Providing Entire Contents of the File

[kerin]

I have provided the entire contents. All the files are attached. Thank you
for your reading and kind help. 
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*glycSim.m*
% "MASS" Simulator of glycolysis 

% This Workbook sets up, analyses, and simulates and graphs the equations
that 
% describe the  glycolytic pathway.   
% 

%%%% SECTION I: SYSTEM DEFINITION AND SETTING UP THE EQUATIONS 

% Loading model 
global model 
load glycModel 

% Dimension of Stoichiometric matrix 
dimS = size(model.S); 
rankS = rank(model.S); 

% Define concentrations variables: pool sizes and external concentrations 
global NADHtotal pyrplasma lacplasma ampplasma hplasma h2oplasma 
NADHtotal = 0.089; 
pyrplasma = 0.06; 
lacplasma = 1.0; 
ampplasma = 0.0001; 
hplasma = 10^-4.2; 
h2oplasma = 1; 

% Calculate the concentrations of the pools at steady state 
poolSize = model.pools*model.ststmet; 

% Create bar chart with pool concentrations 
figure(1) 
bar(poolSize); 
xlabel('1.GP+  2.GP-  3.AP+  4.AP-  5. GR+  6.GR-  7.nadh  8.P+  9.P- 
10.Ptot  11.nadh-tot');ylabel('poolSize'); 

% Compute charge states of pools 
ratiovars = (model.rnum*poolSize)./(model.rden*poolSize); 
figure(2) 
bar(ratiovars); 
ylabel('Ratio');xlabel('1.Glycolytic energy Charge  2.Adenylate energy
charge  3.Glycolytic redox charge  4.NADH redox charge  5.Phosphate recycle
ratio'); 

% Compute the reactions that move into pools 
poolMove = model.pools*model.S; 

% Define exchange fluxes and loads on cofactors 
global gluin ampin 
gluin = 1.12; 
ststloadatp = 2*gluin; 
ststloadnadh = 0.2*gluin; 
ampin = 0.014; 

global k 
k(1) = model.ststflux(1)/(model.ststmet(17)*model.ststmet(1) -
model.ststmet(16)*model.ststmet(2)/model.Keq(1)); 
k(2) = model.ststflux(2)/(model.ststmet(2) - model.ststmet(3)/model.Keq(2)); 
k(3) = model.ststflux(3)/(model.ststmet(3)*model.ststmet(17) -
model.ststmet(4)*model.ststmet(16)/model.Keq(3)); 
k(4) = model.ststflux(4)/(model.ststmet(5) - model.ststmet(6)/model.Keq(4)); 
k(5) = model.ststflux(5)/(model.ststmet(4) -
model.ststmet(6)*model.ststmet(5)/model.Keq(5)); 
k(6) =
model.ststflux(6)/(model.ststmet(18)*model.ststmet(6)*model.ststmet(13) -
model.ststmet(14)*model.ststmet(7)/model.Keq(6)); 
k(7) = model.ststflux(7)/(model.ststmet(7)*model.ststmet(16) -
model.ststmet(8)*model.ststmet(17)/model.Keq(7)); 
k(8) = model.ststflux(8)/(model.ststmet(8) - model.ststmet(9)/model.Keq(8)); 
k(9) = model.ststflux(9)/(model.ststmet(9) -
model.ststmet(10)/model.Keq(9)); 
k(10) = model.ststflux(10)/(model.ststmet(10)*model.ststmet(16) -
model.ststmet(11)*model.ststmet(17)/model.Keq(10)); 
k(11) = model.ststflux(11)/(model.ststmet(11)*model.ststmet(14) -
model.ststmet(12)*model.ststmet(13)/model.Keq(11)); 
k(12) = model.ststflux(12)/(model.ststmet(15) - ampplasma/model.Keq(12)); 
k(13) = 10^6; 
k(14) = model.ststflux(14)/(model.ststmet(11) - pyrplasma); 
k(15) = model.ststflux(15)/(model.ststmet(12) - lacplasma); 
k(16) = model.ststflux(16)/(model.ststmet(17) -
model.ststmet(16)*model.ststmet(18)/model.Keq(16)); 
k(17) = model.ststflux(17)/(model.ststmet(14) -
model.ststmet(13)/model.Keq(17)); 
k(18) = 0; 
k(19) = 0; 
k(20) = 1e5; 
k(21) = 1e5; 

%%%% SECTION II: SIMULATION OF THE NON-LINEAR MASS BALANCE EQUATIONS 
timeRange = [0 50]; 
*/x = lsode(glycODE,0,timeRange);/*

% Check concentrations and fluxes at the start and end of the solution 
begConc = model.ststmet; 
endConc = x(end,:)'; 

figure(3) 
bar([begConc endConc]); 
xlabel('1.Gluc  2.G6P  3.F6P  4.FDP  5.DHAP  6.GAP  7.DPG13  8.PG3  9.PG2 
10.PEP  11.PYR  12.LAC  13.NAD  14.NADH  15.AMP  16.ADP  17.ATP  18.Pi 
19.H+  20.H2O'); 
ylabel('Concentrations');legend('begCon','endConc'); 




*glycODE.m* 
% ODE for Glycolysis Simulator 
% Matlab Conversion 
% AB 01/20/10 


function dxdt = glycODE(x,t) 
x=[]; 
global k model ampplasma gluin ampin pyrplasma lacplasma hplasma h2oplasma 

vhk = k(1)*(x(17)*x(1) - x(16)*x(2)/model.Keq(1)); 
vpgi = k(2)*(x(2) - x(3)/model.Keq(2)); 
vpfk = k(3)*(x(3)*x(17) - x(4)*x(16)/model.Keq(3)); 
vtpi = k(4)*(x(5) - x(6)/model.Keq(4)); 
vald = k(5)*(x(4) - x(6)*x(5)/model.Keq(5)); 
vgapdh = k(6)*(x(18)*x(6)*x(13) - x(14)*x(7)/model.Keq(6)); 
vpgk = k(7)*(x(7)*x(16) - x(8)*x(17)/model.Keq(7)); 
vpglm = k(8)*(x(8) - x(9)/model.Keq(8)); 
veno = k(9)*(x(9) - x(10)/model.Keq(9)); 
vpk = k(10)*(x(10)*x(16) - x(11)*x(17)/model.Keq(10)); 
vldh = k(11)*(x(11)*x(14) - x(12)*x(13)/model.Keq(11)); 
vamp = k(12)*(x(15) - ampplasma/model.Keq(12)); 
vapk = k(13)*(x(16)*x(16) - x(17)*x(15)/model.Keq(13)); 
vpyr = k(14)*(x(11) - pyrplasma/model.Keq(14)); 
vlac = k(15)*(x(12) - lacplasma/model.Keq(15)); 
vatp = k(16)*(x(17) - x(16)*x(18)/model.Keq(16)); 
vnadh = k(17)*(x(14) - x(13)/model.Keq(17)); 
vgluin = gluin; 
vampin = ampin; 
vh = k(20)*(x(19) - hplasma/model.Keq(20)); 
vh2o = k(21)*(x(20) - h2oplasma/model.Keq(21)); 

v =
[vhk;vpgi;vpfk;vtpi;vald;vgapdh;vpgk;vpglm;veno;vpk;vldh;vamp;vapk;vpyr;vlac;vatp;vnadh;vgluin;vampin;vh;vh2o];
 

dxdt = model.S*v; 
endfunction 




*The Error Message:*
octave:9>glycSim 
error: glycODE: A(I): index out of bounds; value 17 out of bound 0 
error: called from: 
error: C:\Octave\Octave3.4.3_gcc4.5.2\glycODE.m at line 10, column 5 
error: evaluating argument list element number 1
error: C:\Octave\Octave3.4.3_gcc4.5.2\glycSim.m at line 77, column 17. 
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http://octave.1599824.n4.nabble.com/file/n4343185/glycSim.m glycSim.m 
http://octave.1599824.n4.nabble.com/file/n4343185/glycODE.m glycODE.m 
http://octave.1599824.n4.nabble.com/file/n4343185/glycModel.mat
glycModel.mat 


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