Step-by-step instructions to getting started

1. Download and install Anaconda
2. Download and install git
3. Download and install Spyder from the standalone
   • Follow this tutorial on scientific data analysis in Spyder
4. Continue to setup your environment for analyzing IBL data
   • Make sure to link Spyder to your iblenv conda env: Settings / Python Interpreter / User the following Python interpreter / anaconda3/envs/iblenvs/bin/python

Python and data analysis references

• Know your way around the command line
  • Basic cheatsheet
• Understand what a virtual environment is
• Understand Git and GitHub
  • GitLectures
  • Git primer by Brad Voytek
  • Even better Git intro
  • Further practice: pull this wiki repo, add something in the Markdown language, and submit a pull request (see Home for instructions on how to contribute to the wiki).
• Learn the basics of Python
  • DataCamp has very good adaptive programming courses. Sign up with your @umail.leidenuniv.nl address using the link for free access.
  • Intro to Python & lab in cognition & perception, both by Todd Gureckis.
  • Students at Leiden University can follow the Introduction to Python course, offered by LIACS.
  • You can also access DataCamp learning resources with your Leiden Uni account.
• Think about the structure of data
  • The structure of data, by Todd Gureckis
  • Learn to work with the pandas and seaborn packages for data handling and visualization.
  • Pandas tutor with helpful dataviz.
• Once your code runs, make it better!
  • The Good Research Code Handbook is a fantastic guide to write elegant, organized code that doesn’t make you want to tear your hair out. Highly recommended.
  • Dan Larremore’s lab guides to clean code
  • Consider code review

Open data, open code, open science

• Might there be a dataset or a tool out there that does what you need? Check out this list of lists.

Computing resources

For most projects (especially those using behavioral data), your laptop will be more than sufficient to run Python . If you need more heavy lifting, there are a few options:

• ALICE supercomputer @ Leiden Uni
  • Get an account
• LISA / Cartesius clusters @ SurfSara
  • Apply through NWO. Very well managed, but since Leiden doesn ’t have a contract with SurfSara you have to apply to extend your account every year.

Remote computing on Windows

• MobaXTerm is your best bet for using ssh on Windows (for transferring data). For MobaXTerm to find your ssh keys, set the env variable in windows to be C:\Users\username, not P-drive! Ask Anne.