Providing Entire Contents of the File

[kerin]

I have provided the entire contents. All the files are attached. Thank you
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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
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http://octave.1599824.n4.nabble.com/file/n4343159/glycSim.m glycSim.m 
http://octave.1599824.n4.nabble.com/file/n4343159/glycODE.m glycODE.m 
http://octave.1599824.n4.nabble.com/file/n4343159/glycModel.mat
glycModel.mat 

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