%% %%%%%% 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.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%% variable_name.m %%
% This file converts all the elements of vector Y[ y(1), y(2),,,,] into
% variable names such as MASS, CLB2 etc. so as to avoid assigning the 
% vector to the variable(MASS=y(1)) and vice versa. It is simply used to
% keep the code more tidy.


varnames = num2cell(zeros(39,1));

for n=1:39
    varnames{n}=n;
end

[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,nSPN,nVi20,...
    nlte1,nBUB2] = deal(varnames{:});

clear n varnames;

[name{1:39}]=deal('MASS','CLN2','CLB2','CLB5','SIC1','CDC6','C2','C5','F2','F5','SIC1P','C2P','C5P',...
    'CDC6P','F2P','F5P','SWI5T','SWI5','IEP','CDC20T','CDC20','CDH1T','CDH1','CDC14T',...
    'CDC14','NET1T','NET1','RENT','TEM1','CDC15','PPX','PDS1','ESP1','ORI','BUD','SPN','Vi20',...
    'lte1','BUB2');