README.md

Awesome Science

A curated list of awesome resources for science and academia with a bias towards free and open source resources. Create a pull request or raise a github issue to add any resources to this list.

Contents

• Contents
• Organizing experiments and ideas
• Data visualization
• Statistics
• Reproducible research
• Coding
• Open source journals
• Writing
• Mentorship

Organizing experiments and ideas

• Obsidian - free and open source mardown-based note taking software. There's a great large community continuously developping more features.

Reading papers

• How to read a paper by S. Keshav
• Pubpeer: platform for discussions on papers post-publication, browser extensions

Data visualization

Principles

• Fundamentals of Data Visualization by Claus O. Wilke
• Ten Simple Rules for Better Figures
• Weissgerber et al., 2015, PLOS Biology
• Friends Don't Let Friends Make Bad Graphs
• How to lie with statistics [and data visualization] by Darrell Huff
• Making figures - basic design principles
• Colormaps:
  • The misuse of colour in science communication, colormap: crameri
  • Perceptually-uniform colormaps - Python
• Colorblind-friendly:
  • Online tool to check your figures: coblis
  • MATLAB tool to check your figures: prettify_matlab

Generating and refining figures

• Inkscape
• Scientific-inkscape plugin
• Getting logos, icons, ect.:
  • Biorender
  • SVG repo
• Python: Seaborn, intro to the ideas behind seaborn here; matplotlib
• MATLAB: Plot beautifier - MATLAB
• R: ggplot2

Statistics

• Common statistical tests are linear models (or: how to teach stats) - Jonas Kristoffer Lindeløv
• One test to rule them all: generating null distributions from your data
  • Blog post by Allen Downey on this
  • Chapter in Elements of Data Science on this
• How to lie with statistics by Darrell Huff
• Spurious correlations

Reproducible research

• Open, rigorous and reproducible research: A practitioner’s handbook
• Open science course - Neuromatch

Coding

Learning to code

• Elements of Data Science by Allen Downey

General design principles and formatting

• General Principles:
  • A Philosophy of Software Design book, talk
  • The Good Research Code Handbook by Patrick J Mineault
• Code formaters:
  • Python: Black
  • MATLAB: MBeautifier
  • R: styler
• Code review

Open source journals

• Scientific results:
  • PLOS
  • eLife
• Code:
  • Peer-reviewed code publication: Journal of Open Source Software (JOSS)
  • Code publication: Zenodo, guide to adding zenodo code to google scholar profile here.

Writing

• Some tips for writing science by Matteo Carandini
• Rules of thumb for writing research articles by Hengl & Gould
• Ten simple rules for structuring papers by Mensh & Kording
• Health care articles with simple and declarative titles were more likely to be in the Altmetric Top 100
• Elsevier series on preparing a manuscript

Mentorship

• Yearly Planning Meetings: Individualized Development Plans Aren’t Just More Paperwork
• Wellcome: Tips for running your own research group

Funny stuff

• xkcd
• The far side
• PhD comics
• Lego grad student
• PhD simulator