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Analog Electronic Neurons project in the Hastings lab.

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Analog Electronic Neurons

This is a project concerning the implementation of biomimetic neurons (of the FitzHugh-Nagumo model) onto analog circuits, with the ultimate goal being to simulate a worm (C. elegans).

Installing dependencies

You will need to have the Julia language installed, on version 1.4 or higher. You can download it at https://julialang.org/downloads/; once you have done that, clone the repo, and run this command in the root directory of the project:

julia --project=. -e 'using Pkg; Pkg.instantiate()'

This will install all the Julia package dependencies.

Project Setup

aen          <- Project's main folder.
│
├── _research        <- WIP scripts, code, notes, comments,
│   |                   to-dos and anything in an alpha state.
│   └── tmp          <- Temporary data folder.
│
├── data             <- **Immutable and add-only!**
│   ├── sims         <- Data resulting directly from simulations.
│   ├── exp_pro      <- Data from processing experiments.
│   └── exp_raw      <- Raw experimental data.
│
├── plots            <- Self-explanatory.
├── notebooks        <- Jupyter, Weave or any other mixed media notebooks.
│
├── papers           <- Scientific papers resulting from the project.
│
├── scripts          <- Various scripts, e.g. simulations, plotting, analysis,
│   │                   The scripts use the `src` folder for their base code.
│   └── intro.jl     <- Simple file that uses DrWatson and uses its greeting.
│
├── src              <- Source code for use in this project. Contains functions,
│                       structures and modules that are used throughout
│                       the project and in multiple scripts.
│
├── test             <- Tests for code in src.
│   └── runtests.jl  <- Script to run all tests.
│
├── README.md        <- You are here.
├── .gitignore       <- ignores latex-compilation related files and filesystem artifacts.
│
├── Manifest.toml    <- Contains full list of exact Julia package versions used currently.
└── Project.toml     <- Main Julia project file, allows activation and installation.
                        Includes DrWatson by default.

Making changes

If you want to make a change to a file, please branch out from master and submit a pull request. Since this is a shared repo, the recommended naming scheme or a branch is <initials>/<short-description>. An example is as/depwarns.

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