 %  DOQCS : http://doqcs.ncbs.res.in/ 
 %  Accession Name = Jak-Stat_Pathway 
 %  Accession Number = 66 
 %  Transcriber = Sharat J. Vayttaden and Prasoon Agarwal, NCBS 
 %  Developer = Yamada S, Shiono S, Joo A, Yoshimura A 
 %  Species = mouse 
 %  Tissue = Liver 
 %  Cell Compartment = Cytosol, Nucleus 
 %  Notes =  This model was taken from the <a href =http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12527385&query_hl=3&itool=pubm?cmded_DocSum>Yamada S et al. FEBS Letters 2003 Jan 16;534(1-3):190-6</a> <br>This model shows the control mechanism of Jak-Stat pathway, here SOCS1 (Suppressor of cytokine signaling-I) was identified as the negative regulator of Jak and STAT signal transduction pathway. <br>Note: There are a few ambiguities in the paper like initial concentration of IFN and some reactions were missing in the paper that were employed for obtaining the results. The graphs are almost similar to the graphs as shown in the paper but still some ambiguities regarding the concentration are there. Thanks to Dr Satoshi Yamada for clarifying some of those ambiguities and providing the values used in the simulations. 
 
   % Note: All the concentrations are in micro Mole (uM)

function moose_convert
%Matlab simulation for chemical kinetics

% Saved on Mon Feb 13 16:44:08 2006
% Automatically generated from kkit model in MOOSE by conv_matlab

global buff;
global t;
global y;

% Define Tables here
tspan=[0, 28800];
% Molecule names
molnames = {
'1 /kinetics/R'
'2 /kinetics/JAK'
'3 /kinetics/RJ'
'4 /kinetics/IFNRJ'
'5 /kinetics/IFNRJ2'
'6 /kinetics/IFNRJ2*'
'7 /kinetics/STAT1c'
'8 /kinetics/IFNRJ2*-STAT1c'
'9 /kinetics/STAT1c*'
'10 /kinetics/IFNRJ2*-STAT1c*'
'11 /kinetics/STAT1c*-STAT1c*'
'12 /kinetics/SHP-2'
'13 /kinetics/IFNRJ2*-SHP-2'
'14 /kinetics/PPX'
'15 /kinetics/PPX-STAT1c*'
'16 /kinetics/PPX-STAT1c*-STAT1c*'
'17 /kinetics/STAT1n*-STAT1n*'
'18 /kinetics/STAT1n*'
'19 /kinetics/PPN'
'20 /kinetics/PPN-STAT1n*'
'21 /kinetics/STAT1n'
'22 /kinetics/PPN-STAT1n*-STAT1n*'
'23 /kinetics/SOCS1'
'24 /kinetics/SOCS1-IFNRJ2*'
'25 /kinetics/SOCS1-IFNRJ2*-STAT1c'
'26 /kinetics/SOCS1-IFNRJ2*-STAT1c-SHP-2'
'27 /kinetics/IFNR'
'28 /kinetics/IFNRJ_'
'29 /kinetics/IFNRJ2*-STAT1c-SHP2'
'30 /kinetics/mRNAVn'
'31 /kinetics/mRNAVc'
'32 /kinetics/AV'
'33 /kinetics/mRNASn'
'34 /kinetics/mRNASc'
'35 /kinetics/SOCS1-IFNRJ2*-SHP2'
};

bufnames = {
'1 /kinetics/IFN'
'2 /kinetics/Transcription_complex'
'3 /kinetics/SOCS1_Deg'
'4 /kinetics/mRNA_remain'
'5 /kinetics/Transcription_comp2'
'6 /kinetics/AV_degraded'
'7 /kinetics/mRNAVc_remain'
};

sumtotnames = {
'1 /kinetics/dup_STAT1n*-STAT1n*'
'2 /kinetics/mRNAVc_dupli'
'3 /kinetics/dup_mRNASc'
};

% Initial concs of 35 molecules
y0(1) = 0.01;
y0(2) = 0.02;
y0(3) = 0;
y0(4) = 0;
y0(5) = 0;
y0(6) = 0;
y0(7) = 1;
y0(8) = 0;
y0(9) = 0;
y0(10) = 0;
y0(11) = 0;
y0(12) = 0.1;
y0(13) = 0;
y0(14) = 0.05;
y0(15) = 0;
y0(16) = 0;
y0(17) = 0;
y0(18) = 0;
y0(19) = 0.06;
y0(20) = 0;
y0(21) = 0;
y0(22) = 0;
y0(23) = 0;
y0(24) = 0;
y0(25) = 0;
y0(26) = 0;
y0(27) = 0;
y0(28) = 0;
y0(29) = 0;
y0(30) = 0;
y0(31) = 0;
y0(32) = 0;
y0(33) = 0;
y0(34) = 0;
y0(35) = 0;
buff(1) = 0.01;
buff(2) = 0.001;
buff(3) = 0;
buff(4) = 0;
buff(5) = 0.001;
buff(6) = 0;
buff(7) = 0;
% Sumtotal eqn for /kinetics/dup_STAT1n*-STAT1n*: sumtot(1) = y(17)
% Sumtotal eqn for /kinetics/mRNAVc_dupli: sumtot(2) = y(31)
% Sumtotal eqn for /kinetics/dup_mRNASc: sumtot(3) = y(34)

% Call the ODE solver and display results
[t, y] = ode23s(@f, tspan, y0);

hold on;
do_plots;

function do_plots()
global t;
global y;
plot(t,y(:,23));
plot(t,y(:,6));
plot(t,y(:,34));
plot(t,y(:,11));
plot(t,y(:,21));
plot(t,y(:,7));
plot(t,y(:,17));

% Evaluation function
function dydt = f(t, y)
global buff;
dydt = [
 - 100 * y(1) * y(2) + 0.05 * y(3) - 20 * buff(1) * y(1) + 0.02 * y(27)
 - 100 * y(1) * y(2) + 0.05 * y(3) - 100 * y(27) * y(2) + 0.05 * y(28)
 + 100 * y(1) * y(2) - 0.05 * y(3) - 20 * y(3) * buff(1) + 0.02 * y(4)
 + 20 * y(3) * buff(1) - 0.02 * y(4) - 40 * y(4) * y(28) + 0.2 * y(5)
 - 0.005 * y(5) + 0.003 * y(13) + 0.003 * y(26) + 0.003 * y(29) + 0.003 * y(35) + 40 * y(4) * y(28) - 0.2 * y(5)
 + 0.005 * y(5) - 8 * y(6) * y(7) + 0.8 * y(8) + 0.4 * y(8) - 5 * y(9) * y(6) + 0.5 * y(10) - 1 * y(6) * y(12) + 0.2 * y(13) - 20 * y(6) * y(23) + 0.1 * y(24) + 0.0005 * y(24)
 - 8 * y(6) * y(7) + 0.8 * y(8) + 0.003 * y(15) + 0.05 * y(21) - 8 * y(7) * y(24) + 0.8 * y(25) + 0.003 * y(26) + 0.003 * y(29) - 8 * y(7) * y(35) + 0.8 * y(26) + 0.003 * y(16)
 + 8 * y(6) * y(7) - 0.8 * y(8) - 0.4 * y(8) - 1 * y(12) * y(8) + 0.2 * y(29) - 20 * y(23) * y(8) + 0.1 * y(25) + 0.0005 * y(25)
 + 0.4 * y(8) - 5 * y(9) * y(6) + 0.5 * y(10) - 40 * y(9)*y(9) + 0.2 * y(11) - 1 * y(9) * y(14) + 0.2 * y(15) + 0.003 * y(16)
 + 5 * y(9) * y(6) - 0.5 * y(10)
 + 20 * y(9)*y(9) - 0.1 * y(11) - 1 * y(14) * y(11) + 0.2 * y(16) - 0.005 * y(11)
 - 1 * y(6) * y(12) + 0.2 * y(13) + 0.003 * y(13) - 1 * y(25) * y(12) + 0.2 * y(26) + 0.003 * y(26) - 1 * y(12) * y(8) + 0.2 * y(29) + 0.003 * y(29) - 1 * y(12) * y(24) + 0.2 * y(35) + 0.003 * y(35)
 + 1 * y(6) * y(12) - 0.2 * y(13) - 0.003 * y(13) - 20 * y(23) * y(13) + 0.1 * y(35) + 0.0005 * y(35)
 - 1 * y(9) * y(14) + 0.2 * y(15) + 0.003 * y(15) - 1 * y(14) * y(11) + 0.2 * y(16) + 0.003 * y(16)
 + 1 * y(9) * y(14) - 0.2 * y(15) - 0.003 * y(15)
 + 1 * y(14) * y(11) - 0.2 * y(16) - 0.003 * y(16)
 + 0.005 * y(11) + 20 * y(18)*y(18) - 0.1 * y(17) - 1 * y(19) * y(17) + 0.2 * y(22)
 - 40 * y(18)*y(18) + 0.2 * y(17) - 1 * y(18) * y(19) + 0.2 * y(20) + 0.005 * y(22)
 - 1 * y(18) * y(19) + 0.2 * y(20) + 0.005 * y(20) - 1 * y(19) * y(17) + 0.2 * y(22) + 0.005 * y(22)
 + 1 * y(18) * y(19) - 0.2 * y(20) - 0.005 * y(20)
 + 0.005 * y(20) - 0.05 * y(21) + 0.005 * y(22)
 + 1 * y(19) * y(17) - 0.2 * y(22) - 0.005 * y(22)
 - 20 * y(6) * y(23) + 0.1 * y(24) + 0.003 * y(26) - 0.0005 * y(23) + 0.01 * y(34) - 20 * y(23) * y(8) + 0.1 * y(25) - 20 * y(23) * y(13) + 0.1 * y(35) - 20 * y(23) * y(29) + 0.1 * y(26) + 0.003 * y(35)
 + 20 * y(6) * y(23) - 0.1 * y(24) - 8 * y(7) * y(24) + 0.8 * y(25) - 0.0005 * y(24) - 1 * y(12) * y(24) + 0.2 * y(35)
 + 8 * y(7) * y(24) - 0.8 * y(25) - 1 * y(25) * y(12) + 0.2 * y(26) + 20 * y(23) * y(8) - 0.1 * y(25) - 0.0005 * y(25)
 + 1 * y(25) * y(12) - 0.2 * y(26) - 0.003 * y(26) - 0.0005 * y(26) + 20 * y(23) * y(29) - 0.1 * y(26) + 8 * y(7) * y(35) - 0.8 * y(26)
 + 20 * buff(1) * y(1) - 0.02 * y(27) - 100 * y(27) * y(2) + 0.05 * y(28)
 + 100 * y(27) * y(2) - 0.05 * y(28) - 40 * y(4) * y(28) + 0.2 * y(5)
 + 1 * y(12) * y(8) - 0.2 * y(29) - 0.003 * y(29) + 0.0005 * y(26) - 20 * y(23) * y(29) + 0.1 * y(26)
 + 0.01 * buff(5) * y(17) / ( 0.4 + y(17) ) - 0.001 * y(30)
 + 0.001 * y(30) - 0.002 * y(31)
 + 0.002 * y(31) - 1e-05 * y(32)
 - 0.001 * y(33) + 0.01 * buff(2) * y(17) / ( 0.4 + y(17) )
 + 0.001 * y(33) - 0.0005 * y(34)
 + 20 * y(23) * y(13) - 0.1 * y(35) + 1 * y(12) * y(24) - 0.2 * y(35) - 0.0005 * y(35) - 0.003 * y(35) - 8 * y(7) * y(35) + 0.8 * y(26)
];

% end of model
