Zeke W. MSc Project Code

This repo contains the code library for the paper "Burst Coding Despite Unimodal Interval Distributions" by Williams et al.

Requirements

Python 3.6.6 was used with anaconda 4.4.0 for the project.

A list of all python libraries contained in the environment used on the project is provided in the file requirements.txt. However, not all of these libraries are needed for this project. I recommend checking the imports in each script and then using requirements.txt to be sure the correct version is used.

Folders

Results

Folder containing data required for plots. Labeled by figure number from paper.

This is not included in the git repo. Email the paper authors to get access.

Files

requirements.txt

Pip freeze of anaconda environment used for project. Note that not all the libraries listed are necessary for the project!

plot_figure3-6:

Code for plotting the associated figure. Each of these require the results folder to be in the current workspace and some of these require extra libraries contained in this repo.

simulate3-6

Code to simulate model and run analysis required for the associated figure of the paper. Requires cell_params3-6, cell_models and main_functions libraries. Note that simulate5 has suffix 1, 2 and simulate6 has suffix BSRM and SRM because two different models were used in the generation of each of these figures.

Note: For the given simulation to run you must change the parameters in the file lba_params so that they match the values used, in the paper, for the given figure. The default values are for figure 3.

main_functions

This library contains the core functions used to implement the decoding cell machinery and Stein's linear information rate analysis.

Uses cell params and lba_params files. Note: to reproduce a figure you must adjust the lba_params file accordingly (see above).

cell_models

This library contains a Gerstner style SRM model, and BSRM models for doublet bursts or a fixed, arbitrary number of intra-burst spikes. Specifically, this library allows one to simulate a population of any number of uncoupled cells, of the given model, with each cell receiving the same Ornstein-Uhlenbeck input.

Contains code to run (i) SRM0 model (simulator: method0) (ii) BSRM with doublets (simulator: method4) or with an arbitrary, fixed number of intra-burst spikes (simulator: method6).

Uses cell_params file.

gamma_renewal

Contains code to simulate a stationary gamma renewal process. This is used in figure 6 of the paper.

analyze_simulated

Contains code for various spiketrain statistics (LV, CV2, etc) and their supporting functions.

cell_params

Dictionary containing cell params used in cell_models code

lba_params ("lower bound analysis")

Dictionary containing params used in the model of decoding cell machinery and in Stein's lower bound information rate analysis.