%% %%%%%% MATLAB ODE Simulation of the Budding Yeast Cell Cycle %%%%%% %%
% The ODE model is taken from Chen(2004): 
% Chen, K.C. and Calzone, L. and Csikasz-Nagy, A. and Cross, F.R. and
% Novak, B. and Tyson, J.J. 2004. Integrative analysis of cell cycle 
% control in budding yeast, Molecular Biology of the Cell 15:3841-3862
% The equations and parameters were downloaded from
% http://mpf.biol.vt.edu/research/budding_yeast_model/model_download/bychen04.ode
% and converted into MATLAB code by Kartik Subramanian (VirginiaTech) and
% Kamaludin Dingle (Oxford Univ.). September 2010.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%% initial_conds.m %%
% This function simply contains all the initial values of the variables in
% the ODEs. The values are taken from Chen(2004).

function y0 = initial_conds
%% Initial conditions
nMASS = 1.206019401550293;
nCLN2 = 0.0652511790394783;
nCLB2 = 0.1469227224588394;

nCLB5=0.05180418863892555;
nSIC1=0.02287768945097923;
nCDC6=0.1075804308056831;
nC2=0.2384047210216522;
nC5=0.07008149474859238;
nF2=0.2360586225986481;
nF5=7.245147571666166*10^-5;

nSIC1P=0.006410160101950169;
nC2P=0.02403404749929905;
nC5P=0.006878305226564407;
nCDC6P=0.01548638287931681;
nF2P=0.02739384770393372;
nF5P=7.90633202996105*10^-6;
nSWI5T=0.9764602780342102;
nSWI5=0.9561624526977539;
nIEP=0.1015391126275063;
nCDC20T=1.916339993476868;
  
nCDC20=0.4442965388298035;
nCDH1T=1;
nCDH1=0.930499255657196;
nCDC14T=2;
nCDC14=0.46834397315979;
nNET1T=2.799999952316284;
nNET1=0.01864561997354031;
nRENT=1.049547672271729;
nTEM1=0.9038969278335571;
nCDC15=0.6565329432487488;
 
nPPX=0.1231788992881775;
nPDS1=0.02561234869062901;
nESP1=0.3013133406639099;
nORI=0.0009094525594264269;
nBUD=0.008473447524011135;
nISPN=0.03056218847632408;
nVI20=0.009999999776482582;
nLTE1=0.1000000014901161;
nBUB2=0.2000000029802322;


%% Now define the vector of initial values used in main_yeast.m
y0 = [nMASS;
nCLN2;
nCLB2;
nCLB5;
nSIC1;
nCDC6;
nC2;
nC5;
nF2;
nF5;
nSIC1P;
nC2P;
nC5P;
nCDC6P;
nF2P;
nF5P;
nSWI5T;
nSWI5;
nIEP;
nCDC20T;
nCDC20;
nCDH1T;
nCDH1;
nCDC14T;
nCDC14;
nNET1T;
nNET1;
nRENT;
nTEM1;
nCDC15;
nPPX;
nPDS1;
nESP1;
nORI;
nBUD;
nISPN;
nVI20;
nLTE1;
nBUB2];