This is a quick package for building small networks of detailed, conductance-based neurons out of ion channels and synapses. The idea is that it's easy to use this template and add your own ion channels / synapses, with your choice of dynamics. Iteratively adding these components to a neuron is done using ModelingToolkit, which makes it scalable to any number of ion channels and synapses.

If you want a more flexible platform to build neuron models, with e.g. multiple compartments, from basic components you should check out the more comprehensive package Conductor.jl (in active development).

NeuronBuilder is available as a registered package and has a tagged release (v0.1.0)

#From Julia REPL
] add NeuronBuilder

Once you exit the package manager (ctrl+c), type using NeuronBuilder.

To try out the demo scripts:

1. From a terminal, clone this repository

git clone https://github.com/Dhruva2/NeuronBuilder.jl
cd NeuronBuilder.jl
git checkout v0.2.5

2. Navigate to the scripts folder. Once there, activate the environment

] activate .

3. Open a Julia session and run the script you want, for example include("neuron_liu.jl")

• A sodium channel is created with Liu.Na(g) or Prinz.Na(g) if the conductance has value g.
• To reproduce sets of channels as reported in the papers Liu et. al. 1998 and Prinz et. al. 2003 use the conversion factors Liu_conversion and Prinz_conversion to get the right units. You can see how these are specifically given in the scripts and are multiplying with the original g value from the papers.
• The g_values.jl file has a small collection of conductances coming from various sources. You can copy-paste any of these into the script that simulates a single neuron.

• The connected_STG.jl script shows how to add synapses between neurons and reproduces the triphasic rhythm of the STG found in Prinz et. al. 2004.
• Synapses also get a conversion factor which depends on the geometry of the somatic compartment.

• Fork NeuronBuilder
• Go to the src/assets folder, you'll find two modules called Liu and Prinz.
• Each module has a list of channels with specified dynamics
• You can copy-paste the structure of those modules, just changing the dynamics and channel names.
• Feel free to send us the library you built to push to the master branch! :)

This work was funded by European Research Council grant 716643 FLEXNEURO and HFSP grant RGY0069/2017, (Principal Investigator Timothy O’Leary).