examples.YeastExample1.mlrj Maven / Gradle / Ivy

Go to download

Show more of this group Show more artifacts with this name
Show all versions of mlrules Show documentation

The main project for the external domain-specific modeling language ML-Rules, which is used to model hierarchical biochemical reaction networks with nested and attributed species

There is a newer version: 2.2.13-headless

Show newest version

// Example 1

////////////////////////////////////////////////////////////////////////////////
//  Multi-level model describing the interplay between intracellular dynamics //
//  and high-level states at cellular level for a single fission yeast cell.  //
////////////////////////////////////////////////////////////////////////////////

// PARAMETERS
dtot:1000;
k1:0.015*dtot;
k2:200;
k3:180;
k3prime:0.018;
k4:4.5;
k5:0.6;
k6:1.0;
k7:1e6;
k8:k7;
k9:k7;
t7:250;
t8:70;
t9:20;
td:116;

// SPECIES DEFINITIONS
C(num,string)[];
Y();
Yp();
D();
Mi();
Ma();

// INITIAL SOLUTION
>>INIT[ C(1.0,'G1')[(dtot-1) D + Ma] ];

// RULE SCHEMATA

// (1) cyclin synthesis 
C(v,p)[s?]:c -> C(v,p)[Y + s?] @ k1*#c;

// (2) formation of inactive MPF complex
Y:y + D:d -> Mi @ k2*#y*#d;

// (3) activation of MPF complex
Mi:i + Ma:a -> 2 Ma @ (k3prime+(k3*((#a/dtot)^(2))))*#i;

// (4) breakage of activated MPF complex
C(v,p)[Ma:a + s?]:c -> C(v,p)[Yp + D + s?] @ if (#a>1) then (k4/v)*#a*#c else 0;

// (5) cyclin degradation
Yp:y -> @ k5*#y;

// (6) cell growth
C(v,p)[s?]:c -> C(v+(1/td),p)[s?] @ if (p=='G1') || (p=='SG2') then k6*#c else 0;

// (7) cell cycle transition from G1->S/G2
C(v,'G1')[Mi:i + s?]:c -> C(v,'SG2')[Mi + s?] @ if (#i>t7) then k7*#c else 0;

// (8) cell cycle transition from S/G2->M
C(v,'SG2')[Ma:a + s?]:c -> C(v,'M')[Ma + s?] @ if (#a>t8) then k8*#c else 0;

// (9) cell division (transition from M->G1)
C(v,'M')[Ma:a + s?]:c -> C(v/2,'G1')[Ma + s?] @ if (#a