 %  DOQCS : http://doqcs.ncbs.res.in/ 
 %  Accession Name = EGFR_MAPK 
 %  Accession Number = 58 
 %  Transcriber = Upinder S. Bhalla, NCBS 
 %  Developer = Upinder S. Bhalla, NCBS 
 %  Species = Generic mammalian 
 %  Tissue = Neuronal 
 %  Cell Compartment = Synapse 
 %  Notes =  Model of MAPK activation by EGFR in the synapse. Demonstration programs using this model are available <a href=http://www.ncbs.res.in/~bhalla/stochnet/demos.html> here</a>.<br>Primary citation:<a href= http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15298883 >Bhalla US. Biophys J. (2004) 87(2):745-53</a>. 
 
   % Note: All the concentrations are in micro Mole (uM)

function moose_convert
%Matlab simulation for chemical kinetics

% Saved on Fri Feb 11 12:39:30 2005

% Automatically generated from kkit model in MOOSE by conv_matlab

global buff;
tspan=[0, 2000];
% Molecule names
molnames = {
'1 /kinetics/PKC-active/PKC-act-raf/PKC-act-raf_cplx'
'2 /kinetics/PKC-active/PKC-inact-GAP/PKC-inact-GAP_cplx'
'3 /kinetics/PKC-active/PKC-act-GEF/PKC-act-GEF_cplx'
'4 /kinetics/MAPK*'
'5 /kinetics/MAPK*/MAPK*-feedback/MAPK*-feedback_cplx'
'6 /kinetics/MAPK*/phosph_Sos/phosph_Sos_cplx'
'7 /kinetics/MAPK/craf-1'
'8 /kinetics/MAPK/craf-1*'
'9 /kinetics/MAPK/MAPKK'
'10 /kinetics/MAPK/MAPK'
'11 /kinetics/MAPK/craf-1**'
'12 /kinetics/MAPK/MAPK-tyr'
'13 /kinetics/MAPK/MAPKK*'
'14 /kinetics/MAPK/MAPKK*/MAPKKtyr/MAPKKtyr_cplx'
'15 /kinetics/MAPK/MAPKK*/MAPKKthr/MAPKKthr_cplx'
'16 /kinetics/MAPK/MAPKK-ser'
'17 /kinetics/MAPK/Raf-GTP-Ras*'
'18 /kinetics/MAPK/Raf-GTP-Ras*/Raf-GTP-Ras*.1/Raf-GTP-Ras*.1_cplx'
'19 /kinetics/MAPK/Raf-GTP-Ras*/Raf-GTP-Ras*.2/Raf-GTP-Ras*.2_cplx'
'20 /kinetics/MKP-1'
'21 /kinetics/MKP-1/MKP1-tyr-deph/MKP1-tyr-deph_cplx'
'22 /kinetics/MKP-1/MKP1-thr-deph/MKP1-thr-deph_cplx'
'23 /kinetics/PPhosphatase2A'
'24 /kinetics/PPhosphatase2A/craf-deph/craf-deph_cplx'
'25 /kinetics/PPhosphatase2A/MAPKK-deph/MAPKK-deph_cplx'
'26 /kinetics/PPhosphatase2A/MAPKK-deph-ser/MAPKK-deph-ser_cplx'
'27 /kinetics/PPhosphatase2A/craf**-deph/craf**-deph_cplx'
'28 /kinetics/Ras/GEF-Gprot-bg'
'29 /kinetics/Ras/GEF-Gprot-bg/GEF-bg_act-ras/GEF-bg_act-ras_cplx'
'30 /kinetics/Ras/inact-GEF'
'31 /kinetics/Ras/GEF*'
'32 /kinetics/Ras/GEF*/GEF*-act-ras/GEF*-act-ras_cplx'
'33 /kinetics/Ras/GTP-Ras'
'34 /kinetics/Ras/GDP-Ras'
'35 /kinetics/Ras/GAP*'
'36 /kinetics/Ras/GAP'
'37 /kinetics/Ras/GAP/GAP-inact-ras/GAP-inact-ras_cplx'
'38 /kinetics/Ras/inact-GEF*'
'39 /kinetics/Ras/CaM-GEF'
'40 /kinetics/Ras/CaM-GEF/CaM-GEF-act-ras/CaM-GEF-act-ras_cplx'
'41 /kinetics/PKA-active/PKA-phosph-GEF/PKA-phosph-GEF_cplx'
'42 /kinetics/Shc*.Sos.Grb2'
'43 /kinetics/Shc*.Sos.Grb2/Sos.Ras_GEF/Sos.Ras_GEF_cplx'
'44 /kinetics/EGFR/EGFR'
'45 /kinetics/EGFR/L.EGFR'
'46 /kinetics/EGFR/L.EGFR/phosph_Shc/phosph_Shc_cplx'
'47 /kinetics/EGFR/SHC'
'48 /kinetics/EGFR/SHC*'
'49 /kinetics/EGFR/Internal_L.EGFR'
'50 /kinetics/Sos/Sos*.Grb2'
'51 /kinetics/Sos/Grb2'
'52 /kinetics/Sos/Sos.Grb2'
'53 /kinetics/Sos/Sos*'
'54 /kinetics/Sos/Sos'
};

bufnames = {
'1 /kinetics/PKC-active'
'2 /kinetics/BetaGamma'
'3 /kinetics/PKA-active'
'4 /kinetics/CaM-Ca4'
'5 /kinetics/EGFR/EGF'
};

sumtotnames = {
};

% Initial concs of 54 molecules
y0(1) = 0;
y0(2) = 0;
y0(3) = 0;
y0(4) = 0;
y0(5) = 0;
y0(6) = 0;
y0(7) = 0.2;
y0(8) = 0;
y0(9) = 0.18;
y0(10) = 0.36;
y0(11) = 0;
y0(12) = 0;
y0(13) = 0;
y0(14) = 0;
y0(15) = 0;
y0(16) = 0;
y0(17) = 0;
y0(18) = 0;
y0(19) = 0;
y0(20) = 0.0024;
y0(21) = 0;
y0(22) = 0;
y0(23) = 0.224;
y0(24) = 0;
y0(25) = 0;
y0(26) = 0;
y0(27) = 0;
y0(28) = 0;
y0(29) = 0;
y0(30) = 0.1;
y0(31) = 0;
y0(32) = 0;
y0(33) = 0;
y0(34) = 0.2;
y0(35) = 0;
y0(36) = 0.002;
y0(37) = 0;
y0(38) = 0;
y0(39) = 0;
y0(40) = 0;
y0(41) = 0;
y0(42) = 0;
y0(43) = 0;
y0(44) = 0.166667;
y0(45) = 0;
y0(46) = 0;
y0(47) = 0.5;
y0(48) = 0;
y0(49) = 0;
y0(50) = 0;
y0(51) = 1;
y0(52) = 0;
y0(53) = 0;
y0(54) = 0.1;
buff(1) = 0.09;
buff(2) = 0.0094;
buff(3) = 0.015;
buff(4) = 0;
buff(5) = 0;
% Call the ODE solver and display results
[t, y] = ode23s(@f, tspan, y0);

hold on;
plot(t,y(:,4));
% Evaluation function
function dydt = f(t, y)
global buff;
dydt = [
 + 0.3 * y(7) * buff(1) - 16 * y(1) - 4 * y(1)
 + 6 * y(36) * buff(1) - 16 * y(2) - 4 * y(2)
 + 6 * y(30) * buff(1) - 16 * y(3) - 4 * y(3)
 - 1.95 * y(8) * y(4) + 40 * y(5) + 10 * y(5) + 0.15 * y(15) - 75 * y(4) * y(20) + 4 * y(22) - 19.5 * y(54) * y(4) + 40 * y(6) + 10 * y(6)
 + 1.95 * y(8) * y(4) - 40 * y(5) - 10 * y(5)
 + 19.5 * y(54) * y(4) - 40 * y(6) - 10 * y(6)
 - 0.3 * y(7) * buff(1) + 16 * y(1) + 6 * y(24)
 + 4 * y(1) - 1.95 * y(8) * y(4) + 40 * y(5) - 1.98 * y(8) * y(23) + 25 * y(24) + 6 * y(27) - 24 * y(8) * y(33) + 0.5 * y(17)
 + 6 * y(26) - 3.3 * y(9) * y(17) + 0.42 * y(18)
 - 16.2 * y(10) * y(13) + 0.6 * y(14) + 1 * y(21)
 + 10 * y(5) - 1.98 * y(11) * y(23) + 25 * y(27)
 + 0.15 * y(14) - 16.2 * y(12) * y(13) + 0.6 * y(15) - 75 * y(12) * y(20) + 4 * y(21) + 1 * y(22)
 - 16.2 * y(10) * y(13) + 0.6 * y(14) + 0.15 * y(14) - 16.2 * y(12) * y(13) + 0.6 * y(15) + 0.15 * y(15) - 1.98 * y(13) * y(23) + 25 * y(25) + 0.105 * y(19)
 + 16.2 * y(10) * y(13) - 0.6 * y(14) - 0.15 * y(14)
 + 16.2 * y(12) * y(13) - 0.6 * y(15) - 0.15 * y(15)
 + 6 * y(25) - 1.98 * y(16) * y(23) + 25 * y(26) + 0.105 * y(18) - 3.3 * y(16) * y(17) + 0.42 * y(19)
 + 24 * y(8) * y(33) - 0.5 * y(17) - 3.3 * y(9) * y(17) + 0.42 * y(18) + 0.105 * y(18) - 3.3 * y(16) * y(17) + 0.42 * y(19) + 0.105 * y(19)
 + 3.3 * y(9) * y(17) - 0.42 * y(18) - 0.105 * y(18)
 + 3.3 * y(16) * y(17) - 0.42 * y(19) - 0.105 * y(19)
 - 75 * y(12) * y(20) + 4 * y(21) + 1 * y(21) - 75 * y(4) * y(20) + 4 * y(22) + 1 * y(22)
 + 75 * y(12) * y(20) - 4 * y(21) - 1 * y(21)
 + 75 * y(4) * y(20) - 4 * y(22) - 1 * y(22)
 - 1.98 * y(8) * y(23) + 25 * y(24) + 6 * y(24) - 1.98 * y(13) * y(23) + 25 * y(25) + 6 * y(25) - 1.98 * y(16) * y(23) + 25 * y(26) + 6 * y(26) - 1.98 * y(11) * y(23) + 25 * y(27) + 6 * y(27)
 + 1.98 * y(8) * y(23) - 25 * y(24) - 6 * y(24)
 + 1.98 * y(13) * y(23) - 25 * y(25) - 6 * y(25)
 + 1.98 * y(16) * y(23) - 25 * y(26) - 6 * y(26)
 + 1.98 * y(11) * y(23) - 25 * y(27) - 6 * y(27)
 - 0.198 * y(34) * y(28) + 0.08 * y(29) + 0.02 * y(29) + 6 * buff(2) * y(30) - 1 * y(28)
 + 0.198 * y(34) * y(28) - 0.08 * y(29) - 0.02 * y(29)
 - 6 * buff(2) * y(30) + 1 * y(28) - 6 * y(30) * buff(1) + 16 * y(3) + 1 * y(31) - 6 * y(30) * buff(3) + 36 * y(41) - 60 * y(30) * buff(4) + 1 * y(39) + 1 * y(38)
 + 4 * y(3) - 1 * y(31) - 0.198 * y(34) * y(31) + 0.08 * y(32) + 0.02 * y(32)
 + 0.198 * y(34) * y(31) - 0.08 * y(32) - 0.02 * y(32)
 + 0.02 * y(29) - 49.4856 * y(33) * y(36) + 40 * y(37) - 0.0001 * y(33) + 0.02 * y(32) + 0.02 * y(40) - 24 * y(8) * y(33) + 0.5 * y(17) + 0.02 * y(43)
 - 0.198 * y(34) * y(28) + 0.08 * y(29) + 10 * y(37) + 0.0001 * y(33) - 0.198 * y(34) * y(31) + 0.08 * y(32) - 0.198 * y(34) * y(39) + 0.08 * y(40) - 0.198 * y(34) * y(42) + 0.08 * y(43)
 + 4 * y(2) - 0.1 * y(35)
 - 49.4856 * y(33) * y(36) + 40 * y(37) + 10 * y(37) - 6 * y(36) * buff(1) + 16 * y(2) + 0.1 * y(35)
 + 49.4856 * y(33) * y(36) - 40 * y(37) - 10 * y(37)
 + 9 * y(41) - 1 * y(38)
 + 60 * y(30) * buff(4) - 1 * y(39) - 0.198 * y(34) * y(39) + 0.08 * y(40) + 0.02 * y(40)
 + 0.198 * y(34) * y(39) - 0.08 * y(40) - 0.02 * y(40)
 + 6 * y(30) * buff(3) - 36 * y(41) - 9 * y(41)
 + 0.49998 * y(52) * y(48) - 0.1 * y(42) - 0.198 * y(34) * y(42) + 0.08 * y(43) + 0.02 * y(43)
 + 0.198 * y(34) * y(42) - 0.08 * y(43) - 0.02 * y(43)
 - 4.2 * y(44) * buff(5) + 0.25 * y(45)
 + 4.2 * y(44) * buff(5) - 0.25 * y(45) - 1.2 * y(47) * y(45) + 0.8 * y(46) + 0.2 * y(46) - 0.002 * y(45) + 0.00033 * y(49)
 + 1.2 * y(47) * y(45) - 0.8 * y(46) - 0.2 * y(46)
 + 0.0016667 * y(48) - 1.2 * y(47) * y(45) + 0.8 * y(46)
 - 0.0016667 * y(48) - 0.49998 * y(52) * y(48) + 0.1 * y(42) + 0.2 * y(46)
 + 0.002 * y(45) - 0.00033 * y(49)
 + 0.0250002 * y(53) * y(51) - 0.0168 * y(50)
 - 0.0250002 * y(51) * y(54) + 0.0168 * y(52) - 0.0250002 * y(53) * y(51) + 0.0168 * y(50)
 + 0.0250002 * y(51) * y(54) - 0.0168 * y(52) - 0.49998 * y(52) * y(48) + 0.1 * y(42)
 + 10 * y(6) - 0.0250002 * y(53) * y(51) + 0.0168 * y(50) - 0.001 * y(53)
 - 0.0250002 * y(51) * y(54) + 0.0168 * y(52) - 19.5 * y(54) * y(4) + 40 * y(6) + 0.001 * y(53)
];

% end of model
