Awesome Bioinformatics Education

A curated list of resources specific to learning bioinformatics. I appreciate any help! For contributing, please see CONTRIBUTING.md.

Contents

• Full courses
• Hands on
• Specific tools or topics
• Further reading
• Uncategorized

Full courses

Full accredited courses

Places where you can directly earn a certificate or where real students are earning real credits

• MIT Open Courseware
  • Computational biology
  • Bioinformatics and Proteomics
  • Foundations of Computational and Systems Biology
• Applied Computational Genomics Course at UU: Sprint 2022
• HarvardX Biomedical Data Science Open Online Training
• Titus Brown's class materials
• Meren Lab's tutorials (central tab)
• Astrobio Mike's tutorials
• Ben Langmead's teaching materials
• SciLifeLab course listings
• Andrea Telatin's tutorials
• Free code camp
• DataCamp
• Udemy
• Coursera
  • Python Basics
  • Data Structures
  • Object Oriented Programming
• Bioinformatics Workbook - Takes you from unix basics and the HPC all the way through advanced concepts. These concepts include computational like bioawk and containers, project management like GitHub and Slack, and all sorts of bioinformatics topics.

Full unaccredited courses

• Pathogen genomics data analysis course - Conor Meehan
• MMB DTP Training - A problem-based learning curriculum for the "Microbes, Microbiomes and Bioinformatics" doctoral training program.
• Computational Genomics and Bioinformatics Class
• Pathogen Bioinformatics Workshop held at SANBI
• Bioinformatics for Genomic Epidemiology - SANBI March 2024
• WCS AMR Africa 24 - NICD March 2024

Hands on

• Rosalind

Specific tools or topics

• Perfect bacterial genome tutorial
• Tools for RNAseq Analyses
• Hi-C with Chromosomal Conformation Course
• GWAS Tutorial
• Analysis of single cell RNA-seq data course
• Metagenome annotation workflow for UBC's MICB405 Microbial Bioinformatics course
• Workshop in microbial metagenome analysis at Michigan State University
• Statistics training from Quadram Institute
• Taming the BEAST (molecular clock analysis)

Phylogenetics or phylogenomics

• Tutorials on phylogenetic and phylogenomic inference
• Genomic epidemiology workshops from bioinformatics.ca
  • Genomic epidemiology workshop 2023
  • Genomic epidemiology workshop 2021

Galaxy

Galaxy is a very large but specific tool with lots of different possible tutorials, e.g.:

• Galaxy Training: Genome Assembly of MRSA using MinION Data
• One-health tag on Galaxy Training Site - Pathogen Bioinformatics
• Galaxy-wide Tutorial Site
• Repository of ~140 hours of Galaxy Lectures+Tutorials - under CC-BY license that can be embedded into your Blackboard/Moodle/etc. (see button at bottom)

Courses:

• Smörgåsbord 2021 (Global Galaxy Course)
• Smörgåsbord 2022 (Tapas)
• Smörgåsbord 2023
• Genomic data analysis

Domain Specific Galaxy Servers

• Metagenomics
• Genome Annotation
• Full List

LLMs

(Help wanted)

Large Language Models (LLMs) include things like ChatGPT, Bing, LLAMA, and Bard.

Genomic epidemiology

• Book: An applied genomic epidemiological handbook
• Book: R for applied epidemiology and public health
• Centre for Genomic Pathogen Surveillance digital epidemiology workshop - Really nice integrated exercises, using EpiCollect, DataFlo, PathogenWatch, Microreact.

Statistics

• Book: Modern Statistics for Modern Biology
• Choosing the correct statistical test in SAS, STATA, SPSS, and R

Further reading

• Integrating Molecular Biology and Bioinformatics Education

Uncategorized

I appreciate any help categorizing these!

• Glittr - Git repositories with bioinformatics training material.
• 5-day OUCRU-MORU bioinformatics fundamentals workshop
• List of genome visualisation tools
• List of training materials at SIB
• List of training materials at GitHub.com/crazyhottommy
• Book: Fundamentals of Data Visualization
• Book: Computational Genomics with R
• Data science in Python - course materials
• CS229: Machine Learning course
• Version Control with Git
• Version Control using Git and GitHub