The In Silico Framework (ISF) - hotzone

.

ISF is an In Silico Framework for multi-scale modeling and analysis of in vivo neuron-network mechanisms. This repository provides a fork of ISF for reproducing simulations of the study 'Thalamus enables active dendritic coupling of inputs arriving at different cortical layers'.

A minimal interactive demo is accessible here:

Documentation

Web-hosted documentation is available here

You can self-host using

pixi r build_docs
pixi r host_docs

Installation

Installation instructions can be found here, but are repeated below for convenience.

This version of ISF is available for Linux and macOS.

For installation and environment management, ISF uses pixi. You can install pixi from the CLI by running:

curl -fsSL https://pixi.sh/install.sh | sh

You may need to restart your shell, or source your shell configuration for the pixi command to be available..

Once pixi is available, you can install this version of ISF by running:

git clone https://github.com/mpinb/in_silico_framework_hot_zone.git --depth 1 &&
cd in_silico_framework_hot_zone &&
pixi install

Usage

Launch a jupyter server:

pixi r launch_jupyter_server

Launch a dask server and workers for parallel computing (optional, but recommended):

pixi r launch_dask_server

pixi r launch_dask_workers

You can then connect to the jupyter server in your browser and start coding using ISF.

Tutorials

Please visit the tutorials (either in getting_started/tutorials or on the documentation page) for a walkthrough of ISF's most important workflows.