NIX-Neo-workshop

---

title: "INCF virtual training weeks 2021" subtitle: "NIX-Neo workshop" author: "Michael Denker, Jan Grewe, Michael Sonntag, and Julia Sprenger"

date: 2021-08-30 to 2021-09-01

NIX-Neo-workshop

This repository contains (to read as will contain) all files required for the INCF NIX-Neo-workshop workshop.

The Workshop is taking place from the 30th August to the 01st September 2021; please check back to this repo during the week before the workshop for any additional information.

Requirements

To benefit from the workshop you need to have to have experience with the Python programming language.

Please make sure you have selected set up an environment as described below before the workshop starts so you can follow along. We cannot debug environment or installation issues during the workshop.

Before attending the workshop please make sure that either the machine you are working on is able to run jupyter notebooks and install python packages.

Either download the contents of the NIX-Neo-workshop repository via the web or use the command line to clone the repository using git clone https://gin.g-node.org/INCF-workshop-2021/NIX-Neo-workshop.git.

To make sure your machine is set up for the workshop, please install the Python requirements running pip install -r requirements.txt and start (jupyter noteboook requirements.jpynb) and run the requirements jupyter notebook before the workshop. We recommend using Anaconda as a Python virtual environment to make sure you are running the workshop in a clean Python environment.

Using Binder to run Jupyter notebooks online

If you are not able to use Jupyter notebooks on your machine, you can use Binder to run the required notebooks online. In this case please be aware, that any changes made to Jupyter notebooks and any files created are remote - you will need to manually save them to your local machine if you want to keep them.

To test running a Jupyter notebook from our course with Binder, either use this link or

• move to https://mybinder.org/
• select "Git repository" and add the URL "https://gin.g-node.org/INCF-workshop-2021/NIX-Neo-workshop".
• enter "requirements.ipynb" as Path to a notebook file.
• press the "launch" button and run the notebook as a test.

Please note that Binder is a free service and it might take a while for Notebooks to start and be available. Also it can happen, that after inactivity a running Binder notebook will be shut down automatically, so save files and progress locally on a regular basis.

Documentation

If you are interested, you can already read into the documentation for the NIX and the NEO projects, but this is not a pre-requisite for the course.