learning-goals.md

Installation and configuration

• A terminal (git bash)

• Miniconda

• git

• IDE (VSCode)

• GitHub account

Learning goals

General

• Working on the terminal (Unix shell)

• Python syntax and basic functionality

• Managing environments with conda

• Python libraries for (data) science

  • numpy

  • pandas

  • matplotlib

  • jupyter

  • scipy?

  • scikit-learn?

• Version control with git

• Collaborative coding via GitHub

• Contributing to open-source projects

• Creating Python packages?

Specific to this placement

• Familiarity with terminology used in analysing animal behaviour

• Familiarity with major pose estimation packages: DeepLabCut & SLEAP

• Familiarity with movement docs and codebase

Study Materials

Python for absolute beginners

• https://learnpythonthehardway.org/

• https://automatetheboringstuff.com/

Python and git for (data) science

• The Real Python Learning Paths

• Software Carpentries

  • The Unix Shell

  • Version Control with git

  • Programming with Python

  • Plotting and Programming in Python

• FreeCodeCamp Data analysis with Python

• Coursera Python for everybody specialisation

More CS-oriented

• CS50

NIU software skills courses

• NIU intro to software development with Python (beginner)

• Collaborating coding and software-dev good practices (intermediate)

• Python packaging (advanced)

Git explainers

• The git parable (conceptual intro)

• How git works zine (for more advanced practitioners)

Courses on analysing animal behaviour

• NIU video-based analysis of animal behaviour

• Cajal modern approaches to behavioural analysis

Papers on analysing animal behaviour

• Neuroscience Needs Behavior: Correcting a Reductionist Bias

• Quantifying behavior to understand the brain

• Open-source tools for behavioral video analysis: Setup, methods, and best practices

NIU docs

• General development guidelines

• Python-specific development guidelines

• Python cookiecutter