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 Computers & Software Setup Instructions

To fully participate in this course students will need access to a modern computer to which they have administrator privileges (that is a computer where they can install software without restriction).

I much prefer Mac and Linux based computers as they already have a UNIX base. If you can, please use 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 windows desktop for classwork.

Regardless of your computer 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 Zoom virtual meeting software

We will use Zoom on a weekly basis for office hours and other meetings. Please make sure you have Zoom installed and running to allow you to join these meetings.

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 18) the latest release (2020-06-22, “Taking Off Again”) is R-4.0.2.

After installing R itself we recommend installing RStudio Desktop (version 1.1.456 or above), a slick visual interface for R. N.B. You will want the Open Source FREE desktop version.

The Bash Shell

Bash is a commonly-used UNIX shell that gives you the power to do simple tasks more quickly.

Mac OS X: You do not need to install anything. You can access bash from the Terminal (found in /Applications/Utilities). You may want to keep Terminal in your dock for this class.

Linux: There is no need to install anything.

Windows: Install Git for Windows from https://gitforwindows.org by downloading their latest .exe installer file and then following the steps bellow:

• Run your downloaded installer file (e.g. Git-2.16.3-32-bit.exe) by double clicking on it.
• Click on “Next”.
• Click on “Next”.
• Select “Use Git from the Windows Command Prompt” and click on “Next”.
• Click on “Next”.
• Keep “Checkout Windows-style, commit Unix-style line endings” selected and click “Next”.
• Select “Use Windows default console window” selected and click on “Next”.
• Click on “Install” (this may take a little while).
• Once done click on “Finish”.

To check if your install worked you can click on the “Windows Menu button” > “All Apps” and scroll down to Git and click to expand and select Git Bash. This should open a mostly black command line window. Success!! We can go ahead and close this for now.

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 connecting 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.

We will cover all of these together in class.