Bioinformatics Workshops & Training

Jump to: In-person courses, online material, or other resources.

In-person Courses

Last updated: 2015-03-06

Note that many of the courses shown below also have course materials from past years publicly available online.

Cold Spring Harbor Courses: meetings.cshl.edu/courses.html

Cold Spring Harbor has been offering advanced workshops and short courses in the life sciences for years. Relevant workshops include the Genome Access Course, Genetics of Complex Human Diseases, Statistical Methods for Functional Genomics, Programming for Biology, Computational and Comparative Genomics, and others. Unlike most of the others below, you won't find material from past years' CSHL courses available online.

Canadian Bioinformatics Workshops: bioinformatics.ca/workshops

Bioinformatics.ca through its Canadian Bioinformatics Workshops (CBW) series began offering one and two week short courses in bioinformatics, genomics and proteomics in 1999. The more recent workshops focus on training researchers using advanced high-throughput technologies on the latest approaches being used in computational biology to deal with the new data. Course material from past workshops is freely available online, including both audio/video lectures and slideshows. Topics include microarray analysis, RNA-seq analysis, genome rearrangements, copy number alteration, pathway analysis, genome visualization, gene function prediction, functional annotation, data analysis using R, statistics for metabolomics, and much more.

UC Davis Bioinformatics Training Program: training.bioinformatics.ucdavis.edu

The UC Davis Bioinformatics Training program offers several intensive short bootcamp workshops on RNA-seq, data analysis and visualization, and cloud computing with a focus on Amazon's computing resources. They also offer a week-long Bioinformatics Short Course, covering in-depth the practical theory and application of cutting-edge next-generation sequencing techniques. Every course's documentation is freely available online, even if you didn't take the course.

MSU NGS Summer Course: http://bioinformatics.msu.edu/ngs-summer-course-2014

This intensive two week summer course will introduce attendees with a strong biology background to the practice of analyzing short-read sequencing data from Illumina and other next-gen platforms. The first week will introduce students to computational thinking and large-scale data analysis on UNIX platforms. The second week will focus on mapping, assembly, and analysis of short-read data for resequencing, ChIP-seq, and RNAseq. Materials from previous courses are freely available online under a CC-by-SA license.

UAB Short Course on Statistical Genetics and Genomics: soph.uab.edu/ssg/...

Focusing on the state-of-art methodology to analyze complex traits, this five-day course will offer an interactive program to enhance researchers' ability to understand & use statistical genetic methods, as well as implement & interpret sophisticated genetic analyses. Topics include GWAS Design/Analysis/Imputation/Interpretation; Non-Mendelian Disorders Analysis; Pharmacogenetics/Pharmacogenomics; ELSI; Rare Variants & Exome Sequencing; Whole Genome Prediction; Analysis of DNA Methylation Microarray Data; Variant Calling from NGS Data; RNAseq: Experimental Design and Data Analysis; Analysis of ChIP-seq Data; Statistical Methods for NGS Data; Discovering new drugs & diagnostics from 300 billion points of data. Video recording from the 2013 course are available online.

MBL Molecular Evolution Workshop: hermes.mbl.edu/education/...

One of the longest-running courses listed here (est. 1988), the Workshop on Molecular Evolution at Woods Hole presents a series of lectures, discussions, and bioinformatic exercises that span contemporary topics in molecular evolution. The course addresses phylogenetic analysis, population genetics, database and sequence matching, molecular evolution and development, and comparative genomics, using software packages including AWTY, BEAST, BEST, Clustal W/X, FASTA, FigTree, GARLI, MIGRATE, LAMARC, MAFFT, MP-EST, MrBayes, PAML, PAUP*, PHYLIP, STEM, STEM-hy, and SeaView. Some of the course materials can be found by digging around the course wiki.

UW Summer Institute in Statistical Genetics: sisg.biostat.washington.edu

consists of a series of two-and-a-half day modules over a 3-week period designed to introduce geneticists to modern methods of statistical analysis and to introduce statisticians to the statistical challenges posed by modern genetic data. Prerequisites are minimal, and the modular nature of the Institute enables participants to design a program best suited to their backgrounds and interests. Most participants take two or three modules. See the schedule and the list of SISG modules for details.

Online Material

Last updated: 2015-03-06
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Canadian Bioinformatics Workshops: bioinformatics.ca/workshops

(In person workshop described above). Course material from past workshops is freely available online, including both audio/video lectures and slideshows. Topics include microarray analysis, RNA-seq analysis, genome rearrangements, copy number alteration, network/pathway analysis, genome visualization, gene function prediction, functional annotation, data analysis using R, statistics for metabolomics, and much more.

UC Davis Bioinformatics Training Program: training.bioinformatics.ucdavis.edu

(In person workshop described above). Every course's documentation is freely available online, even if you didn't take the course. Past topics include Galaxy, Bioinformatics for NGS, cloud computing, and RNA-seq.

MSU NGS Summer Course: bioinformatics.msu.edu/ngs-summer-course-2013

(In person workshop described above). Materials from previous courses are freely available online under a CC-by-SA license, which cover mapping, assembly, and analysis of short-read data for resequencing, ChIP-seq, and RNAseq.

More of Titus Brown's Courses: ivory.idyll.org/blog//...

Titus Brown taught a 3.5 day microbial bioinformatics course at Caltech, two days of intro computing for biologists at MSU, and another two-day intro computing for biologists workshop at UW. The Caltech workshop was sponsored by CEMI, the Caltech Environmental Microbial Initiative; the MSU workshop was co-sponsored by BEACON and iCER; and the UW workshop was co-sponsored by BEACON and the eScience Institute. All three of the workshops made use of Amazon Web Services. All workshop materials are on GitHub and freely available for use and reuse under CC0 (see Caltech, MSU, and UW materials). See Titus's blog post about the courses above for course experiences, reactions, and other thoughts.

EMBL-EBI Train Online: www.ebi.ac.uk/training/online

Train online provides free courses on Europe's most widely used data resources, created by experts at EMBL-EBI and collaborating institutes. Topics include Genes and Genomes, Gene Expression, Interactions, Pathways, and Networks, and others. Of particular interest may be the Practical Course on Analysis of High-Throughput Sequencing Data, which covers Bioconductor packages for short read analysis, ChIP-Seq, RNA-seq, and allele-specific expression & eQTLs.

UC Riverside Bioinformatics Manuals: manuals.bioinformatics.ucr.edu

This is an excellent collection of manuals and code snippets. Topics include Programming in R, R+Bioconductor, Sequence Analysis with R and Bioconductor, NGS analysis with Galaxy and IGV, basic Linux skills, and others.

Software Carpentry: software-carpentry.org

Software Carpentry helps researchers be more productive by teaching them basic computing skills. We recently ran a our second 2-day Software Carpentry Bootcamp here at UVA. Check out the online lectures for some introductory material on Unix, Python, Version Control, Databases, Automation, and many other topics.

Coursera: coursera.org/courses

Coursera partners with top universities to offer courses online for anytone to take, for free. Courses are usually 4-6 weeks, and consist of video lectures, quizzes, assignments, and exams. Joining a course gives you access to the course's forum where you can interact with the instructor and other participants. Relevant courses include Data Analysis, Computing for Data Analysis using R, and Bioinformatics Algorithms, among others. You can also view all of Jeff Leek's Data Analysis lectures on Youtube.

OpenHelix: openhelix.com

OpenHelix provides tutorials and training materials (video lectures, screencasts, slides, exercises) on over 100 bioinformatics tools, databases, and web servers. Most of the tutorials require a subscription, but there are a handful of free tutorials on topics such as OMIM, UCSC genome browser (beginner, advanced, and more), and a few others.

Rosalind: http://rosalind.info

Quite different from the others listed here, Rosalind is a platform for learning bioinformatics through gaming-like problem solving. Visit the Python Village to learn the basics of Python. Arm yourself at the Bioinformatics Armory, equipping yourself with existing ready-to-use bioinformatics software tools. Or storm the Bioinformatics Stronghold, implementing your own algorithms for computational mass spectrometry, alignment, dynamic programming, genome assembly, genome rearrangements, phylogeny, probability, string algorithms and others.

Bioconductor Course Materials: bioconductor.org/help/course-materials

Bioconductor provides training in computational and statistical methods for the analysis of genomic data. In particular, the course materials from the useR! 2013 R/Bioconductor for Analyzing High-Throughput Genomic Data are especially useful, containing R code and a PDF tutorial on sequence alignment, RNA-seq, ChIP-seq, and sequence annotation with various Bioconductor packages.

Google Developers R Programming Video Lectures: http://www.youtube.com/...

Google Developers recognized that most developers learn R in bits and pieces, which can leave significant knowledge gaps. To help fill these gaps, they created a series of introductory R programming videos. These videos provide a solid foundation for programming tools, data manipulation, and functions in the R language and software. The series of short videos is organized into four subsections: intro to R, loading data and more data formats, data processing and writing functions. Start watching the YouTube playlist here.

Univ. of Oslo De Novo Assembly Course: github.com/lexnederbragt/...

Lex Nederbragt at the Norwegian Sequencing Center put together this course on de novo genome assembly and released all the course materials on Github under CC0/public domain. Course material includes slideshow presentations and exercises (in the practicals directory), which give code examples from everything from quality control, assembly, and assembly evaluation.

Other Resources

Last updated: 2015-03-06
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