Introduction to Biocomputing: From files to functions to plots
- Matt Bramble
Welcome to the class! This is the home page for the Introduction to Biocomputing class. From this page, you can link to all of the content needed to work through the course.
Logistics:
We will meet at FNT 1.104 from Tuesday May 27 to Friday May 30 at 1:30-4:30pm for our class.
In-person attendance is recommended, because the course is designed to be interactive, and following code remotely is sometimes difficult. However, if you would like to attend virtually, use this zoom link:
Join our Cloud HD Video Meeting
Zoom Instructions:
Please make sure your zoom version is updated ( and that you have a zoom account )
-- this is required to join a UT-sponsored Zoom session. See this link for more details about zoom requirements: Home
Other setup:
Please make sure you have an ssh client installed on your computer. All macs come with terminal, so no installation is required. For windows laptops, install putty and winSCP.
Course Overview
This course is designed to give you an introduction to methods for data manipulation and analysis in a hands-on manner. It will consist of lectures and guided tutorials.
The course has the following objectives:
To teach you about the Unix (Bash) environment and its tools in order to allow you to work effectively at the command line.
To familiarize you with R and RStudio and how to perform basic data analysis tasks in R.
To use the above skills in an integrated manner to take data from raw files and produce clean visualizations in R.
Your Instructor
Name | Affiliation | Expertise | How to contact? |
|---|---|---|---|
Matt Bramble | CBRS, bioinformatics group | R, Python | matthew.bramble@austin.utexas.edu or come to FNT1.206D |
Setup
Logging in to the POD
If you are using a terminal (Mac/Linux), open the terminal, and type:
ssh username@gsafcbig01.ccbb.utexas.edu
(replace username with your student username – studentNN)
If you are using windows Powershell, use the same command as above (for Mac/Linux)
To set up Powershell: powershell
If you are using putty (Windows PC), open it and enter the following:
host name: gsafcbig01.ccbb.utexas.edu
Upon prompting, enter your username and the password
Putty Setup
If your Windows version does not support ssh, you can download PuTTY from:
Download PuTTY: latest release (0.83)
Logging in with PuTTY
If you're using PuTTY as your Terminal from Windows:
Double-click the Putty icon
In the PuTTY Configuration window
make sure the Connection type is
SSHenter gsafcbig01.ccbb.utexas.edu for Host Name
Optional: to save this configuration for further use:
Enter gsafcomp into the Saved Sessions text box, then click Save
Next time, select gsafcomp from the Saved Sessions list, and click Load.
click the Open button
answer Yes to the SSH security question
In the PuTTY Terminal
enter your student account name after the "login as:" prompt, then Enter
enter the password associated with our student accounts
for security reasons, the text that you enter will not be displayed
If your Terminal has a dark background, the default shell colors can be hard to read. Execute this line to display directory names in yellow.
export LS_COLORS=$LS_COLORS:'di=01;33:' |
We'll see later how to set this environment variable in your login script (~/.profile) so that it gets executed every time you login to this server.
For now, just copy the appropriate line above, paste it into your Terminal window (after logging on), then press Enter.
Terminal via RStudio web
If you're attending remotely or do not have access to the UT VPN, you can use the Terminal functionality in the RStudio web application.
To access the Terminal built into RStudio Server.
Click on this link:
Enter your studentNN account name and our password, then click the Sign In button
In the RStudio web application, select the Terminal tab above the text entry window on the left.
You should now see a command line in the RStudio window.
In the RStudio Terminal, if the default color for directories is difficult to see against its white background, execute this line to display directory names in blue.
export LS_COLORS=$LS_COLORS:'di=1;34:fi=01:ln=01;36:' |
We'll see later how to set this environment variable in your login script (~/.profile) so that it gets executed every time you login to this server.
For now, just copy the appropriate line above, paste it into your Terminal window (after logging on), then press Enter.
Introduction to Unix
Open the following link in a new window or tab. Be sure to bookmark this introduction page. We will be returning here.
R and RStudio Part 1