Students in BGGN 213 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 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.

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 MobaXterm, an enhanced terminal with bash for Windows. Note that the default ‘Personal Edition install’ typically places the MobaXterm executable in C:\Program Files (x86)\Mobatek\MobaXterm Personal Edition.

Please also install the Plugin CygUtils. Once downloaded please move the CygUtils.plugin file to the folder C:\Program Files (x86)\Mobatek\MobaXterm Personal Edition. Launching mobaxterm will complete the install.

Text Editor

When you’re writing code, it’s nice to have a text editor that is optimized for writing code, with features like automatic color-coding of key words. The default text editor on Mac OS X and Linux is usually set to Vim, which is not famous for being intuitive. if you accidentally find yourself stuck in it, try typing the escape key, followed by :q! (colon, lower-case ‘q’, exclamation mark), then hitting Return to return to the shell. Nano is a basic editor and the default that we will use during this course.

Mac OS X: nano should be pre-installed.

Linux: nano should be pre-installed.

Windows: Nano can be installed as a plugin to mobaxterm (see above). First start mobaxterm and then in the mobaxterm terminal type: mobapt Pressing Return will bring up a panel listing available additions. Please select nano by clicking on its entry and then the “Install/Update” button.

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.