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https://github.com/Julie-Fabre/awesome_science

A curated list of awesome resources for science and academia.
https://github.com/Julie-Fabre/awesome_science

List: awesome_science

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A curated list of awesome resources for science and academia.

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README 

        
# Awesome Science  [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://github.com/sindresorhus/awesome)



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](#contents)

* [Organizing experiments and ideas](#organizing-experiments-and-ideas)

* [Data visualization](#data-visualization)

* [Statistics](#statistics)

* [Reproducible research](#reproducible-research)

* [Learning to code](#learning-to-code)

* [Publication-ready plots](#publication-ready-plots)

* [Publication-ready code](#publication-ready-code)

* [Open source journals](#open-source-journals)

* [Writing](#writing)



## Organizing experiments and ideas



- [Obsidian](https://obsidian.md/) - 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](HowtoReadPaper.pdf)

- [Pubpeer: platform  for discussions on papers post-publication](https://pubpeer.com/), [browser extensions](https://www.pubpeer.com/static/extensions)



## Data visualization



- [Fundamentals of Data Visualization by Claus O. Wilke](https://clauswilke.com/dataviz)

- [Ten Simple Rules for Better Figures](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003833)

  [Weissgerber et al., 2015, PLOS Biology](https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002128)

- [Friends Don't Let Friends Make Bad Graphs](https://github.com/cxli233/FriendsDontLetFriends)

- Colormaps:

  - [The misuse of colour in science communication](https://www.nature.com/articles/s41467-020-19160-7), colormap: [crameri](https://www.fabiocrameri.ch/colourmaps/)

  - [Perceptually-uniform colormaps - Python](https://github.com/holoviz/colorcet)

- Colorblind-friendly:

  - Online tool to check your figures: [coblis](https://www.color-blindness.com/coblis-color-blindness-simulator/)

  - MATLAB tool to check your figures: [prettify_matlab](https://github.com/Julie-Fabre/prettify_matlab)

 

## Statistics

- [Common statistical tests are linear models (or: how to teach stats) - Jonas Kristoffer Lindeløv](https://lindeloev.github.io/tests-as-linear/)

- One test to rule them all: generating null distributions from your data

  - [Blog post by Allen Downey on this](https://allendowney.blogspot.com/2011/05/there-is-only-one-test.html)

  - [Chapter in Elements of Data Science on this](https://allendowney.github.io/ElementsOfDataScience/13_hypothesis.html#the-hypothesis-testing-framework)



## Reproducible research 



- [Open, rigorous and reproducible research: A practitioner’s handbook](https://stanforddatascience.github.io/best-practices/index.html)



## Learning to code 

- [Elements of Data Science by Allen Downey](https://allendowney.github.io/ElementsOfDataScience/)



## Publication-ready plots



- [Inkscape](https://inkscape.org/)

- [Scientific-inkscape plugin](https://github.com/burghoff/Scientific-Inkscape)

- Getting logos, icons, ect.:

   - [Biorender](https://www.biorender.com/)

   - [SVG repo](https://www.svgrepo.com/)

- Python: [Seaborn](https://seaborn.pydata.org/), intro to the ideas behind seaborn [here](https://seaborn.pydata.org/tutorial/introduction.html); [matplotlib](https://matplotlib.org/)

- MATLAB: [Plot beautifier - MATLAB](https://github.com/Julie-Fabre/prettify_matlab)

- R: [ggplot2](https://ggplot2.tidyverse.org/)



## Publication-ready code 



- General Principles:

  - A Philosophy of Software Design [book](https://milkov.tech/assets/psd.pdf), [talk](https://www.youtube.com/watch?v=bmSAYlu0NcY&ab_channel=TalksatGoogle)

  - [The Good Research Code Handbook by Patrick J Mineault](https://goodresearch.dev/)

- Code formaters: 

  - Python: [Black](https://github.com/psf/black)

  - MATLAB: [MBeautifier](https://github.com/davidvarga/MBeautifier)

  - R: [styler](https://styler.r-lib.org/)

  

## Open source journals



- Scientific results:

  - [PLOS](https://plos.org/)

  - [eLife](https://elifesciences.org/)

- Code:

  - Peer-reviewed code publication: [Journal of Open Source Software (JOSS)](https://joss.theoj.org/)

  - Code publication: [Zenodo](https://zenodo.org/), guide to adding zenodo code to google scholar profile [here](addingZenodoToGoogleScholar.md). 



## Writing



- [Some tips for writing science by Matteo Carandini](https://www.eneuro.org/content/9/6/ENEURO.0497-22.2022.abstract)

- [Rules of thumb for writing research articles by Hengl & Gould](https://webapps.itc.utwente.nl/librarywww/papers/hengl_rules.pdf)

- [Ten simple rules for structuring papers by Mensh & Kording](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005619)

- [Health care articles with simple and declarative titles were more likely to be in the Altmetric Top 100](https://www.sciencedirect.com/science/article/pii/S0895435616308538?via%3Dihub)

- [Elsevier series on preparing a manuscript](https://www.elsevier.com/connect/11-steps-to-structuring-a-science-paper-editors-will-take-seriously)



## Because we all need a laugh sometimes.. 

- [xkcd](https://xkcd.com/)

- [The far side](https://www.thefarside.com/)