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  • Defining initial concentrations and rate equations in PySCeS ?

    I'm trying to create a model file for PySCeS (Python module) and I have all of the reactions mapped out (internal and external). I'm at the point of assigning values to the initial concentrations of metabolites and defining the rate equations. I'm new at metabolics and I'm not sure how to figure out these values. I've looked through Dr. Olivier's Input File Resource (http://pysces.sourceforge.net/pdf/PySCeS-InputFile.pdf) as well as his thesis (http://pysces.sourceforge.net/pdf/bg...phd_thesis.pdf).



    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

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