Welcome to parPE’s documentation!

Contents:

• Usage
  • Examples
    • Model simulation, optimization, analysis
    • Hierarchical optimization
    • Mini-batch optimization
  • Parameter estimation for PEtab/SBML models using parPE
    • Introduction
    • Workflow overview
    • Notation
    • Building PEtab
    • Model processing
    • Building parameter estimation executable
    • Generating an HDF5 input file for parPE parameter optimization
    • Running parameter optimization and further analyses
  • Running parameter optimization for an AMICI model using parpe::OptimizationApplication
    • Command line options
    • Output explained
    • Environment variables
  • Running AMICI simulations for parameters from an optimization result file using main_simulator.cpp
  • Using parPE with charliecloud
    • parPE base docker image
    • Running the example model
    • Optimizing a PEtab model
  • Using parPE with Snakemake
    • Parameter estimation
  • HDF5 data file structure
    • Parameter estimation input files
    • Parameter estimation output files
    • Simulation result files
  • Mini-batch optimization with parPE
    • Using the mini-batch optimization solver of parPE
    • Setting mini-batch optimization specific hyperparameters
    • Choosing hyperparameters
    • Reporting of objective function values and gradients: Important differences
• parPE C++ API
  • Class Hierarchy
  • File Hierarchy
  • Full API
    • Namespaces
    • Classes and Structs
    • Enums
    • Functions
    • Variables
    • Defines
    • Typedefs
• Python package
• FAQ

Indices and tables

• Index

• Module Index

• Search Page