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.