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simulation_protocol_fitting_CollectedTimeCourse.m
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simulation_protocol_fitting_CollectedTimeCourse.m
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function [time,observables] = simulation_protocol_fitting_CollectedTimeCourse(params)
%A = [0.616000000000000;3;0.726154480000000;0.108367000000000;0.659000000000000;0.00700000000000000;18.5478285800000;0.00191000000000000;1;0.299000000000000;1.00064013300000;2.36164831900000;0.00211000000000000;0.00423000000000000;77.3800000000000;0.00261149000000000;0.00963821300000000;0.00344545400000000;0.00143820600000000;0.0205015600000000;0.0759752810000000;0.00122000000000000;0.170000000000000;6.29000000000000e-06;0.102500000000000;0.0630000000000000;0.360000000000000;0.420000000000000;0.400000000000000;0.294100000000000;2.95000000000000;0.0650000000000000;0.500000000000000;0.00450000000000000;1.60000000000000;3.03000000000000;4.65000000000000e-05;2.68000000000000;0.00450000000000000;1.97000000000000e-05;0.225000000000000;4.72000000000000e-05;4.44750337500000;0.0720000000000000;0.0720000000000000;8.44445922300000;0.0240000000000000;0.450000000000000;4.50000000000000;0.700000000000000;4.77000000000000e-06;0.0146347570000000;1.00000000000000e-06;0.0164989410000000;0.379987684000000;0.272335568000000];
A = [0.542125648135445;3.76168895009916;0.454448540472248;0.706990028881560;0.0156565460978362;0.478582126811771;4.39031164654454;0.168038706461350;4.21968660787895;0.0560506065370617;0.397377606983681;0.583587181302951;0.716708019845057;0.000154147902632731;0.136501997249423;0.132939511019276;0.00456400046649098;0.000733943694403398;0.00134582377890930;0.00483413989498314;0.0379963772949342;0.00192408120909374;4.23518730127469;2.45107434802339e-06;0.000771217660846397;2.09292143332501;0.288669565535384;0.00779378981985000;0.224895886981259;12.6827767477872;6.03285037234089e-05;6.77882129684873e-05;0.000309121127035145;1.74318833008063e-06;1.45680249381982e-05;2.94658145921870;3.12055381157148e-05;0.797796208874077;2.65472943228149e-07;2.85338922615892e-05;0.0240841285605586;1.05706088817784e-05;3.31601148362778;0.0170013921210288;0.00150069872532053;2.47590966892564;0.0300000000000000;2.15537701634457e-07;4.94999978446232;3.43977996188819;1.51575084594245e-06;0.0400301566013678;1.72526016292169;0.0300000000000000;1.03960000000000;0.0480000000000000];
%A = params(73:126);
options = odeset('RelTol',1e-12,...
'AbsTol',1e-19,...
'NormControl','on',...
'Stats','off',...
'BDF','off',...
'NonNegative',1:56,...
'MaxOrder', 5);
%% Spegel 2013
tspan = [0:120];
% Afirst = A;
initvalue = A;
params(71,1) = 2.8;
[~, BASE_Spegel2013] = ode15s(@INS1Epathway,tspan,initvalue,options,params);
tspan = [0:15];
initvalue = (BASE_Spegel2013(end,:))';
params(71,1) = 16.7;
[time, END_Spegel2013] = ode15s(@INS1Epathway,tspan,initvalue,options,params);
Spegel_3_2pg = END_Spegel2013(3,12) / BASE_Spegel2013(end, 12);
Spegel_6_2pg = END_Spegel2013(6,12) / BASE_Spegel2013(end, 12);
Spegel_10_2pg = END_Spegel2013(10,12) / BASE_Spegel2013(end, 12);
Spegel_15_2pg = END_Spegel2013(end,12) / BASE_Spegel2013(end, 12);
Spegel_3_3pg = END_Spegel2013(3,11) / BASE_Spegel2013(end, 11);
Spegel_6_3pg = END_Spegel2013(6,11) / BASE_Spegel2013(end, 11);
Spegel_10_3pg = END_Spegel2013(10,11) / BASE_Spegel2013(end, 11);
Spegel_15_3pg = END_Spegel2013(end,11) / BASE_Spegel2013(end, 11);
Spegel_3_akg = (END_Spegel2013(3,41)+END_Spegel2013(3,29)) / (BASE_Spegel2013(end, 41)+BASE_Spegel2013(end, 29));
Spegel_6_akg = (END_Spegel2013(6,41)+END_Spegel2013(6,29)) / (BASE_Spegel2013(end, 41)+BASE_Spegel2013(end, 29));
Spegel_10_akg = (END_Spegel2013(10,41)+END_Spegel2013(10,29)) / (BASE_Spegel2013(end, 41)+BASE_Spegel2013(end, 29));
Spegel_15_akg = (END_Spegel2013(end,41)+END_Spegel2013(end,29)) / (BASE_Spegel2013(end, 41)+BASE_Spegel2013(end, 29));
Spegel_3_ala = END_Spegel2013(3,50) / BASE_Spegel2013(end, 50);
Spegel_6_ala = END_Spegel2013(6,50) / BASE_Spegel2013(end, 50);
Spegel_10_ala = END_Spegel2013(10,50) / BASE_Spegel2013(end, 50);
Spegel_15_ala = END_Spegel2013(end,50) / BASE_Spegel2013(end, 50);
Spegel_3_asp = (END_Spegel2013(3,35)+END_Spegel2013(3,37)) / (BASE_Spegel2013(end, 35)+BASE_Spegel2013(end, 37));
Spegel_6_asp = (END_Spegel2013(6,35)+END_Spegel2013(6,37)) / (BASE_Spegel2013(end, 35)+BASE_Spegel2013(end, 37));
Spegel_10_asp = (END_Spegel2013(10,35)+END_Spegel2013(10,37)) / (BASE_Spegel2013(end, 35)+BASE_Spegel2013(end, 37));
Spegel_15_asp = (END_Spegel2013(end,35)+END_Spegel2013(end,37)) / (BASE_Spegel2013(end, 35)+BASE_Spegel2013(end,37));
Spegel_3_cit = (END_Spegel2013(3,27)+END_Spegel2013(3,42)) / (BASE_Spegel2013(end, 27)+BASE_Spegel2013(end, 42));
Spegel_6_cit = (END_Spegel2013(6,27)+END_Spegel2013(6,42)) / (BASE_Spegel2013(end, 27)+BASE_Spegel2013(end, 42));
Spegel_10_cit = (END_Spegel2013(10,27)+END_Spegel2013(10,42)) / (BASE_Spegel2013(end, 27)+BASE_Spegel2013(end, 42));
Spegel_15_cit = (END_Spegel2013(end,27)+END_Spegel2013(end,42)) / (BASE_Spegel2013(end, 27)+BASE_Spegel2013(end,42));
Spegel_3_fum = END_Spegel2013(3,32) / BASE_Spegel2013(end, 32);
Spegel_6_fum = END_Spegel2013(6,32) / BASE_Spegel2013(end, 32);
Spegel_10_fum = END_Spegel2013(10,32) / BASE_Spegel2013(end, 32);
Spegel_15_fum = END_Spegel2013(end,32) / BASE_Spegel2013(end, 32);
Spegel_3_g3p = END_Spegel2013(3,8) / BASE_Spegel2013(end, 8);
Spegel_6_g3p = END_Spegel2013(6,8) / BASE_Spegel2013(end, 8);
Spegel_10_g3p = END_Spegel2013(10,8) / BASE_Spegel2013(end, 8);
Spegel_15_g3p = END_Spegel2013(end,8) / BASE_Spegel2013(end, 8);
Spegel_3_lac = END_Spegel2013(3,15) / BASE_Spegel2013(end, 15);
Spegel_6_lac = END_Spegel2013(6,15) / BASE_Spegel2013(end, 15);
Spegel_10_lac = END_Spegel2013(10,15) / BASE_Spegel2013(end, 15);
Spegel_15_lac = END_Spegel2013(end,15) / BASE_Spegel2013(end, 15);
Spegel_3_mal = (END_Spegel2013(3,33)+END_Spegel2013(3,40)) / (BASE_Spegel2013(end, 33)+BASE_Spegel2013(end, 40));
Spegel_6_mal = (END_Spegel2013(6,33)+END_Spegel2013(6,40)) / (BASE_Spegel2013(end, 33)+BASE_Spegel2013(end, 40));
Spegel_10_mal = (END_Spegel2013(10,33)+END_Spegel2013(10,40)) / (BASE_Spegel2013(end, 33)+BASE_Spegel2013(end, 40));
Spegel_15_mal = (END_Spegel2013(end,33)+END_Spegel2013(end,40)) / (BASE_Spegel2013(end, 33)+BASE_Spegel2013(end,40));
Spegel_3_pep = END_Spegel2013(3,13) / BASE_Spegel2013(end, 13);
Spegel_6_pep = END_Spegel2013(6,13) / BASE_Spegel2013(end, 13);
Spegel_10_pep = END_Spegel2013(10,13) / BASE_Spegel2013(end, 13);
Spegel_15_pep = END_Spegel2013(end,13) / BASE_Spegel2013(end, 13);
Spegel_3_pyr = (END_Spegel2013(3,14)+END_Spegel2013(3,25)) / (BASE_Spegel2013(end, 14)+BASE_Spegel2013(end, 25));
Spegel_6_pyr = (END_Spegel2013(6,14)+END_Spegel2013(6,25)) / (BASE_Spegel2013(end, 14)+BASE_Spegel2013(end, 25));
Spegel_10_pyr = (END_Spegel2013(10,14)+END_Spegel2013(10,25)) / (BASE_Spegel2013(end, 14)+BASE_Spegel2013(end, 25));
Spegel_15_pyr = (END_Spegel2013(end,14)+END_Spegel2013(end,25)) / (BASE_Spegel2013(end, 14)+BASE_Spegel2013(end,25));
Spegel_3_r5p = END_Spegel2013(3,20) / BASE_Spegel2013(end, 20);
Spegel_6_r5p = END_Spegel2013(6,20) / BASE_Spegel2013(end, 20);
Spegel_10_r5p = END_Spegel2013(10,20) / BASE_Spegel2013(end, 20);
Spegel_15_r5p = END_Spegel2013(end,20) / BASE_Spegel2013(end, 20);
Spegel_3_suc = END_Spegel2013(3,31) / BASE_Spegel2013(end, 31);
Spegel_6_suc = END_Spegel2013(6,31) / BASE_Spegel2013(end, 31);
Spegel_10_suc = END_Spegel2013(10,31) / BASE_Spegel2013(end, 31);
Spegel_15_suc = END_Spegel2013(end,31) / BASE_Spegel2013(end, 31);
%% Graham 30 minute
tspan = [0:30];
% Afirst = A;
initvalue = A;
params(71,1) = 1e-6;
[~, BASE] = ode15s(@INS1Epathway,tspan,initvalue,options,params);
%% Low Glucose no Ex, extGluc = 2.8
tspan = [0:30];
%initvalue = (BASE(end,:))';
%Change this for L,M, H
params(71,1) = 2.8;
initvalue = (BASE(end,:))';
[time, END_GrahamL] = ode15s(@INS1Epathway,tspan,initvalue,options,params);
tspan = [0:30];
%initvalue = (BASE(end,:))';
%Change this for L,M, H
params(71,1) = 16.7;
initvalue = (BASE(end,:))';
[time, END_GrahamH] = ode15s(@INS1Epathway,tspan,initvalue,options,params);
Graham_3PG = END_GrahamH(end,11) / END_GrahamL(end,11);
Graham_AKG = (END_GrahamH(end, 41) + END_GrahamH(end, 29)) / (END_GrahamL(end, 41) + END_GrahamL(end, 29));
Graham_ALA = END_GrahamH(end, 50) / END_GrahamL(end, 50);
Graham_ASP = (END_GrahamH(end,35) + END_GrahamH(end,37)) / (END_GrahamL(end,35) + END_GrahamL(end,37));
Graham_FUM = END_GrahamH(20,32) / END_GrahamL(20,32);
Graham_G6P = END_GrahamH(end,3) / END_GrahamL(end,3);
Graham_GLC = END_GrahamH(end,1) / END_GrahamL(end,1);
Graham_glut= (END_GrahamH(end, 36) + END_GrahamH(end, 38)) / (END_GrahamL(end, 36) + END_GrahamL(end, 38));
Graham_G3P = END_GrahamH(end, 8) / END_GrahamL(end, 8);
Graham_LAC = END_GrahamH(end,15) / END_GrahamL(end,15);
Graham_MAL = (END_GrahamH(end,33) + END_GrahamH(end,40)) / (END_GrahamL(end,33) + END_GrahamL(end,40));
Graham_SUC = END_GrahamH(end,31) / END_GrahamL(end,31);
%% Malmgren-60mins
tspan = [0:120];
initvalue = A;
params(71,1) = 2.8;
[~, BASE] = ode15s(@INS1Epathway,tspan,initvalue,options,params);
tspan = [0:60];
params(71,1) = 2.8;
initvalue = (BASE(end,:))';
[time, END_MalmgrenL] = ode15s(@INS1Epathway,tspan,initvalue,options,params);
params(71,1) = 16.7;
initvalue = (BASE(end,:))';
[time, END_MalmgrenH] = ode15s(@INS1Epathway,tspan,initvalue,options,params);
Malmgren_AKG = END_MalmgrenH(end, 41) + END_MalmgrenH(end, 29) / END_MalmgrenL(end, 41) + END_MalmgrenL(end, 29);
Malmgren_ALA = END_MalmgrenH(end, 50) / END_MalmgrenL(end, 50);
Malmgren_ASP = END_MalmgrenH(end,35) + END_GrahamH(end,37) / END_MalmgrenL(end,35) + END_MalmgrenL(end,37);
Malmgren_CIT = (END_MalmgrenH(end,27)+END_MalmgrenH(end,42)) / (END_MalmgrenL(end, 27)+END_MalmgrenL(end, 42));
Malmgren_FUM = END_MalmgrenH(end,32) / END_MalmgrenL(end,32);
Malmgren_G6P = END_MalmgrenH(end,3) / END_MalmgrenL(end,3);
Malmgren_GLC = END_MalmgrenH(end,1) / END_MalmgrenL(end,1);
Malmgren_glut= (END_MalmgrenH(end, 36) + END_MalmgrenH(end, 38)) / (END_MalmgrenL(end, 36) + END_MalmgrenL(end, 38));
Malmgren_G3P = END_MalmgrenH(end, 8) / END_MalmgrenL(end, 8);
Malmgren_ICIT= (END_MalmgrenH(end,28)+END_MalmgrenH(end,51)) / (END_MalmgrenL(end, 28)+END_MalmgrenL(end, 51));
Malmgren_LAC = END_MalmgrenH(end,15) / END_MalmgrenL(end,15);
Malmgren_MAL = (END_MalmgrenH(end,33) + END_MalmgrenH(end,40)) / (END_MalmgrenL(end,33) + END_MalmgrenL(end,40));
Malmgren_PYR = (END_MalmgrenH(end,14)+END_MalmgrenH(end,25)) / (END_MalmgrenL(end, 14)+END_MalmgrenL(end, 25));
Malmgren_SUC = END_MalmgrenH(end,31) / END_MalmgrenL(end,31);
%% Goehring 45min
Goehring_3PG = END_MalmgrenH(45,11) / END_MalmgrenL(45,11);
Goehring_3PG_60 = END_MalmgrenH(end,11) / END_MalmgrenL(end,11);
Goehring_AKG = END_MalmgrenH(45, 41) + END_MalmgrenH(45, 29) / END_MalmgrenL(45, 41) + END_MalmgrenL(45, 29);
Goehring_CIT = (END_MalmgrenH(45,27)+END_MalmgrenH(45,42)) / (END_MalmgrenL(45, 27)+END_MalmgrenL(45, 42));
Goehring_FUM = END_MalmgrenH(45,32) / END_MalmgrenL(45,32);
Goehring_G6P = END_MalmgrenH(45,3) / END_MalmgrenL(45,3);
Goehring_GLC = END_MalmgrenH(45,1) / END_MalmgrenL(45,1);
Goehring_LAC = END_MalmgrenH(45,15) / END_MalmgrenL(45,15);
Goehring_MAL = (END_MalmgrenH(45,33) + END_MalmgrenH(45,40)) / (END_MalmgrenL(45,33) + END_MalmgrenL(45,40));
Goehring_PEP = END_MalmgrenH(45,13) / END_MalmgrenL(45,13);
Goehring_PEP_60 = END_MalmgrenH(end,13) / END_MalmgrenL(end,13);
Goehring_PYR = (END_MalmgrenH(45,14)+END_MalmgrenH(45,25)) / (END_MalmgrenL(45, 14)+END_MalmgrenL(45, 25));
Goehring_R5P = END_MalmgrenH(45,20) / END_MalmgrenL(45,20);
Goehring_R5P_60 = END_MalmgrenH(end,20) / END_MalmgrenL(end,20);
Goehring_SUC = END_MalmgrenH(45,31) / END_MalmgrenL(45,31);
Goehring_FRU = END_MalmgrenH(45,55) / END_MalmgrenL(45,55);
%% Huang 2012 - 120mins
% initvalue = A;
% tspan = [0:120];
% params(71,1) = 2;
% [time, END_HuangL] = ode15s(@INS1Epathway,tspan,initvalue,options,params);
%
% params(71,1) = 16.7;
% initvalue = (BASE(end,:))';
% [time, END_HuangH] = ode15s(@INS1Epathway,tspan,initvalue,options,params);
%
% Huang_3PG = END_HuangH(end,11) / END_HuangL(end,11);
% Huang_AKG = (END_HuangH(end, 41) + END_HuangH(end, 29)) / (END_HuangL(end, 41) + END_HuangL(end, 29));
% Huang_ALA = END_HuangH(end, 50) / END_HuangL(end, 50);
% Huang_ASP = (END_HuangH(end,35) + END_HuangH(end,37)) / (END_HuangL(end,35) + END_HuangL(end,37));
% Huang_FUM = END_HuangH(end,32) / END_HuangL(end,32);
% Huang_ICIT= (END_HuangH(end,28)+END_HuangH(end,51)) / (END_HuangL(end, 28)+END_HuangL(end, 51));
% Huang_MAL = (END_HuangH(end,33) + END_HuangH(end,40)) / (END_HuangL(end,33) + END_HuangL(end,40));
% Huang_r5p = END_HuangH(end,20) / END_HuangL(end, 20);
% Huang_SOR = END_HuangH(end,20) / END_HuangL(end, 20);
% Huang_SUC = END_HuangH(end,31) / END_HuangL(end,31);
%%
observables = [Spegel_3_2pg
Spegel_3_3pg
Spegel_3_akg
Spegel_3_ala
Spegel_3_asp
Spegel_3_cit
Spegel_3_fum
Spegel_3_g3p
Spegel_3_lac
Spegel_3_mal
Spegel_3_pep
Spegel_3_pyr
Spegel_3_r5p
Spegel_3_suc
Spegel_6_2pg
Spegel_6_3pg
Spegel_6_akg
Spegel_6_ala
Spegel_6_asp
Spegel_6_cit
Spegel_6_fum
Spegel_6_g3p
Spegel_6_lac
Spegel_6_mal
Spegel_6_pep
Spegel_6_pyr
Spegel_6_r5p
Spegel_6_suc
Spegel_10_2pg
Spegel_10_3pg
Spegel_10_akg
Spegel_10_ala
Spegel_10_asp
Spegel_10_cit
Spegel_10_fum
Spegel_10_g3p
Spegel_10_lac
Spegel_10_mal
Spegel_10_pep
Spegel_10_pyr
Spegel_10_r5p
Spegel_10_suc
Spegel_15_2pg
Spegel_15_3pg
Spegel_15_akg
Spegel_15_ala
Spegel_15_asp
Spegel_15_cit
Spegel_15_fum
Spegel_15_g3p
Spegel_15_lac
Spegel_15_mal
Spegel_15_pep
Spegel_15_pyr
Spegel_15_r5p
Spegel_15_suc
Malmgren_AKG
Malmgren_ALA
Malmgren_ASP
Malmgren_CIT
Malmgren_FUM
Malmgren_G6P
Malmgren_GLC
Malmgren_glut
Malmgren_G3P
Malmgren_ICIT
Malmgren_LAC
Malmgren_MAL
Malmgren_PYR
Malmgren_SUC
Goehring_FRU
];
% Goehring_3PG
% Goehring_3PG_60
% Goehring_AKG
% Goehring_CIT
% Goehring_FUM
% Goehring_G6P
% Goehring_GLC
% Goehring_LAC
% Goehring_MAL
% Goehring_PEP
% Goehring_PEP_60
% Goehring_PYR
% Goehring_R5P
% Goehring_R5P_60
% Goehring_SUC];
%
% observables = [Spegel_3_lac
% Spegel_6_lac
% Spegel_10_lac
% Spegel_15_lac
% Graham_LAC
% Malmgren_LAC];
%% With Graham
% Spegel_3_2pg
% Spegel_3_3pg
% Spegel_3_akg
% Spegel_3_ala
% Spegel_3_asp
% Spegel_3_cit
% Spegel_3_fum
% Spegel_3_g3p
% Spegel_3_lac
% Spegel_3_mal
% Spegel_3_pep
% Spegel_3_pyr
% Spegel_3_r5p
% Spegel_3_suc
% Spegel_6_2pg
% Spegel_6_3pg
% Spegel_6_akg
% Spegel_6_ala
% Spegel_6_asp
% Spegel_6_cit
% Spegel_6_fum
% Spegel_6_g3p
% Spegel_6_lac
% Spegel_6_mal
% Spegel_6_pep
% Spegel_6_pyr
% Spegel_6_r5p
% Spegel_6_suc
% Spegel_10_2pg
% Spegel_10_3pg
% Spegel_10_akg
% Spegel_10_ala
% Spegel_10_asp
% Spegel_10_cit
% Spegel_10_fum
% Spegel_10_g3p
% Spegel_10_lac
% Spegel_10_mal
% Spegel_10_pep
% Spegel_10_pyr
% Spegel_10_r5p
% Spegel_10_suc
% Spegel_15_2pg
% Spegel_15_3pg
% Spegel_15_akg
% Spegel_15_ala
% Spegel_15_asp
% Spegel_15_cit
% Spegel_15_fum
% Spegel_15_g3p
% Spegel_15_lac
% Spegel_15_mal
% Spegel_15_pep
% Spegel_15_pyr
% Spegel_15_r5p
% Spegel_15_suc
% Graham_AKG
% Graham_ALA
% Graham_ASP
% Graham_FUM
% Graham_G6P
% Graham_GLC
% Graham_glut
% Graham_LAC
% Graham_MAL
% Graham_SUC
% Malmgren_AKG
% Malmgren_ALA
% Malmgren_ASP
% Malmgren_CIT
% Malmgren_FUM
% Malmgren_G6P
% Malmgren_GLC
% Malmgren_glut
% Malmgren_G3P
% Malmgren_ICIT
% Malmgren_LAC
% Malmgren_MAL
% Malmgren_PYR
% Malmgren_SUC];
end