├── image.png ├── HowtoReadPaper.pdf ├── addingZenodoToGoogleScholar.md └── README.md /image.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Julie-Fabre/awesome_science/HEAD/image.png -------------------------------------------------------------------------------- /HowtoReadPaper.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Julie-Fabre/awesome_science/HEAD/HowtoReadPaper.pdf -------------------------------------------------------------------------------- /addingZenodoToGoogleScholar.md: -------------------------------------------------------------------------------- 1 | To add your code on zenodo to your google scholar profile (and get citations show up): 2 | 3 | - Your code on zenodo needs to be cited in a format like this: 4 | 5 | > Julie M.J. Fabre, Enny H. van Beest, Andrew J. Peters, Matteo Carandini, & Kenneth D. Harris. (2023). Bombcell: automated curation and cell classification of spike-sorted electrophysiology data. Zenodo. https://doi.org/10.5281/zenodo.8172821 6 | 7 | - You need to add it to google scholar like this: 8 | ![GoogleScholar](image.png) -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # Awesome Science [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://github.com/sindresorhus/awesome) 2 | 3 | A curated list of awesome resources for science and academia with a bias towards free and open source resources. This is essentially a compilation of guides and tips I find/found helpful and of science software that I use and love. Create a pull request or raise a github issue to add any resources to this list. 4 | 5 | ### Contents 6 | 7 | 8 | 9 | * [Contents](#contents) 10 | * [Organizing experiments and ideas](#organizing-experiments-and-ideas) 11 | * [Data visualization](#data-visualization) 12 | * [Statistics](#statistics) 13 | * [Reproducible research](#reproducible-research) 14 | * [Coding](#coding) 15 | * [Open source journals](#open-source-journals) 16 | * [Writing](#writing) 17 | * [Equipment](#equipment) 18 | * [Mentorship](#mentorship) 19 | * [PhD resources](#phd-resources) 20 | * [Funny stuff](#funny-stuff) 21 | 22 | 23 | ### Organizing experiments and ideas 24 | 25 | - [Obsidian](https://obsidian.md/) - free and open source mardown-based note taking software. There's a great large community continuously developping more features. 26 | 27 | ### Choosing a topic 28 | - [How to Choose a Good Scientific Problem by U Alon](https://www.cell.com/molecular-cell/fulltext/S1097-2765(09)00641-8) 29 | 30 | ### Reading papers 31 | - Guides: 32 | - [How to read a paper by S. Keshav](HowtoReadPaper.pdf) 33 | - Finding papers: 34 | - [connected papers](https://www.connectedpapers.com/) 35 | - [inciteful](https://inciteful.xyz) 36 | - Discussion forum: 37 | - [Pubpeer: platform for discussions on papers post-publication](https://pubpeer.com/), [browser extensions](https://www.pubpeer.com/static/extensions) 38 | 39 | ### Data visualization 40 | #### Principles 41 | - [Fundamentals of Data Visualization by C. Wilke](https://clauswilke.com/dataviz) 42 | - [Ten Simple Rules for Better Figures](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003833) 43 | - [Weissgerber et al., 2015, PLOS Biology](https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002128) 44 | - [Friends Don't Let Friends Make Bad Graphs](https://github.com/cxli233/FriendsDontLetFriends) 45 | - [How to lie with statistics [and data visualization] by D. Huff](https://archive.org/details/HowToLieWithStatistics_201608) 46 | - [Making figures - basic design principles](https://www.nature.com/articles/d41586-024-03477-0) 47 | - Colormaps: 48 | - [The misuse of colour in science communication](https://www.nature.com/articles/s41467-020-19160-7), colormap: [crameri](https://www.fabiocrameri.ch/colourmaps/) 49 | - [Perceptually-uniform colormaps - Python](https://github.com/holoviz/colorcet) 50 | - Colorblind-friendly: 51 | - Online tool to check your figures: [coblis](https://www.color-blindness.com/coblis-color-blindness-simulator/) 52 | - MATLAB tool to check your figures: [prettify_matlab](https://github.com/Julie-Fabre/prettify_matlab) 53 | 54 | #### Generating and refining figures 55 | ##### Editing software 56 | - [Inkscape](https://inkscape.org/) 57 | - [Scientific-inkscape plugin](https://github.com/burghoff/Scientific-Inkscape) 58 | ##### Getting logos, icons, ect. 59 | - [Biorender](https://www.biorender.com/) 60 | - [SVG repo](https://www.svgrepo.com/) 61 | ##### Plotting toolboxes 62 | - Python: [Seaborn](https://seaborn.pydata.org/), intro to the ideas behind seaborn [here](https://seaborn.pydata.org/tutorial/introduction.html); [matplotlib](https://matplotlib.org/) 63 | - R: [ggplot2](https://ggplot2.tidyverse.org/) 64 | ##### Tips and automated toolboxes to beautify figures 65 | - MATLAB: [Plot beautifier - MATLAB](https://github.com/Julie-Fabre/prettify_matlab) 66 | - Python: [Pylustrator](https://github.com/rgerum/pylustrator) 67 | - [Python] [tips by Guido Meijer](https://bsky.app/profile/guidomeijer.com/post/3m3cdjoedfk2l) 68 | 69 | 70 | ### Statistics 71 | - [Youtube series on statistics - R. McElreath](https://www.youtube.com/playlist?list=PLDcUM9US4XdPz-KxHM4XHt7uUVGWWVSus) 72 | - [Common statistical tests are linear models (or: how to teach stats) - J. Lindeløv](https://lindeloev.github.io/tests-as-linear/) 73 | - One test to rule them all: generating null distributions from your data 74 | - [Blog post by Allen Downey on this](https://allendowney.blogspot.com/2011/05/there-is-only-one-test.html) 75 | - [Chapter in Elements of Data Science on this](https://allendowney.github.io/ElementsOfDataScience/13_hypothesis.html#the-hypothesis-testing-framework) 76 | - [How to lie with statistics by D. Huff](https://archive.org/details/HowToLieWithStatistics_201608) 77 | - [Spurious correlations](https://www.tylervigen.com/spurious-correlations) 78 | - [P-hacking](https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002106) 79 | - [Anscombe's quartet](https://en.wikipedia.org/wiki/Anscombe%27s_quartet) 80 | 81 | ### Reproducible research 82 | - [Open, rigorous and reproducible research: A practitioner’s handbook](https://stanforddatascience.github.io/best-practices/index.html) 83 | - [Open science course - Neuromatch](https://openscience.neuromatch.io/) 84 | 85 | ### Coding 86 | #### Learning to code 87 | - [Elements of Data Science by A. Downey](https://allendowney.github.io/ElementsOfDataScience/) 88 | 89 | #### General design principles and formatting 90 | - General Principles: 91 | - A Philosophy of Software Design [book](https://milkov.tech/assets/psd.pdf), [talk](https://www.youtube.com/watch?v=bmSAYlu0NcY&ab_channel=TalksatGoogle) 92 | - [The Good Research Code Handbook by P. Mineault](https://goodresearch.dev/) 93 | - Code formaters: 94 | - Python: [Black](https://github.com/psf/black) 95 | - MATLAB: [MBeautifier](https://github.com/davidvarga/MBeautifier) 96 | - R: [styler](https://styler.r-lib.org/) 97 | - [Code review](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1012375) 98 | 99 | ### Open source journals 100 | - Scientific results: 101 | - [PLOS](https://plos.org/) 102 | - [eLife](https://elifesciences.org/) 103 | - Code: 104 | - Peer-reviewed code publication: [Journal of Open Source Software (JOSS)](https://joss.theoj.org/) 105 | - Code publication: [Zenodo](https://zenodo.org/), guide to adding zenodo code to google scholar profile [here](addingZenodoToGoogleScholar.md). 106 | 107 | ### Writing 108 | - Books on writing: 109 | - [How to write a scientific paper by C. Mack](https://spie.org/samples/9781510619142.pdf) 110 | - Videos on writing: 111 | - [The craft of writing effectively - UChicago](https://youtu.be/vtIzMaLkCaM?si=DHqD5IsoSB4xQjQy) 112 | - Articles on writing: 113 | - [Some tips for writing science by M. Carandini](https://www.eneuro.org/content/9/6/ENEURO.0497-22.2022.abstract) 114 | - [Whitesides' group: writing a paper](https://www.gmwgroup.harvard.edu/files/gmwgroup/files/895.pdf) 115 | - [Rules of thumb for writing research articles by Hengl & Gould](https://webapps.itc.utwente.nl/librarywww/papers/hengl_rules.pdf) 116 | - [Ten simple rules for structuring papers by Mensh & Kording](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005619) 117 | - [10 tips on how we write papers by E. Sargent](https://www.sciencedirect.com/science/article/pii/S2590238522005434) 118 | - [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) 119 | - [Elsevier series on preparing a manuscript](https://www.elsevier.com/connect/11-steps-to-structuring-a-science-paper-editors-will-take-seriously) 120 | - [How to write clearly](http://www.harmonize.com/probe/BulletinEditors/BE-Manual/Write_cl.htm) 121 | - [How to write consistently boring scientific literature by Sand-Jensen](https://nsojournals.onlinelibrary.wiley.com/doi/epdf/10.1111/j.0030-1299.2007.15674.x) 122 | - [How to write an excellent Review article](https://www.nature.com/articles/s44222-024-00256-4) 123 | - Courses on writing: 124 | - [Writing in the Sciences on Coursera](https://www.coursera.org/learn/sciwrite) 125 | 126 | ### Equipment 127 | - Designs to 3D print: https://www.thingiverse.com/ 128 | - Open source 3D design software: [solvespace](https://solvespace.com/index.pl) 129 | 130 | ### Mentorship/starting your lab 131 | - [Yearly Planning Meetings: Individualized Development Plans Aren’t Just More Paperwork](https://www.cell.com/molecular-cell/fulltext/S1097-2765(15)00307-X) 132 | - [Wellcome: Tips for running your own research group](https://wellcome.org/sites/default/files/research-careers-tips-running-research-group-2018-05-17.pdf) 133 | - [Advice on starting your lab from Tim Behrens](https://users.fmrib.ox.ac.uk/~behrens/Startingalab.htm) 134 | - [getting-a-job-in-french-academia](https://trialsanderrors.substack.com/p/getting-a-job-in-french-academia) 135 | - ["The SAFE Labs Handbook: community-driven commitments for group leaders to improve lab culture"](https://www.biorxiv.org/content/10.1101/2025.05.27.655799v1.full.pdf) 136 | 137 | ### PhD resources 138 | - [How to Pick a Graduate Advisor by Ben Barres](https://www.cell.com/neuron/pdf/S0896-6273(13)00907-0.pdf) 139 | - [How to Be a Graduate Advisee](https://www.cell.com/neuron/fulltext/S0896-6273(13)01191-4) 140 | - [Doing a PhD: ten golden rules](https://www.nature.com/articles/s41390-022-01950-y.pdf) 141 | - [The importance of stupidity in scientific research by M Schwartz](https://journals.biologists.com/jcs/article/121/11/1771/30038/The-importance-of-stupidity-in-scientific-research) 142 | 143 | 144 | ### Blogs 145 | - https://labrigger.com (General) 146 | - https://matt.might.net/articles/ (General & Computer Science) 147 | - https://backreaction.blogspot.com/ (General & Physics) 148 | - https://terrytao.wordpress.com/ (General & Maths) 149 | - https://www.thetransmitter.org/ (Neuroscience) 150 | 151 | ### Funny stuff 152 | - [xkcd](https://xkcd.com/) 153 | - [The far side](https://www.thefarside.com/) 154 | - [PhD comics](https://phdcomics.com/comics/most_popular.php) 155 | - [Lego grad student](https://brickademics.com/gallery) 156 | - [PhD simulator](https://research.wmz.ninja/projects/phd/index.html) 157 | 158 | ### Other awesome lists 159 | - https://github.com/deverte/awesome-science 160 | - https://github.com/helenahartmann/awesome-PhD 161 | - https://github.com/alirezasamar/awesome-phd 162 | - https://github.com/pliang279/awesome-phd-advice 163 | - https://phd-resources.github.io/general 164 | - https://x.com/lei_zhang_lz/status/1474174707788304387?s=20 165 | --------------------------------------------------------------------------------