pyABC
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User's guide

  • What is pyABC about?
  • Installation und Upgrading
  • Examples
    • Parameter inference
    • Model selection
    • Early stopping of model simulations
    • Resuming stored ABC runs
    • Using R with pyABC
    • Ordinary Differential Equations: Conversion Reaction
    • Markov Jump Process: Reaction Network
    • Multi-scale model: Tumor spheroid growth
    • Stochastic Differential Equation: Ion channel noise in Hodgkin-Huxley neurons
    • Adaptive Distances
    • Aggregating and weighting diverse data
    • Script based external simulators
    • Data plots
    • Noise
    • PEtab import and yaml2sbml
    • PEtab application example
    • Discrete parameters
    • Download the examples as notebooks
  • Parallel and Distributed Sampling
  • Data store
  • Visualization and analysis

About

  • Release Notes
  • About
  • References

Developer's guide

  • Contribute
  • Deploy

API reference

  • API reference
pyABC
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  • Examples
  • Edit on GitHub

Examples¶

The following examples should help to get a better idea of how to use pyABC.

  • Parameter inference
  • Model selection
  • Early stopping of model simulations
  • Resuming stored ABC runs
  • Using R with pyABC
  • Ordinary Differential Equations: Conversion Reaction
  • Markov Jump Process: Reaction Network
  • Multi-scale model: Tumor spheroid growth
  • Stochastic Differential Equation: Ion channel noise in Hodgkin-Huxley neurons
  • Adaptive Distances
  • Aggregating and weighting diverse data
  • Script based external simulators
  • Data plots
  • Noise
  • PEtab import and yaml2sbml
  • PEtab application example
  • Discrete parameters

Download the examples as notebooks¶

  • Parameter inference

  • Model selection

  • Early stopping of model simulations

  • Resuming stored ABC runs

  • Using R with pyABC

  • Ordinary Differential Equations: Conversion Reaction

  • Markov Jump Process: Reaction Network

  • Multi-scale model: Tumor spheroid growth

  • Stochastic Differential Equation: Ion channel noise in Hodgkin-Huxley neurons

  • Adaptive Distances

  • Aggregated Distances

  • External Simulators

  • Data plots

  • Measurement noise assessment

  • PEtab import and yaml2sbml

  • PEtab application example

  • Discrete parameters

Warning

Upgrade to the latest pyABC version before running the examples. If you installed pyABC some weeks (or days) a ago, some new features might have been added in the meantime. Refer to the Upgrading section on how to upgrade pyABC.

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