NeuroHackademy 2026 Curriculum

This repository contains the curriculum for the 2026 NeuroHackademy! Instructors can put course materials in this repository, and they will appear in your home directory on the NeuroHackademy 2026 JupyterHub.

This README file additionally contains some general information on using the JupyterHub.

Using a terminal on the JupyterHub

When you first open the JupyterLab interface on the NeuroHackademy JupyterHub, it should open a "launcher" panel. You can also open such a panel by pressing the blue "+" button in the upper left corner of the interface. One of the options toward the bottom of the launcher panel is to launch a terminal. The terminal that is launched is just like a terminal on your local machine except that it is running in the cloud on the JupyterHub. You can use this interface to run shell commands including git commands.

Setting up Git and GitHub on the NeuroHackademy JupyterHub

Git is used heavily in the NeuroHackademy. It has already been installed on the NeuroHackademy JupyterHub, but you'll need to configure it before you can use it. Configuring git requires just a few steps:

1. Tell git your name and email address.
2. Create an ssh key for authentication on the JupyterHub and provide GitHub with this key.
3. Optionally, configure other items such as your preferred editor.

These steps are explained in detail by the Software Carpentry tutorial on Git and GitHub. In particular, this page explains the basic git configuration and this page explains how to set up SSH keys.

If you are unfamiliar with these steps, we recommend that you attend the introductory session on Git and GitHub on Tuesday (July 14th) at 1:30pm where we will walk through them as a group.

Uploading and Downloading Data

You can upload data to the JupyterHub by dragging files into the left-side panel (the file browser) in the JupyterLab interface. You can also right-click on a file in the same panel to download it.

If you need to download several files or an entire directory, you can first tar/zip the files then untar/unzip them once you download them. For example, if you want to download everything in a directory called "work/" that exists in your home directory on the Hub:

tar zcf work.tar.gz work/

This creates a file work.tar.gz that contains the work/ folder and all of its contents. You can then download that file and unzip it locally.