Documentation for ecmpy

Contents:

• 1.Model_Preview
  • Import related functions
• 2.Get_Reaction_Kcat_AutoPACMEN
  • Import related functions
  • Input and output files
  • Get reaction kcat_mw using AutoPacmen
    • Step 1: get bigg metbolite
    • Step 2: BRENDA kcat
    • Step 3: Select Brenda kcat for model
    • Step 4: SABIO-RK kcat for model
    • Step 5: Brenda and SABIO-RK kcat combined
    • Step 6: subunit number of each reaction
    • Step 7: get mw for model gene (must be uniprot ID)
    • Step 8: kcat assignment for model(include sa)
    • Step 9: get_reaction_kcat_mw for model
• 3.Get_Reaction_Kcat_AutoPACMEN
  • Import related functions
  • Input and output files
  • Get reaction kcat_mw using DLKcat
    • Step 0: read GEM
    • Step 1: subunit number of each reaction
    • Step 2: convert metbolites bigg id to smiles
    • Step 3: get protein sequence and mass in model
    • Step 4: split the substrate of reactions to match the gene
    • Step 5: combine the reaction–substrate–gene–protein_sequnce–mass and formate DLKcat input file
    • Step 6: use DLKcat calculate kcat
    • Step 7: get the kcat_mw file
• 4.Get ecModel using ECMpy
  • Import related functions
  • Input and output files
  • Get ecModel and simulation
• 5.EcModel_Calibration
  • Import related functions
  • Input and output files
  • Calibration kcat according Enzyme usage
• 6.EcModel_Analysis
  • Import related functions
  • Cumulative distribution figure
    • Input and output files
  • Phenotype Phase Plane (PhPP) Analysis
    • Input and output files
  • Overflow simulation
    • Input and output files
  • Trade-off simulation
  • Phenotype Simulation
• 7.EcModel_ME
  • Import related functions
  • Input and output files
  • Directly determining targets based on enzyme abundance
  • Determine targets based on the fold changes of enzyme cost
  • Determine targets based on FESOF
• 8.One Click Modeling
  • Use AutoPACMEN data to reconstruct ecGEM
  • Use DLKcat data to reconstruct ecGEM
  • Use user’s data to reconstruct ecGEM
• 9.BiGG_to_ecGEM
  • Batch construction of ecGEM from BiGG models
    • Download BiGG Model
    • Model add UniProt ID

Indices and tables

• Index

• Module Index

• Search Page