I can see a pattern in the sample input file with the kinetic equations but the reactions are very simple.
i) What resource can help me in defining the kinetic equations for more complicated reactions like R5 below?
The initial concentrations are "guesses" that get adjusted (at least that's what I got from the documentation).
ii) How can I "guess" which values to use as my initial concentrations for accurate modeling?
An example of a complete reaction step including the name, stoichiometry and rate equation:
Code:
R5: Fru + ATP = Hex_P + ADP Fru/Ki5_Fru)*(Fru/Km5_Fru)*(ATP/Km5_ATP)/(1 + Vmax5/(1 + Fru/Ki5_Fru)*(Fru/Km5_Fru)*(ATP/Km5_ATP)/(1 + Fru/Km5_Fru + ATP/Km5_ATP + Fru*ATP/(Km5_Fru*Km5_ATP) + ADP/Ki5_ADP) Here is an example of the PySCeS input file:
Code:
# PySCeS input file # Simple linear pathway (2004) FIX: x0 x3 R1: x0 = s0 k1*x0 - k2*s0 R2: s0 = s1 k3*s0 - k4*s1 R3: s1 = s2 k5*s1 - k6*s2 R4: s2 = x3 k7*s2 - k8*x3 # InitExt x0 = 10.0 x3 = 1.0 # InitPar k1 = 10.0 k2 = 1.0 k3 = 5.0 k4 = 1.0 k5 = 3.0 k6 = 1.0 k7 = 2.0 k8 = 1.0 # InitVar s0 = 1.0 s1 = 1.0 s2 = 1.0