Software Resources

Overview of resources related to programming, Python, Git(Hub), Shell and programming communities.

General Resources

• The Turing Way

• Overview of guided workshops, R/Python/SQL/Git/Shell courses

• Stack Overflow

• Research Reproducibility and Open Science by Hao Ye

• Social coding: sharing and citing software by CodeRefinery

• Debugging Bingo by Ji Son

• Computational Tools for Reproducible Science (with an R focus)

• NixOS

• Nextjournal

• How to make your script ready for publication

• Example of a workflow: ‘The task is a quantum of workflow’

• Open Research Primers

• Calmcode.io

• Text editors for Mac: Atom, Subline Text, TextEdit, BBEdit, Visual Studio Code

• Top Tips to Start Coding in Academia

• Presentation by Daniel Katz on Computational Reproducibility (intermediate/advanced)

• Writing clear code by Karl Broman

• Writing Clean Scientific Software by Nicolas Murphy

Shell/Unix

• Five reasons why researchers should learn to love the command line

• Recording of the Automating Task lessonby SoftwareSaved

• Data Science at the Command Line by Jeroen Janssen

• Learn Linux commands by playing a simple text adventure

• Learning Bash

Git(Hub)

• OLS GitHub intro (OLS1) and a more extensive intro for OLS2

• GitHub intro by Vicky Steeves (repository)

• GitHub’s introduction on branches

• A successful Git branching model

• Git + social coding from Code Refinery

• Recording of the Git lessonby SoftwareSaved

• The Git Parable by Tom Preston-Werner

• Getting the most out of git (Intermediate)

• Pro Git

• Git flow

• Git/GitHub primer (beginner)

• Git Resources by Paula Andrea Martinez

• Git configuration files

• Learn Git Branching

• OHBM Brainhack 2021 - Traintrack: Version control

• What is Github (3-4 min video)

• Version Control Systems: Keep Your Code in Order!

• Ten Simple Rules for Taking Advantage of Git and GitHub (Perez-Riverol et al. 2016)

• Introduction to Git (more theoretical + GitLab)

Python

• Practical Python Programming by David Beazley 

• Packages

  • Python Package Best Practices

  • Jupytext

• Recording of a Python Carpentry Workshop by SoftwareSaved using Jupyter Lab (part 1) (part 2)

• Teaching and Learning with Jupyter

• Hypothesis library

• Python videos (beginner?)

• Can you speak Python?

• Research Software Engineering with Python

• Maneage 

• Jupyter notebooks: Friends or foes?

• Ten simple rules for writing and sharing Computational analyses in Jupyter Notebooks (Rule et al. 2019)

• Intermediate Python Workshop

• Build a Dashboard with Python Plotly Dash (webinar by Laura Gutierrez Funderburk)

R

Please find a curated list for R resources at the TU Delft R Café

Communities

• Code Newbies (@CodeNewbies)

• Codecademy (@Codecademy)

• Stackademic (@StackademicHQ)

• Code .org (@codeorg)

• Women Who Code (@WomenWhoCode)

• Girls Who Code (@GirlsWhoCode)

• Free Code Camp (@freeCodeCamp)

• Black Girls Code (@BlackGirlsCode)

• Design+Code (@designcodeio)

• Microsoft Make Code (@MSMakeCode)

• CodeHS (@CodeHS)

Funding

• Sovereign Tech Fund