This syllabus covers material that Cat Munro, Jacob Musser, and Andi Hejnol will present at the 2019 EvoCELL workshop in place of Casey Dunn.
These days will include morning workshops on general computing skills based on the book Practical Computing for Biologists. Morning workshops will be followed by afternoon workshops on specific applications of bioinformatics.
A few general notes about the course structure:
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Many details of the course are specific to UNIX-like operating systems, which include Linux and Apple macOS.
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We will also use UNIX for local command line, programing, and data processing exercises. This means that it will not be possible to use Microsoft Windows alone for most course activities. If your primary laptop is Microsoft Windows, you can install Linux on a Virtual Machine and run it from within Windows. We will also be using docker containers to keep things consistent,
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Course content, schedule, code, and other files will be distributed on github.
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Bring a copy of Practical Computing for Biologists (abbreviated in this document as PCfB). Complete the reading for the first class (see Schedule below) prior to arrival. Also download an familiarize yourself with the example files provided at the book website.
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Create a github account. If you use an academic email address, you may be eligible for free upgrades.
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Install the required software listed below.
Please install the following tools on your laptop before you arrive. This will reduce network load during the course, and also allow us to get started right away.
- macOS command line developer tools. To see if you have them installed, open /Applications/Utilities/Terminal and type
git --versionat the command line. Ifgit --versionruns, you are probably all set. If it asks you if you would like to install the Developer tools, follow the instructions to do so. This will installgit.
This syllabus focuses on the classes to be taught by Cat, Jake, and Andi.
The course activities will walk through material covered in the following reading.
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Haddock, SHD and CW Dunn (2011). Practical Computing for Biologists. amazon Casey wrote this book with his colleague Steve Haddock as an introduction to general computing skills for biologists. If you are not already comfortable at the command line then you should get this book as a reference.
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Whickham, H (2017). R for Data Science. http://r4ds.had.co.nz This book is free online at the provided link. It is an excellent introduction to data analysis in R, and more broadly how to think about data structure and analysis. It presents a coherent introduction to the Tidyverse, a set of R packages for general data manipulation and analysis. Our R coding will follow conventions in this book.
9:00 - 13:00 - Practical - Setting up your computer, regular expressions, introduction to the unix command line (Cat)
11:00 Coffee Break
14:00 - 16:00 - The Unix command line (Cat)
16:00 Coffee Break
18:00 - 19:30 - Jaime Huerta-Cepas talk
9:00 - 13:00 - Version control with git (Cat)
11:00 Coffee Break
14:00 - 15:30 - Working with text (Cat)
15:30 Coffee break
16:00 - 17:00 - Integrating tools and designing workflows (Cat)
18:30 - 19:10 - Jennifer Rainsford
9:00 - 13:00 - Intro to R and tidyverse (Jacob)
11:00 Coffee break
14:00 - 15:00 - Principles of data visualization (Jacob)
15:00 - 18:00 - Intro to Phylogenetic Comparative methods (Andi)
16:00 Coffee break
18:00 - 19:30 - Andi Hejnol: Comparative methods in EvoDevo
9:00 - 13:00 - Phylogenetic comparative analyses in R (Cat)
https://github.com/Phylogenetics-Brown-BIOL1425/independent_contrasts
11:00 Coffee Break
14:00 - 15:30 - Amy, Career in Science Journalism
16:00 Coffee break
16:30 - 17:00 - Recap
18:00 - 19:30 - Amy Podium
Haddock and Dunn 2011. Practical Computing for Biologists. Sinauer and Associates.