A collection of random and not so random learning materials for computation/biology/bioinformatics. I did not screen all of the material presented here. Some might/will be inappropriate for what you want to do or learn. Please give me feedback (open a New issue) if some of the material was either useful or not. Send through more material (preferable via a pull request, clone this repo at https://github.com/sschmeier/elearningcollection) if you have any that you think are particular useful and would like to see included here. Also, some web-links that worked at the time of creating this page might not work anymore (open a New issue or sent me a correction via a pull request).
- 1. General computation/statistics/biology
- 1.1 Online courses
- 1.2 University course material
- 1.3 Other material/tutorials/books/etc.
- 2. Bioinformatics/genomics/transcriptomics/etc.
- 2.1 Online courses
- 2.2 University course material
- 2.3 Other material/tutorials/books/etc.
- Software Carpentry
- Data Carpentry
- Introduction to Linux - edX course
- Introduction to Computer Science and Programming Using Python - edX course
- Genes and the Human Condition (From Behavior to Biotechnology) - Coursera course
- Experimental Genome Science - Coursera course
- Methods in Biostatistics I - JHSPHOPEN
- Case-Based Introduction to Biostatistics - Coursera course
- Data Analysis - Coursera course
- Data Science - A Sequence of Courses: Learn to be a Data Scientist and Apply Your Skills in a Capstone Project
- The Data Scientist’s Toolbox - Coursera course
- Exploratory Data Analysis - Coursera course
- Practical Machine Learning - Coursera course
- R programming - Coursera course
- An Introduction to Interactive Programming in Python - Coursera course
- UC Davis genome center instructional videos - Instructional videos about linux and some simple bioinformatics tasks
- Stanford Open Classroom video lecture - Practical Unix
- Data Analysis and Visualization Course - UC Davis, 2012
- Unix, Perl, and Python - Course material from Bioinformatics and Research Computing at the Whitehead Institute
- Dive into Python - Free online book to learn Python programming
- A Primer on Python for Life Science Researchers
- PLoS collections, e.g.:
- Nature Review Genetics series, e.g.:
- Nature Review Molecular Cell Biology series, e.g.:
- Nature Review Microbiology series, e.g.:
A recent article in PLoS, "A New Online Computational Biology Curriculum", by David Searls (PLoS Comput Biol 2014 10(6): e1003662. doi: 10.1371/journal.pcbi.1003662) provides a comprehensive supplementary with many programs and courses regarding bioinformatics education. Find the document here.
- Quantitative Biology Workshop - edX course
- Data Analysis for Genomics - edX course
- Bioinformatics: Life Sciences on Your Computer - Coursera course
- Bioinformatic Methods I - Coursera course
- Bioinformatic Methods II - Coursera course
- Systems Biology - A Sequence of Courses: Learn to be a Systems Biologist and Apply Your Skills in a Capstone Project
- Genomics, Bioinformatics & Medicine - Stanford University, Doug Brutlag
- Computational Molecular Biology - Stanford University, Doug Brutlag
- Introduction to Statistical and Computational Genomics - University of Washington, Borenstein-lab, 2013
- Introduction to Statistical and Computational Genomics - University of Washington, Borenstein-lab, 2014
- Genomic Informatics - University of Washington, Borenstein-lab, 2013
- Genomic Informatics - University of Washington, Borenstein-lab, 2014
- Canadian Bioinformatics Workshops material - Different courses with PDFs and VIDEOs, some examples:
- Bioinformatics and Computational Methods - Material from different courses from the Weill Medical College and Memorial Sloan-Kettering Cancer Center
- Next-Gen Sequence Analysis Workshop (2013) - Yearly workshop by Titus
- Courses focusing on different aspects of bioinformatics - UC Davis course material of past bioinformatics courses
- EBI train online - Online learning material from past courses at the European Bioinformatics Institute, e.g.
- Computational Biology: Genomes, Networks, Evolution - MIT video lectures
- De Novo Assembly Course - Univ. of Oslo: PDF lectures and examples free on github
- Schmeier Group bioinformatics course @ Massey University
- NCBI Handbook - Free online book explaining the tools and processes at NCBI
- WikiBooks: Next Generation Sequencing (NGS)
- A Primer of Genome Science, 3rd ed, Greg Gibson and Spencer Muse
- Bioinformatics: Sequence and Genome Analysis, Second Edition, 2nd ed, David Mount
- Essential Bioinformatics, Jin Xiong
- Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids, Richard Durbin, S. Eddy, A. Krogh, G. Mitchison
- Bioinformatics: Sequence, Structure and Databanks, Des Higgins and Willie Taylor
- Bioinformatics: The Machine Learning Approach, 2nd ed, Pierre Baldi and Søren Brunak
- An Introduction to Bioinformatics Algorithms, Neil C. Jones and Pavel A. Pevzner
- Algorithms on Strings, Trees and Sequences, Dan Gusfield
- Genome speak - Speak the language of genomics
- Beginner’s guide to comparative bacterial genome analysis using next-generation sequence data
- GAGE-B: an evaluation of genome assemblers for bacterial organisms.
- GAGE: A critical evaluation of genome assemblies and assembly algorithms
- A survey of sequence alignment algorithms for next-generation sequencing
- PLoS collections, e.g.:
- Nature Review Genetics series, e.g.:
- Computational tools - Reviews on tools for analyzing genetic and genomic data
- Modelling
- Study design
- Applications of next-generation sequencing
- Genome-wide association studies
- Translational genetics
- BioStars - An Online Question & Answer Resource for the Bioinformatics Community
- SEQanswers - the next generation sequencing community
- NCBI Education Resources - Mostly tutorials about NCBI tools and databases.
- BaRC Standard operating procedures - Standard operating procedures from Bioinformatics and Research Computing at the Whitehead Institute
- BioLinux - Linux distribution based on Ubuntu Linux that pre-installed many bioinformatics tools
- Illumina online courses - Online training videos about Illumina's sequencing technology