pyMechT’s documentation

pyMechT is a Python package for simulating the mechanical response of soft biological tissues. To start using, install it via pip as follows

$ conda create -n pymecht python=3.9 ipykernel
$ conda activate pymecht
$ pip install pymecht

Tutorial provided in this documentation is a good place to start, followed by several detailed examples.

pyMechT is a collection of modules for:

  • MatModel: defining material models

  • SampleExperiment: simulating experiments, such as uniaxial extension, biaxial extension, and inflation-extension. Simulations can be either disp_controlled() or force_controlled()

  • ParamDict: a custom dictionary class of a datastructure called Param, which facilitates storing/varying/fitting parameters

  • ParamFitter: fitting parameters to experimental data

  • RandomParameters and MCMC: Bayesian inference by running Monte Carlo (MC) and Markov chain Monte Carlo (MCMC) simulations

Structure of pyMechT

This package is developed and maintained by the Computational Biomechanics Research Group at the University of Glasgow and is hosted at github.

The ethos of pyMechT is to create simplified virtual experimental setups, rather than finite element analyses. Thus, varying parameters and running simulations is much faster, making it feasible to perform Bayesian inference and Markov Chain Monte Carlo analyses.

Tutorials:

Examples:

Theory:

Package Reference:

Indices and tables