Students in this course will learn that Bioinformatics frequently requires analyzing large complex datasets. The recommended approach to such analysis is to work with a computer that offers UNIX integration. Together we will lean the fundamentals of the UNIX command line and the R environment for data analysis and graphics.

Student Laptops & Software Setup Instructions

To fully participate in this course students will need to bring a laptop to class. I much prefer Mac and Linux based laptops as they already have a UNIX base. If you can, please bring one of these. However, don’t worry if you are running Windows as we will be able to login to a campus based UNIX machine from your laptop or use a classroom Mac for classwork.

Regardless of your laptop type you will need to install the software described below.

An up-to-date web browser

Current versions of Chrome, Firefox and Safari are preferred.

The data analysis environment R and RStudio

R Binaries for Windows, MacOSX and Linux can be downloaded and installed from CRAN (Comprehensive R Archive Network). If possible download the latest binary version of R for your operating system. As of course launch (Sept 17) the latest release (2017/06/07, “Single Candle”) is R-3.4.1.

After installing R itself we recommend installing RStudio Desktop (v1.0.153 or above), a slick visual interface for R. N.B. You will want the Open Source FREE version.

Using Jetstream

Jetstream is a cloud-based on-demand virtual machine system funded by the National Science Foundation. It will provide us with UNIX based computers (what we call “virtual machine instances”) that look and feel just like a regular Linux workstation but with thousands of times the computing power!

We will cover configuring and conecting to Jetstream in class. You can also find detailed step-by-step instructions for:

• Starting a Jetstream Computer Instance,
• Logging in to jetstream from your local terminal,
• Adding password to a Jetstream instance.