PAMparametrizer
1.0.0

Table of Contents

  • PAMparametrizer - parametrizing Protein Allocation Models with Flux Data
    • Why do we need a PAMparametrizer?
    • What does the PAMparametrizer do?
    • What can you find where in this repository?
      • PAMparametrizer functionality
    • Code structure
    • Dependencies
    • License
  • Genetic Algorithm for Protein Allocation Model Parameter Estimation
    • Software Structure
    • Genetic Algorithm workflow
    • Fitness Evaluation adjustment
  • Example usage of the PAMparametrizer
    • Example 1: Parametrizing the E. coli Protein Allocation Model with glucose as sole carbon source
      • Step 0: Initiate the sectors
        • Step 0.1 Initialize the active enzyme parameter set using GotEnzymes
        • Step 0.1 The Translational Protein Sector
        • Step 0.2 The Unused Enzyme Sector
      • Step 1: Organize the data
      • Step 2: Build the Protein Allocation Model
      • Step 3: Create the data objects required for the PAMparametrizer
        • i. Parse the sector configuration
        • ii. Get the ValidationData
        • iii. Define the HyperParameters
        • iv. ParametrizationResults and FluxResults
      • Step 4: Build the PAMparametrizer object
      • Step 5: Run!
      • Step 6: Analyze the Results
    • Example 2: Parametrizing the E. coli Protein Allocation Model with multiple carbon sources
      • Step 0: Initiate the sectors
      • Step 1: Organize the data
      • Step 2: Build the PAM
      • Step 3: Create the data objects required for the PAMparametrizer
        • i. Parse the sector configuration
        • i. Get the ValidationData
        • ii. Define the HyperParameters
      • Step 4: Build the PAMparametrizer object
      • Step 5: Run!
      • Step 6: Analyze the Results
  • Workflow for Protein Allocation Model Parameter Estimation
    • Software Structure
    • PAM parametrizer workflow
    • Data objects
      • SectorConfig
      • ValidationData
      • HyperParameters
      • ParametrizationResults
      • FluxResults
  • Parametrizing a PAM: from GEM to PAM
    • 1. The Genome-Scale Metabolic Model Sanity Check
    • 2. Building the Protein Sectors
      • 2.1 Initiating the ActiveEnzymesSector
      • 2.2 Parametrizing the TranslationalProteinSector
      • 2.3 Parametrizing the UnusedEnzymesSector
    • 3. Design Choices
      • 3.1 Total protein content
      • 3.2 Scaling kcat values
      • 3.3 Which conditions?
      • 3.4 Getting the validation data
    • 4. Working with the PAMparametrizer
      • 4.1 Building and running the PAMparametrizer
      • 4.2 Creating an ensemble of models
    • 5. Analyzing the Paramaterization Results
      • 5.1 The output
        • 5.1.1 Best_Individuals
        • 5.1.2 Computational_time
        • 5.1.3 Final_Errors
        • 5.1.4 sector_parameters
        • 5.1.5 reaction_weights
      • 5.2 Prebuilt analyses
        • 5.2.1 kcat distribution
        • 5.2.2 Flux prediction accuracy
        • 5.2.3 Protein Prediction accuracy
  • API reference
    • PAM_parametrizer
      • PAMparametrizer.PAM_parametrizer.KcatConstraintConfig
      • PAMparametrizer.PAM_parametrizer.PAM_data_classes
      • PAMparametrizer.PAM_parametrizer.pam_parametrizer
      • PAMparametrizer.PAM_parametrizer
    • genetic_algorithm_parametrization
      • PAMparametrizer.genetic_algorithm_parametrization.Evaluation.Fitfun_params_gaussian
      • PAMparametrizer.genetic_algorithm_parametrization.Evaluation.Fitfun_params_uniform
      • PAMparametrizer.genetic_algorithm_parametrization.Evaluation
      • PAMparametrizer.genetic_algorithm_parametrization.core_parametrization_gaussian
      • PAMparametrizer.genetic_algorithm_parametrization.core_parametrization_uniform
      • PAMparametrizer.genetic_algorithm_parametrization.ga_param
      • PAMparametrizer.genetic_algorithm_parametrization
    • utils
      • PAMparametrizer.utils.error_calculation
      • PAMparametrizer.utils.genetic_algorithm_analysis
      • PAMparametrizer.utils.pam_generation
      • PAMparametrizer.utils.pamparametrizer_analysis
      • PAMparametrizer.utils.pamparametrizer_setup
      • PAMparametrizer.utils.pamparametrizer_visualization
      • PAMparametrizer.utils.preprocessing
      • PAMparametrizer.utils.sampling_functions
      • PAMparametrizer.utils.sector_config_functions
      • PAMparametrizer.utils
PAMparametrizer
  • API reference
  • utils
  • View page source

utils

utils

  • PAMparametrizer.utils.error_calculation
  • PAMparametrizer.utils.genetic_algorithm_analysis
  • PAMparametrizer.utils.pam_generation
  • PAMparametrizer.utils.pamparametrizer_analysis
  • PAMparametrizer.utils.pamparametrizer_setup
  • PAMparametrizer.utils.pamparametrizer_visualization
  • PAMparametrizer.utils.preprocessing
  • PAMparametrizer.utils.sampling_functions
  • PAMparametrizer.utils.sector_config_functions
  • PAMparametrizer.utils
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