// conceptual galactose model in Dizzy format
// options to obtain estimated variance in batch mode:  
//  -simulator ODEtoJava-dopr54-adaptive -computeFluctuations -stopTime 1000.0
// this runs model for 1000 minutes to obtain steady-state
// then estimates the standard deviation of a stochastic simulation
// time required to obtain steady-state depends on initial condition
// see Help for instructions

//list of species
iGa=1e7;
inductflag = 1;  //set to zero for no induction
g4 = 22;       // GAL4
g4d = 50;      // GAL4 dimer
g7 = 1384;      // GAL7
g7d = 1126;      // GAL7 dimer
g80 = 183;     // GAL80
g80d = 20;     // GAL80 dimer
g3 = 326;      // GAL3
GAI = (1*10^7 – 1975) * inductflag;         // internal galactose
g3i = 4 * inductflag;       // GAL3-galactose
g4dg80d = 54;  // GAL4-dimer-GAL80-dimer
g80g3i = 1971 * inductflag;    // GAL80-GAL3-galactose
r3 = 4;        // mRNA-GAL3
r80 = 4;       // mRNA-GAL80
r7 = 3;        // mRNA-GAL7

//gal3 and gal 80 promoters in bound or unbound states
d3b1 = 1;
d3b1g4d = 0;
d3b1g4dg80d = 0;
d80b1 = 1;
d80b1g4d = 0;
d80b1g4dg80d = 0;

//gal7 promoters in bound or unbound states
d7xxxx = 1.0;
d7g4xx = 0.0;
d7xxg4 = 0.0;
d7g4g4 = 0.0;
d7g8xx = 0.0;
d7xxg8 = 0.0;
d7g4g8 = 0.0;
d7g8g4 = 0.0;
d7g8g8 = 0.0;

//dimerization and complex formation
c1,  g4 + g4 -> g4d , 0.1;
c2,  g4d  -> g4 + g4, 1.0;
c3,  g7 + g7 -> g7d , 0.1;
c4,  g7d  -> g7 + g7, 170.2;
c5,  g80 + g80 -> g80d , 0.1;
c6,  g80d  -> g80 + g80, 170.2;
c7,  g3 + GAI -> g3i , 0.001;
c8,  g3i  -> g3 + GAI, 8.9*10^5;
c9,  g4d + g80d -> g4dg80d , 0.1;
c10,  g4dg80d  -> g4d + g80d, 1.82588;
c11,  g80 + g3i -> g80g3i , 0.1;
c12,  g80g3i  -> g80 + g3i, 0.03023*20;

//binding and unbinding with gal3 and gal80 promoter regions
b3r1,  d3b1 + g4d -> d3b1g4d , 0.1;
b3r2,  d3b1g4d  -> d3b1 + g4d, 1.14676;
b3r3,  d3b1g4d + g80d -> d3b1g4dg80d , 0.1;
b3r4,  d3b1g4dg80d  -> d3b1g4d + g80d, 1.82588;
b80r1,  d80b1 + g4d -> d80b1g4d , 0.1;
b80r2,  d80b1g4d  -> d80b1 + g4d, 1.14676;
b80r3,  d80b1g4d + g80d -> d80b1g4dg80d , 0.1;
b80r4,  d80b1g4dg80d  -> d80b1g4d + g80d, 1.82588;

//binding and unbinding with gal7 promoter regions
q = 30.0;  //cooperativity factor
b7r1, d7xxxx + g4d -> d7g4xx, 0.1;           
b7r2, d7g4xx -> d7xxxx + g4d, 1.14676;
b7r3, d7xxxx + g4d -> d7xxg4, 0.1;
b7r4, d7xxg4 -> d7xxxx + g4d, 1.14676;
b7r5, d7xxg4 + g4d -> d7g4g4, 0.1;
b7r6, d7g4g4 -> d7xxg4 + g4d, 1.14676;
b7r7, d7xxg4 + g80d -> d7xxg8, 0.1;
b7r8, d7xxg8 -> d7xxg4 + g80d, 1.82588;
b7r9, d7g4xx + g4d -> d7g4g4, 0.1;
b7r10, d7g4g4 -> d7g4xx + g4d, 1.14676;
b7r11, d7g4xx + g80d -> d7g8xx, 0.1;
b7r12, d7g8xx -> d7g4xx + g80d, 1.82588;
b7r13, d7g4g4 + g80d -> d7g8g4, 0.1;
b7r14, d7g8g4 -> d7g4g4 + g80d, 1.82588;
b7r15, d7g4g4 + g80d -> d7g4g8, 0.1;
b7r16, d7g4g8 -> d7g4g4 + g80d, 1.82588;
b7r17, d7g8g4 + g80d -> d7g8g8, q * 0.1;
b7r18, d7g8g8 -> d7g8g4 + g80d, 1.82588;
b7r19, d7g4g8 + g80d -> d7g8g8, q * 0.1;
b7r20, d7g8g8 -> d7g4g8 + g80d, 1.82588;
b7r21, d7xxg8 + g4d -> d7g4g8, 0.1;
b7r22, d7g4g8 -> d7xxg8 + g4d, 1.14676;
b7r23, d7g8xx + g4d -> d7g8g4, 0.1;
b7r24, d7g8g4 -> d7g8xx + g4d, 1.14676;

// RNA creation
r3r1,   d3b1g4d -> d3b1g4d + r3 , 1.44385;     
r80r1,  d80b1g4d -> d80b1g4d + r80 , 1.44385;      
r7r1,   d7g4xx -> d7g4xx + r7 , 5.3284; 
r7r2,   d7xxg4 -> r7 + d7xxg4, 5.3284; 
r7r3,   d7g4g4 -> r7 + d7g4g4, 5.3284; 
r7r4,   d7g4g8 -> r7 + d7g4g8,  5.3284;
r7r5,   d7g8g4 -> r7 + d7g8g4,  5.3284;

// translation and species creation
p1,  r3  -> r3 + g3, 4.3807;          // gal3 translation
p2,  r80  -> r80 + g80, 2.19036;       // gal80 translation
p3,  r7  -> r7 + g7, 4.3807;          // gal7 translation 
p4,   -> g4 , 0.86181;
p5, -> GAI , 1.0*10^7 * 0.003747 * inductflag; 

// RNA decay
dr1,  r3  -> , 0.159193;
dr2,  r80  -> , 0.159193;
dr3,  r7  -> , 0.159193;

// protein decay
dp1,  g3  -> , 0.003747;
dp2,  g80  -> , 0.003747;
dp3,  g7  -> , 0.003747;
dp4,  g4  -> , 0.003747;
dp5,  g80d  -> , 0.003747;
dp6,  g7d  -> , 0.003747;
dp7,  g4d  -> , 0.003747;
dp8,  g3i  -> , 0.003747;
dp9,  g4dg80d  -> , 0.003747;
dp10,  g80g3i  -> , 0.003747;
dp11, GAI -> , 0.003747;