This syllabus covers material that Casey Dunn will present, with help from Cat Munro, at the 2019 EvoCELL workshop.

These days will include morning workshops on general computing skills based on the book Practical Computing for Biologists. These will be taught be Casey Dunn. Morning workshops will be followed by afternoon workshops on specific applications of bioinformatics.

A few general notes about the course structure:

• Many details of the course are specific to UNIX-like operating systems, which include Linux and Apple macOS.

• 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, there are a couple options. We suggest that you borrow a Mac laptop for the course. Alternatively, if you prefer you can install Linux on a Virtual Machine and run it from within Windows.

• Course content, schedule, code, and other files will be distributed on github. Course materials are available at neptune2016.

• 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.

• Create a github account. If you use an academic email address, you may be eligible for free upgrades.

• 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.

• Atom text editor

• RStudio

• Docker

• macOS command line developer tools. To see if you have them installed, open /Applications/Utilities/Terminal and type gcc at the command line. If gcc runs, 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 install git.

• git

This syllabus focuses on the classes to be taught by Casey.

The course activities will walk through material covered in the following reading.

• Haddock, SHD and CW Dunn (2011). Practical Computing for Biologists. amazon I wrote this book with my 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.

• 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 - Setting up your computer, regular expressions

14:00 - 15:30 - The Unix command line

18:00 - 19:30 - Jaime Huerta-Cepas talk

9:00 - 13:00 - Version control with git

14:00 - 15:30 - Working with text

18:00 - 19:30 - Jennifer Rainsford

9:00 - 13:00 - Intro to R and tidyverse

14:00 - 15:30 - Principles of data visualization

18:00 - 19:30 - Andi Hejnol: Comparative methods in EvoDevo

9:00 - 13:00 - Phylogenetic comparative analyses in R

14:00 - 15:30 - Recap

18:00 - 19:30 - Amy

Amy will also give a 1-2 hour workshop on this day

Haddock and Dunn 2011. Practical Computing for Biologists. Sinauer and Associates.