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
• Equipment
• Mentorship
• PhD resources
• Funny stuff

Organizing experiments and ideas

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

Choosing a topic

• How to Choose a Good Scientific Problem by U Alon

Reading papers

• Guides:
  • How to read a paper by S. Keshav
• Finding papers:
  • connected papers
  • inciteful
• Discussion forum:
  • Pubpeer: platform for discussions on papers post-publication, browser extensions

Data visualization

Principles

• Fundamentals of Data Visualization by C. 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 D. 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
  • Pylustrator
• MATLAB: Plot beautifier - MATLAB
• R: ggplot2

Statistics

• Common statistical tests are linear models (or: how to teach stats) - J. 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 D. Huff
• Spurious correlations
• P-hacking
• Anscombe's quartet

Reproducible research

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

Coding

Learning to code

• Elements of Data Science by A. Downey

General design principles and formatting

• General Principles:
  • A Philosophy of Software Design book, talk
  • The Good Research Code Handbook by P. 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

• Books:
  • How to write a scientific paper by C. Mack
• Videos:
  • The craft of writing effectively - UChicago
• Articles:
  • Some tips for writing science by M. Carandini
  • Whitesides' group: writing a paper
  • Rules of thumb for writing research articles by Hengl & Gould
  • Ten simple rules for structuring papers by Mensh & Kording
  • 10 tips on how we write papers by E. Sargent
  • Health care articles with simple and declarative titles were more likely to be in the Altmetric Top 100
  • Elsevier series on preparing a manuscript
  • How to write clearly
  • How to write consistently boring scientific literature by Sand-Jensen
  • How to write an excellent Review article
• Courses:
  • Writing in the Sciences on Coursera

Equipment

• Designs to 3D print: https://www.thingiverse.com/

Mentorship

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

PhD resources

• How to Pick a Graduate Advisor by Ben Barres
• How to Be a Graduate Advisee
• Doing a PhD: ten golden rules
• The importance of stupidity in scientific research by M Schwartz

Blogs

• https://labrigger.com (General)
• https://matt.might.net/articles/ (General & Computer Science)
• https://backreaction.blogspot.com/ (General & Physics)
• https://terrytao.wordpress.com/ (General & Maths)
• https://www.thetransmitter.org/ (Neuroscience)

Funny stuff

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

Other awesome lists

• https://github.com/deverte/awesome-science
• https://github.com/helenahartmann/awesome-PhD
• https://github.com/alirezasamar/awesome-phd
• https://github.com/pliang279/awesome-phd-advice
• https://phd-resources.github.io/general
• https://x.com/lei_zhang_lz/status/1474174707788304387?s=20