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 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 1.3.0 or above), a slick visual interface for R. N.B. You will want the Open Source FREE 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 or above) 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.

Other Software

In individual classes we will make use of the following software. Having these installed in advance of class start will be highly advantageous.

• Cytoscape,
• VMD ,
• MUSCLE,
• MGL Tools.

We will review each tools setup and configuration in class together as the need arises. However, we note from past experience that download time can be substantial on slow classroom WiFi networks - hence the recommendation to at least download before class start.

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 and thus no pre-class configuration is required.