Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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

Latest Articles

Collapse

  • seqadmin
    Current Approaches to Protein Sequencing
    by seqadmin


    Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
    04-04-2024, 04:25 PM
  • seqadmin
    Strategies for Sequencing Challenging Samples
    by seqadmin


    Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
    03-22-2024, 06:39 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 04-11-2024, 12:08 PM
0 responses
25 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 10:19 PM
0 responses
29 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 09:21 AM
0 responses
25 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-04-2024, 09:00 AM
0 responses
52 views
0 likes
Last Post seqadmin  
Working...
X