Tripod Neuron model

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The code presented here simulates a three-compartments neuron model. This package serves for reproducibility and future work based on two journal articles:

1. The Tripod neuron: a minimal structural reduction of the dendritic tree

2. Nonlinear dendritic integration supports Up-Down states in single neurons

The code in the branch master correspond to the one used in the second paper. It should be compatible also for the experiments in (1); if it is not, please use the code in the branch 'JPhysol2022'.

The package is composed of five folders:

• src: contains the source code of the Tripod model, with detailed Readme of the package.
• papers: contains the files for reproducing all the figures of the paper
• scripts: contains utilities
• data
• plots

This code base is using the Julia Language and DrWatson to make a reproducible scientific project named

Tripod

The Julia version used: julia = "1.8.2"

To (locally) reproduce this project, do the following:

0. Download this code base. Notice that raw data are typically not included in the git-history and may need to be downloaded independently.
1. Open a Julia console and do:

   julia> using Pkg
   julia> Pkg.add("DrWatson") # install globally, for using `quickactivate`
   julia> Pkg.activate("path/to/this/project")
   julia> Pkg.instantiate()
   

This will install all necessary packages for you to be able to run the scripts and everything should work out of the box, including correctly finding local paths.

The Tripod Neuron; A minimal reduction of the dendritic tree"

In the papers/dendritic_memory there are eight folders, one for each figure of the paper. Within it, there are the scripts that are used to reproduce the results and the panels.

Fig6 to Fig9 are obtained with data from relatively long simulations (between 5 mins to 1 hour on server for calculus with 24-threads). In order to facilitate testing of the package, we added pre-computed data in the folder data/dendritic_memory, the plot file will load the data from there. If you intend to re-compute it, the DrWatson.safesave function will automatically swap the files, the newer one will become accessible and the old data file will be renamed with filename_#1.

In scripts there is one file that is used to generate the style for the plots and one file that automatically run all the scripts in the paper folder. The run_all.jl file include all the files that have plot functions and generates the plots in plots/dendritic_memory; it does not run the files marked with <filename>_run.jl. These files may require long computation and should be run only if intended. If the run_all.jl script won't work for some unpredicted reason - we suggest to run it from within a REPL-, it is possible to reproduce the figures running each script separatedly. The scripts with the _long.jl will take time to run, but can be skipped if the data are in the folder.

The figures generated may present small variations to the ones presented in the paper becasue during the refactoring of the code small variations were made; for example, for consistency across the several stimuli patterns used in the experiments. The results are in agreement with the conclusion drawn in the manuscript.

This code base is using the Julia Language and DrWatson to make a reproducible scientific project named

Tripod