biophysics_fitting ❭ exploration_from_seedpoint

exploration_from_seedpoint

Explore viable biophysical models from a given seedpoint. Given the following empirical constraints:

  • a set of biophysical parameters

  • a morphology

  • empirically recorded responses to defined stimulus protocols (see e.g. get_hay_problem_description()).

this package provides methods and full workflows that allow you to make random variations on the input biophysical parameters, run the stimulus protocols on the cell, and evaluate how much they deviate from the empirically recorded mean. Eventually, this random walk through parameter space can explore very diverse biophysical models that are all within the empirical constraints.

Functions

evaluation_function_incremental_helper(p, s, cutoffs, stim_order, verbose, evaluators_by_stimulus, additional_evaluation_functions, objectives_by_stimulus)

Helper function for the evaluation function.

Modules

RW

Perform a random walk through parameter space starting from a seed point.

RW_analysis

This module provides routines to analyze the results of a random walk exploration through biophysical parameter space.

utils

Convenience functions for the exploration_from_seedpoint module.