A-microbiologist-wants-to-compute

In June 2020, I started to learn how to (properly!) compute the microbiome data.

Here, I'm collecting online resources that made this learning journey easier and fun.

WIP: Still learning and updating this collection! If you have some of your favourite bioinformatics learning material, feel free to let me know.

KUDOS to all bioinformaticians and computational scientists who are sharing their knowledge!

✅ PARTICULARLY worked for me

Bioinformatics for beginners

✅ Code Club by @PatSchloss
✅ Modern Statistics for Modern Biology by @SherlockpHolmes and @wolfgangkhuber
Biostar Handbook by István Albert
Bioinformatics data skills by @vsbuffalo
Examples from Practical computing for biologists by @caseywdunn @beroe
The Missing Semester of Your CS Education by @anishathalye @jonhoo @jjgort
Python Scripting for Computational Molecular Science by @jessica_a_nash @ARingerMcDonald
Canadian Bioinformatics Workshops by @Bioinfodotca *Past workshop content is available under a Creative Commons License here or here.
Bioinformatics Algorithms: An Active Learning Approach by Phillip Compeau and Pavel Pevzner
Rosalind exercises
2021 Microbiome Informatics Webinars by OSU Center of Microbiome Science
Bioinformatics Workbook A tutorial to help scientists design their projects and analyze their data.
An Introduction to Applied Bioinformatics by Gregory Caporaso.
✅ Metagenomics tools etc. by Big Data Biology Lab.

PLUS, check out this list of bioinformatics books here,

📻 podcasts:

✅ The bioinformatics chat produced by Roman Cheplyaka and hosted by Roman and Jacob Schreiber
The Bioinformatics and Beyond Podcast by Leo Elworth and Ep: Wet Lab / Dry Lab Transitioning with Dr. Willian da Silveira

& What is a bioinformatics postdoc? The experienced bioinformaticians Fatemeh Vafaee, Matt Field, Nikeisha Caruana, Philipp Bayer, Thomas Quinn, Ignatius Pang answering questions such as:

What is a bioinformatics postdoc?

Tips for landing a postdoc position?

Finding a mentor?

What are the challenges?

How to handle these challenges?

A cartoon guide to bioinformatics by a novice coder by Ed Himelblau

Shell

✅ Software Carpentry Lessons
The Missing Semester of Your CS Education by @anishathalye @jonhoo @jjgort
UNIX crash course by @AstrobioMike
Basic Linux commands

Git and GitHub

✅ Git for Scientists by Simon Cockell
✅ Git: Reference Sheet
Learn Git Branching - the most visual and interactive way to learn Git on the web.
LCSB-BioCore/basic-git-practice + slides
Git for humans
Basic writing and formatting syntax
Understand how to write a good commit message through memes 😉 by Hritik Jaiswal

Python

✅ Biology meets Programming - Introduction to Bioinformatics using Python by deNBI
30 Days of Python by Justin Mitchel *first 8 lessons
✅ LxMLS2020 Intro to Python by Luis Pedro Coelho
Python Scripting for Computational Molecular Science
Exploring and understanding Python through surprising snippets What the f*ck Python! 😱
A Gentle Introduction to Data Science with Python
✅ Tips & tricks for large scale processing with Python by Big Data Biology Lab

Matplotlib cheatsheets

Pandas

Machine Learning

A visual introduction to machine learning by @stephaniejyee and @tonyhschu
How to Critically Evaluate Machine Learning Methods by @tpq__
A guide to machine learning for biologists by Greener, J.G., Kandathil, S.M., Moffat, L. et al. Nat Rev Mol Cell Biol (2021)
Machine Learning for Biology ml4bio-workshop

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