_25_n_SPC_1678_mitochondrion, x(17)); % Reaction: id = REAC_26 % Local Parameter: id = Ki_SPC_1679_mitochondrion, name = Ki_dTTP reaction_REAC_26_Ki_SPC_1679_mitochondrion=7.0E-6; reaction_REAC_26=KL_41767(reaction_REAC_26_Ki_SPC_1679_mitochondrion, x(16), x(17)); % Reaction: id = REAC_27 % Local Parameter: id = Km_SPC_5404_Cell, name = Km_SAdenosylmethioninamine reaction_REAC_27_Km_SPC_5404_Cell=7.0E-6; reaction_REAC_27=KL_39577(x(58), reaction_REAC_27_Km_SPC_5404_Cell, reaction_REAC_27_Vmax); % Reaction: id = REAC_28 % Local Parameter: id = Km_SPC_1941_Cell, name = Km_Putrescine reaction_REAC_28_Km_SPC_1941_Cell=8.0E-5; reaction_REAC_28=KL_39576(reaction_REAC_28_Vmax, x(59), reaction_REAC_28_Km_SPC_1941_Cell); % Reaction: id = REAC_29 % Local Parameter: id = IC_50_SPC_5060_Cell, name = IC_50_Heparin reaction_REAC_29_IC_50_SPC_5060_Cell=2.083375E-5; reaction_REAC_29=KL_48160(x(65), reaction_REAC_29_IC_50_SPC_5060_Cell); % Reaction: id = REAC_30 % Local Parameter: id = IC_50_SPC_5060_Cell, name = IC_50_Heparin reaction_REAC_30_IC_50_SPC_5060_Cell=2.083375E-5; reaction_REAC_30=KL_48161(reaction_REAC_30_IC_50_SPC_5060_Cell, x(65)); % Reaction: id = REAC_31 % Local Parameter: id = Km_SPC_23010_Cell, name = Km_4MethylumbelliferylbetaNacetylglucosaminide reaction_REAC_31_Km_SPC_23010_Cell=6.7E-4; reaction_REAC_31=KL_48158(reaction_REAC_31_Km_SPC_23010_Cell, reaction_REAC_31_Vmax, x(65)); % Reaction: id = REAC_32 % Local Parameter: id = Km_SPC_23010_Cell, name = Km_4MethylumbelliferylbetaNacetylglucosaminide reaction_REAC_32_Km_SPC_23010_Cell=6.7E-4; reaction_REAC_32=KL_48159(reaction_REAC_32_Km_SPC_23010_Cell, reaction_REAC_32_Vmax, x(65)); % Reaction: id = REAC_33 % Local Parameter: id = Km_SPC_21081_lysosome, name = Km_NDodecanoylsphingosine reaction_REAC_33_Km_SPC_21081_lysosome=1.49E-4; % Local Parameter: id = Vmax, name = Vmax reaction_REAC_33_Vmax=3.777778E-8; reaction_REAC_33=KL_21313(reaction_REAC_33_Km_SPC_21081_lysosome, x(73), reaction_REAC_33_Vmax); % Reaction: id = REAC_34 % Local Parameter: id = EA, name = EA reaction_REAC_34_EA=7.777778E-9; reaction_REAC_34=KL_21319(x(77), reaction_REAC_34_EA); % Reaction: id = REAC_35 % Local Parameter: id = EA, name = EA reaction_REAC_35_EA=5.277778E-9; reaction_REAC_35=KL_21316(x(80), reaction_REAC_35_EA); % Reaction: id = REAC_36 % Local Parameter: id = EA, name = EA reaction_REAC_36_EA=1.111111E-9; reaction_REAC_36=KL_21321(reaction_REAC_36_EA, x(83)); % Reaction: id = REAC_37 % Local Parameter: id = EA, name = EA reaction_REAC_37_EA=2.972222E-8; reaction_REAC_37=KL_21314(x(73), reaction_REAC_37_EA); % Reaction: id = REAC_38 % Local Parameter: id = EA, name = EA reaction_REAC_38_EA=5.833333E-9; reaction_REAC_38=KL_21315(reaction_REAC_38_EA, x(88)); % Reaction: id = REAC_39 % Local Parameter: id = EA, name = EA reaction_REAC_39_EA=8.333333E-9; reaction_REAC_39=KL_21317(reaction_REAC_39_EA, x(91)); % Reaction: id = REAC_40 % Local Parameter: id = EA, name = EA reaction_REAC_40_EA=4.722222E-9; reaction_REAC_40=KL_21318(reaction_REAC_40_EA, x(94)); % Reaction: id = REAC_41 % Local Parameter: id = EA, name = EA reaction_REAC_41_EA=8.333333E-10; reaction_REAC_41=KL_21320(reaction_REAC_41_EA, x(97)); xdot=zeros(98,1); % Species: id = SPC_2122_cytosol, name = Phosphatidylinositol, affected by kineticLaw xdot(1) = (1/(compartment_compart_cytosol))*((-1.0 * reaction_REAC_0)); % Species: id = SPC_40_cytosol, name = H2O, affected by kineticLaw xdot(2) = (1/(compartment_compart_cytosol))*((-1.0 * reaction_REAC_0)); % Species: id = SPC_5013_cytosol, name = Diacylglycerol, affected by kineticLaw xdot(3) = (1/(compartment_compart_cytosol))*(( 1.0 * reaction_REAC_0)); % Species: id = SPC_5422_cytosol, name = 1D-myo-Inositol 1-phosphate, affected by kineticLaw xdot(4) = (1/(compartment_compart_cytosol))*(( 1.0 * reaction_REAC_0)); % Species: id = ENZ_225573_cytosol, name = phosphoinositide phospholipase C(Enzyme) wildtype % Warning species is not changed by either rules or reactions xdot(5) = ; % Species: id = SPC_2122_membrane, name = Phosphatidylinositol, affected by kineticLaw xdot(6) = (1/(compartment_compart_membrane))*((-1.0 * reaction_REAC_1)); % Species: id = SPC_40_membrane, name = H2O, affected by kineticLaw xdot(7) = (1/(compartment_compart_membrane))*((-1.0 * reaction_REAC_1)); % Species: id = SPC_5013_membrane, name = Diacylglycerol, affected by kineticLaw xdot(8) = (1/(compartment_compart_membrane))*(( 1.0 * reaction_REAC_1)); % Species: id = SPC_5422_membrane, name = 1D-myo-Inositol 1-phosphate, affected by kineticLaw xdot(9) = (1/(compartment_compart_membrane))*(( 1.0 * reaction_REAC_1)); % Species: id = ENZ_225568_membrane, name = phosphoinositide phospholipase C(Enzyme) wildtype % Warning species is not changed by either rules or reactions xdot(10) = ; % Species: id = SPC_40_lysosome, name = H2O, affected by kineticLaw xdot(11) = (1/(compartment_compart_lysosome))*((-1.0 * reaction_REAC_2) + (-1.0 * reaction_REAC_33) + (-1.0 * reaction_REAC_34) + (-1.0 * reaction_REAC_35) + (-1.0 * reaction_REAC_36) + (-1.0 * reaction_REAC_37) + (-1.0 * reaction_REAC_38) + (-1.0 * reaction_REAC_39) + (-1.0 * reaction_REAC_40) + (-1.0 * reaction_REAC_41)); % Species: id = SPC_28371_lysosome, name = 4-Methylumbelliferyl-alpha-D-galactoside, affected by kineticLaw xdot(12) = (1/(compartment_compart_lysosome))*((-1.0 * reaction_REAC_2)); % Species: id = SPC_90_lysosome, name = alpha-D-Galactose, affected by kineticLaw xdot(13) = (1/(compartment_compart_lysosome))*(( 1.0 * reaction_REAC_2)); % Species: id = SPC_6439_lysosome, name = 4-Methylumbelliferone, affected by kineticLaw xdot(14) = (1/(compartment_compart_lysosome))*(( 1.0 * reaction_REAC_2)); % Species: id = ENZ_286858_lysosome, name = alpha-galactosidase(Enzyme) wildtype % Warning species is not changed by either rules or reactions xdot(15) = ; % Species: id = SPC_1315_mitochondrion, name = Thymidine, affected by kineticLaw xdot(16) = (1/(compartment_compart_mitochondrion))*((-1.0 * reaction_REAC_3) + (-1.0 * reaction_REAC_4) + (-1.0 * reaction_REAC_5) + (-1.0 * reaction_REAC_6) + (-1.0 * reaction_REAC_7) + (-1.0 * reaction_REAC_9) + (-1.0 * reaction_REAC_12) + (-1.0 * reaction_REAC_13) + (-1.0 * reaction_REAC_21) + (-1.0 * reaction_REAC_25) + (-1.0 * reaction_REAC_26)); % Species: id = SPC_34_mitochondrion, name = ATP, affected by kineticLaw xdot(17) = (1/(compartment_compart_mitochondrion))*((-1.0 * reaction_REAC_3) + (-1.0 * reaction_REAC_4) + (-1.0 * reaction_REAC_5) + (-1.0 * reaction_REAC_6) + (-1.0 * reaction_REAC_7) + (-1.0 * reaction_REAC_8) + (-1.0 * reaction_REAC_10) + (-1.0 * reaction_REAC_12) + (-1.0 * reaction_REAC_13) + (-1.0 * reaction_REAC_14) + (-1.0 * reaction_REAC_15) + (-1.0 * reaction_REAC_16) + (-1.0 * reaction_REAC_17) + (-1.0 * reaction_REAC_18) + (-1.0 * reaction_REAC_19) + (-1.0 * reaction_REAC_20) + (-1.0 * reaction_REAC_21) + (-1.0 * reaction_REAC_22) + (-1.0 * reaction_REAC_23) + (-1.0 * reaction_REAC_24) + (-1.0 * reaction_REAC_25) + (-1.0 * reaction_REAC_26)); % Species: id = SPC_65_mitochondrion, name = dTMP, affected by kineticLaw xdot(18) = (1/(compartment_compart_mitochondrion))*(( 1.0 * reaction_REAC_3) + ( 1.0 * reaction_REAC_4) + ( 1.0 * reaction_REAC_5) + ( 1.0 * reaction_REAC_6) + ( 1.0 * reaction_REAC_7) + ( 1.0 * reaction_REAC_9) + ( 1.0 * reaction_REAC_12) + ( 1.0 * reaction_REAC_13) + ( 1.0 * reaction_REAC_21) + ( 1.0 * reaction_REAC_25) + ( 1.0 * reaction_REAC_26)); % Species: id = SPC_35_mitochondrion, name = ADP, affected by kineticLaw xdot(19) = (1/(compartment_compart_mitochondrion))*(( 1.0 * reaction_REAC_3) + ( 1.0 * reaction_REAC_4) + ( 1.0 * reaction_REAC_5) + ( 1.0 * reaction_REAC_6) + ( 1.0 * reaction_REAC_7) + ( 1.0 * reaction_REAC_8) + ( 1.0 * reaction_REAC_10) + ( 1.0 * reaction_REAC_12) + ( 1.0 * reaction_REAC_13) + ( 1.0 * reaction_REAC_14) + ( 1.0 * reaction_REAC_15) + ( 1.0 * reaction_REAC_16) + ( 1.0 * reaction_REAC_17) + ( 1.0 * reaction_REAC_18) + ( 1.0 * reaction_REAC_19) + ( 1.0 * reaction_REAC_20) + ( 1.0 * reaction_REAC_21) + ( 1.0 * reaction_REAC_22) + ( 1.0 * reaction_REAC_23) + ( 1.0 * reaction_REAC_24) + ( 1.0 * reaction_REAC_25) + ( 1.0 * reaction_REAC_26)); % Species: id = SPC_27857_mitochondrion, name = 2',3'-Didehydro-2',3'-dideoxythymidine % Warning species is not changed by either rules or reactions xdot(20) = ; % Species: id = ENZ_236178_mitochondrion, name = thymidine kinase(Enzyme) wildtype % Warning species is not changed by either rules or reactions xdot(21) = ; % Species: id = SPC_13796_mitochondrion, name = 5-Fluorodeoxyuridine, affected by kineticLaw xdot(22) = (1/(compartment_compart_mitochondrion))*((-1.0 * reaction_REAC_24)); % Species: id = ENZ_236184_mitochondrion, name = thymidine kinase(Enzyme) wildtype % Warning species is not changed by either rules or reactions xdot(23) = ; % Species: id = SPC_27854_mitochondrion, name = 3'-Azido-2',3'-dideoxythymidine, affected by kineticLaw xdot(24) = (1/(compartment_compart_mitochondrion))*((-1.0 * reaction_REAC_10)); % Species: id = ENZ_236166_mitochondrion, name = thymidine kinase(Enzyme) wildtype % Warning species is not changed by either rules or reactions xdot(25) = ; % Species: id = SPC_27856_mitochondrion, name = 3'-Fluoro-2',3'-dideoxythymidine % Warning species is not changed by either rules or reactions xdot(26) = ; % Species: id = ENZ_236172_mitochondrion, name = thymidine kinase(Enzyme) wildtype % Warning species is not changed by either rules or reactions xdot(27) = ; % Species: id = ENZ_236145_mitochondrion, name = thymidine kinase(Enzyme) wildtype % Warning species is not changed by either rules or reactions xdot(28) = ; % Species: id = SPC_2178_mitochondrion, name = 2'-Deoxycytidine, affected by kineticLaw xdot(29) = (1/(compartment_compart_mitochondrion))*((-1.0 * reaction_REAC_8) + (-1.0 * reaction_REAC_11) + (-1.0 * reaction_REAC_14) + (-1.0 * reaction_REAC_15) + (-1.0 * reaction_REAC_16) + (-1.0 * reaction_REAC_22)); % Species: id = SPC_63_mitochondrion, name = dCMP, affected by kineticLaw xdot(30) = (1/(compartment_compart_mitochondrion))*(( 1.0 * reaction_REAC_8) + ( 1.0 * reaction_REAC_11) + ( 1.0 * reaction_REAC_14) + ( 1.0 * reaction_REAC_15) + ( 1.0 * reaction_REAC_16) + ( 1.0 * reaction_REAC_22)); % Species: id = ENZ_236155_mitochondrion, name = thymidine kinase(Enzyme) wildtype % Warning species is not changed by either rules or reactions xdot(31) = ; % Species: id = SPC_1286_mitochondrion, name = CTP, affected by kineticLaw xdot(32) = (1/(compartment_compart_mitochondrion))*((-1.0 * reaction_REAC_9) + (-1.0 * reaction_REAC_11)); % Species: id = SPC_1302_mitochondrion, name = CDP, affected by kineticLaw xdot(33) = (1/(compartment_compart_mitochondrion))*(( 1.0 * reaction_REAC_9) + ( 1.0 * reaction_REAC_11)); % Species: id = ENZ_236150_mitochondrion, name = thymidine kinase(Enzyme) wildtype % Warning species is not changed by either rules or reactions xdot(34) = ; % Species: id = SPC_27853_mitochondrion, name = 3'-Azido-2',3'-dideoxythymidine 5'-phosphate, affected by kineticLaw xdot(35) = (1/(compartment_compart_mitochondrion))*(( 1.0 * reaction_REAC_10)); % Species: id = ENZ_236140_mitochondrion, name = thymidine kinase(Enzyme) wildtype % Warning species is not changed by either rules or reactions xdot(36) = ; % Species: id = ENZ_236160_mitochondrion, name = thymidine kinase(Enzyme) wildtype % Warning species is not changed by either rules or reactions xdot(37) = ; % Species: id = SPC_2074_mitochondrion, name = 2'-Deoxyuridine, affected by kineticLaw xdot(38) = (1/(compartment_compart_mitochondrion))*((-1.0 * reaction_REAC_17) + (-1.0 * reaction_REAC_18) + (-1.0 * reaction_REAC_19) + (-1.0 * reaction_REAC_20) + (-1.0 * reaction_REAC_23)); % Species: id = ENZ_236190_mitochondrion, name = thymidine kinase(Enzyme) wildtype % Warning species is not changed by either rules or reactions xdot(39) = ; % Species: id = ENZ_236196_mitochondrion, name = thymidine kinase(Enzyme) wildtype % Warning species is not changed by either rules or reactions xdot(40) = ; % Species: id = ENZ_236238_mitochondrion, name = thymidine kinase(Enzyme) wildtype % Warning species is not changed by either rules or reactions xdot(41) = ; % Species: id = ENZ_236232_mitochondrion, name = thymidine kinase(Enzyme) wildtype % Warning species is not changed by either rules or reactions xdot(42) = ; % Species: id = ENZ_236226_mitochondrion, name = thymidine kinase(Enzyme) wildtype % Warning species is not changed by either rules or reactions xdot(43) = ; % Species: id = SPC_1334_mitochondrion, name = dUMP, affected by kineticLaw xdot(44) = (1/(compartment_compart_mitochondrion))*(( 1.0 * reaction_REAC_17) + ( 1.0 * reaction_REAC_18) + ( 1.0 * reaction_REAC_19) + ( 1.0 * reaction_REAC_20) + ( 1.0 * reaction_REAC_23)); % Species: id = ENZ_236220_mitochondrion, name = thymidine kinase(Enzyme) wildtype % Warning species is not changed by either rules or reactions xdot(45) = ; % Species: id = ENZ_236214_mitochondrion, name = thymidine kinase(Enzyme) wildtype % Warning species is not changed by either rules or reactions xdot(46) = ; % Species: id = ENZ_236202_mitochondrion, name = thymidine kinase(Enzyme) wildtype % Warning species is not changed by either rules or reactions xdot(47) = ; % Species: id = ENZ_236208_mitochondrion, name = thymidine kinase(Enzyme) wildtype % Warning species is not changed by either rules or reactions xdot(48) = ; % Species: id = ENZ_236120_mitochondrion, name = thymidine kinase(Enzyme) wildtype % Warning species is not changed by either rules or reactions xdot(49) = ; % Species: id = ENZ_236125_mitochondrion, name = thymidine kinase(Enzyme) wildtype % Warning species is not changed by either rules or reactions xdot(50) = ; % Species: id = ENZ_236130_mitochondrion, name = thymidine kinase(Enzyme) wildtype % Warning species is not changed by either rules or reactions xdot(51) = ; % Species: id = SPC_27852_mitochondrion, name = 5-Fluorodeoxyuridine 5'-phosphate, affected by kineticLaw xdot(52) = (1/(compartment_compart_mitochondrion))*(( 1.0 * reaction_REAC_24)); % Species: id = ENZ_236135_mitochondrion, name = thymidine kinase(Enzyme) wildtype % Warning species is not changed by either rules or reactions xdot(53) = ; % Species: id = SPC_1678_mitochondrion, name = dCTP % Warning species is not changed by either rules or reactions xdot(54) = ; % Species: id = ENZ_236250_mitochondrion, name = thymidine kinase(Enzyme) wildtype % Warning species is not changed by either rules or reactions xdot(55) = ; % Species: id = SPC_1679_mitochondrion, name = dTTP % Warning species is not changed by either rules or reactions xdot(56) = ; % Species: id = ENZ_236244_mitochondrion, name = thymidine kinase(Enzyme) wildtype % Warning species is not changed by either rules or reactions xdot(57) = ; % Species: id = SPC_5404_Cell, name = S-Adenosylmethioninamine, affected by kineticLaw xdot(58) = (1/(compartment_compart_Cell))*((-1.0 * reaction_REAC_27) + (-1.0 * reaction_REAC_28)); % Species: id = SPC_1941_Cell, name = Putrescine, affected by kineticLaw xdot(59) = (1/(compartment_compart_Cell))*((-1.0 * reaction_REAC_27) + (-1.0 * reaction_REAC_28)); % Species: id = SPC_3088_Cell, name = Spermidine, affected by kineticLaw xdot(60) = (1/(compartment_compart_Cell))*(( 1.0 * reaction_REAC_27) + ( 1.0 * reaction_REAC_28)); % Species: id = SPC_1960_Cell, name = 5'-Deoxy-5'-(methylthio)adenosine, affected by kineticLaw xdot(61) = (1/(compartment_compart_Cell))*(( 1.0 * reaction_REAC_27) + ( 1.0 * reaction_REAC_28)); % Species: id = ENZ_224044_Cell, name = spermidine synthase(Enzyme) wildtype % Warning species is not changed by either rules or reactions xdot(62) = ; % Species: id = ENZ_224039_Cell, name = spermidine synthase(Enzyme) wildtype % Warning species is not changed by either rules or reactions xdot(63) = ; % Species: id = SPC_40_Cell, name = H2O, affected by kineticLaw xdot(64) = (1/(compartment_compart_Cell))*((-1.0 * reaction_REAC_29) + (-1.0 * reaction_REAC_30) + (-1.0 * reaction_REAC_31) + (-1.0 * reaction_REAC_32)); % Species: id = SPC_23010_Cell, name = 4-Methylumbelliferyl-beta-N-acetylglucosaminide, affected by kineticLaw xdot(65) = (1/(compartment_compart_Cell))*((-1.0 * reaction_REAC_29) + (-1.0 * reaction_REAC_30) + (-1.0 * reaction_REAC_31) + (-1.0 * reaction_REAC_32)); % Species: id = SPC_6916_Cell, name = N-Acetyl-beta-D-glucosamine, affected by kineticLaw xdot(66) = (1/(compartment_compart_Cell))*(( 1.0 * reaction_REAC_29) + ( 1.0 * reaction_REAC_30) + ( 1.0 * reaction_REAC_31) + ( 1.0 * reaction_REAC_32)); % Species: id = SPC_6439_Cell, name = 4-Methylumbelliferone, affected by kineticLaw xdot(67) = (1/(compartment_compart_Cell))*(( 1.0 * reaction_REAC_29) + ( 1.0 * reaction_REAC_30) + ( 1.0 * reaction_REAC_31) + ( 1.0 * reaction_REAC_32)); % Species: id = SPC_5060_Cell, name = Heparin % Warning species is not changed by either rules or reactions xdot(68) = ; % Species: id = ENZ_273848_Cell, name = beta-N-acetylhexosaminidase(Enzyme) wildtype isoform A % Warning species is not changed by either rules or reactions xdot(69) = ; % Species: id = ENZ_273854_Cell, name = beta-N-acetylhexosaminidase(Enzyme) wildtype isoform B % Warning species is not changed by either rules or reactions xdot(70) = ; % Species: id = ENZ_273837_Cell, name = beta-N-acetylhexosaminidase(Enzyme) wildtype isoform A % Warning species is not changed by either rules or reactions xdot(71) = ; % Species: id = ENZ_273842_Cell, name = beta-N-acetylhexosaminidase(Enzyme) wildtype isoform B % Warning species is not changed by either rules or reactions xdot(72) = ; % Species: id = SPC_21081_lysosome, name = N-Dodecanoylsphingosine, affected by kineticLaw xdot(73) = (1/(compartment_compart_lysosome))*((-1.0 * reaction_REAC_33) + (-1.0 * reaction_REAC_37)); % Species: id = SPC_5042_lysosome, name = Sphingosine, affected by kineticLaw xdot(74) = (1/(compartment_compart_lysosome))*(( 1.0 * reaction_REAC_33) + ( 1.0 * reaction_REAC_34) + ( 1.0 * reaction_REAC_35) + ( 1.0 * reaction_REAC_37) + ( 1.0 * reaction_REAC_38) + ( 1.0 * reaction_REAC_39) + ( 1.0 * reaction_REAC_40)); % Species: id = SPC_2488_lysosome, name = Dodecanoate, affected by kineticLaw xdot(75) = (1/(compartment_compart_lysosome))*(( 1.0 * reaction_REAC_33) + ( 1.0 * reaction_REAC_37)); % Species: id = ENZ_112389_lysosome, name = ceramidase(Enzyme) wildtype % Warning species is not changed by either rules or reactions xdot(76) = ; % Species: id = SPC_25141_lysosome, name = N-Oleoyl-D-sphingosine, affected by kineticLaw xdot(77) = (1/(compartment_compart_lysosome))*((-1.0 * reaction_REAC_34)); % Species: id = SPC_2139_lysosome, name = Oleate, affected by kineticLaw xdot(78) = (1/(compartment_compart_lysosome))*(( 1.0 * reaction_REAC_34)); % Species: id = ENZ_112419_lysosome, name = ceramidase(Enzyme) wildtype % Warning species is not changed by either rules or reactions xdot(79) = ; % Species: id = SPC_25149_lysosome, name = N-Hexanoyl-D-erythro-sphingosine, affected by kineticLaw xdot(80) = (1/(compartment_compart_lysosome))*((-1.0 * reaction_REAC_35)); % Species: id = SPC_2297_lysosome, name = Hexanoate, affected by kineticLaw xdot(81) = (1/(compartment_compart_lysosome))*(( 1.0 * reaction_REAC_35)); % Species: id = ENZ_112404_lysosome, name = ceramidase(Enzyme) wildtype % Warning species is not changed by either rules or reactions xdot(82) = ; % Species: id = SPC_25159_lysosome, name = N-Palmitoylsphinganine, affected by kineticLaw xdot(83) = (1/(compartment_compart_lysosome))*((-1.0 * reaction_REAC_36)); % Species: id = SPC_1990_lysosome, name = Palmitate, affected by kineticLaw xdot(84) = (1/(compartment_compart_lysosome))*(( 1.0 * reaction_REAC_36)); % Species: id = SPC_5264_lysosome, name = Sphinganine, affected by kineticLaw xdot(85) = (1/(compartment_compart_lysosome))*(( 1.0 * reaction_REAC_36) + ( 1.0 * reaction_REAC_41)); % Species: id = ENZ_112429_lysosome, name = ceramidase(Enzyme) wildtype % Warning species is not changed by either rules or reactions xdot(86) = ; % Species: id = ENZ_112394_lysosome, name = ceramidase(Enzyme) wildtype % Warning species is not changed by either rules or reactions xdot(87) = ; % Species: id = SPC_25148_lysosome, name = N-Acetyl-D-sphingosine, affected by kineticLaw xdot(88) = (1/(compartment_compart_lysosome))*((-1.0 * reaction_REAC_38)); % Species: id = SPC_1278_lysosome, name = Acetate, affected by kineticLaw xdot(89) = (1/(compartment_compart_lysosome))*(( 1.0 * reaction_REAC_38)); % Species: id = ENZ_112399_lysosome, name = ceramidase(Enzyme) wildtype % Warning species is not changed by either rules or reactions xdot(90) = ; % Species: id = SPC_25150_lysosome, name = N-Octanoyl-D-sphingosine, affected by kineticLaw xdot(91) = (1/(compartment_compart_lysosome))*((-1.0 * reaction_REAC_39)); % Species: id = SPC_2889_lysosome, name = Octanoate, affected by kineticLaw xdot(92) = (1/(compartment_compart_lysosome))*(( 1.0 * reaction_REAC_39) + ( 1.0 * reaction_REAC_41)); % Species: id = ENZ_112409_lysosome, name = ceramidase(Enzyme) wildtype % Warning species is not changed by either rules or reactions xdot(93) = ; % Species: id = SPC_25151_lysosome, name = N-Stearoyl-D-sphingosine, affected by kineticLaw xdot(94) = (1/(compartment_compart_lysosome))*((-1.0 * reaction_REAC_40)); % Species: id = SPC_20032_lysosome, name = Stearate, affected by kineticLaw xdot(95) = (1/(compartment_compart_lysosome))*(( 1.0 * reaction_REAC_40)); % Species: id = ENZ_112414_lysosome, name = ceramidase(Enzyme) wildtype % Warning species is not changed by either rules or reactions xdot(96) = ; % Species: id = SPC_25130_lysosome, name = N-Octanoylsphinganine, affected by kineticLaw xdot(97) = (1/(compartment_compart_lysosome))*((-1.0 * reaction_REAC_41)); % Species: id = ENZ_112424_lysosome, name = ceramidase(Enzyme) wildtype % Warning species is not changed by either rules or reactions xdot(98) = ; end function z=KL_50493(Vmax,S,Km), z=(Vmax*S/(S+Km));end function z=KL_41750(Km,A,Vmax,S), z=(Vmax*S/(Km+S));end function z=KL_41752(S,A,Km,Vmax), z=(Vmax*S/(Km+S));end function z=KL_41751(S,Vmax,Km,A), z=(Vmax*S/(Km+S));end function z=KL_41753(S,Vmax,Km,A), z=(Vmax*S/(Km+S));end function z=KL_41746(Vmax_Km,S,Vmax,Km,A), z=(Vmax*S/(Km+S));end function z=KL_41747(A,Vmax_Km,Vmax,Km,S), z=(Vmax*S/(Km+S));end function z=KL_41748(Km,S,Vmax_Km,A,Vmax), z=(Vmax*S/(Km+S));end function z=KL_39577(S,Km,Vmax), z=(Vmax*S/(Km+S));end function z=KL_39576(Vmax,S,Km), z=(Vmax*S/(Km+S));end function z=KL_48158(Km,Vmax,A), z=(Vmax*A/(Km+A));end function z=KL_48159(Km,Vmax,A), z=(Vmax*A/(Km+A));end function z=KL_21313(Km,S,Vmax), z=(Vmax*S/(Km+S));end % adding few functions representing operators used in SBML but not present directly % in either matlab or octave. function z=pow(x,y),z=x^y;end function z=root(x,y),z=y^(1/x);end function z = piecewise(varargin) numArgs = nargin; result = 0; foundResult = 0; for k=1:2: numArgs-1 if varargin{k+1} == 1 result = varargin{k}; foundResult = 1; break; end end if foundResult == 0 result = varargin{numArgs}; end z = result; end