CSHL

Python material for the Cold Spring Harbor Laboratory Ion Channel and Neural Circuits Summer School.

Installation

Clone git repo to your computer

• You can use the desktop git : https://desktop.github.com/
• Or use the command line :

cd <path where you want to store the CSHL folder>

git clone https://github.com/afmontarras/CSHL.git

Copy the folder (create your playground)

During the course, the reference notebooks will be updated daily following your progress. You will want to create/modify them yourself day by day. So copy the cloned folder so that your own changes will not be affected by updating (pull) the git.

Environment Manager

You need to install Miniforge:

• Miniforge/mamba: https://github.com/conda-forge/miniforge (https://mamba.readthedocs.io/en/latest/index.html)

Create your CSHL environment

Write in your terminal:

cd <path to CSHL directory>

conda update -n base -c conda-forge conda

conda env create --name CSHL --file CSHL.yml

This will create a CSHL python environment based on the CSHL.yml file present in the CSHL folder. It contains every package you need to start working with th notebooks. You need to activate the environment to work with it: conda activate CSHL.

Launch jupyter lab

conda activate CSHL
jupyter lab

Update actions :

- CSHL git repo

cd <path to CSHL directory>
git pull

- CSHL environment

You need to be on the base environment (easiest way is to open a new terminal):

conda env update --name CSHL --file CSHL.yml