Getting Started

About Anna

Anna is a member of the Center for Biomedical Research Support (CBRS), which is home to a number of core facilities: GSAF, Proteomics/Mass Spec, Microscopy, Crystallography, Mouse Genetic Engineering....

Anna Battenhouse, Associate Research Scientist, abattenhouse@utexas.edu
- BA English literature, 1978, Carleton College
- Commercial software development 1982 – 2007
  - Texas Instruments, Motorola ...
  - lots of software development experience but limited Unix/Linux
- Joined Iyer Lab 2007 (functional genomics)
  - “retirement career”
  - began to appreciate Linux & bash (slowly)
- BS Biochemistry, 2013, UT
- Current affiliations:
  - Biomedical Research Computing Facility (BRCF)
  - Bioinformatics Consulting Group (BCG)
  - Genome Sequencing and Analysis Facility (GSAF)
  - Marcotte lab (systems biology/proteomics)

The Biomedical Research Computing Facility (BRCF) is the CBRS core facility that supports local research computing.

About You

Tell us a bit about yourself, such as:

your lab or organization
research interests or staff role
computational background, including any programming languages you use
why you're interested in advanced bash scripting

Overview

This class is designed to be hands-on, to provide you with the enjoyment ( ) of working in the Linux command line environment.

However, all steps and scripts are detailed on this Wiki, and you will see me exercising processes on the command line interactively. So you may decide (at any time) to just watch and listen.

Note that you will have access to this Wiki even after the class, and I will email you a link to a video of the course.

Setup to follow hands-on

If you choose to follow hands-on, you'll be using the BRCF "GSAF POD", a set of 3 compute servers attached to a large, shared storage server.

Accounts

We have set up 75 "student" accounts, named student01 , student02 ... student75 . You have each been assigned one as follows, along with a server to use:

These credentials are active for the next few days, but will be de-activated on Monday October 31, 2022.

Servers

With your studentNN account you can ssh into one of the following servers, according to the assignments given.

Here's how to access the servers:

# From the UT campus network, or if you have the UT VPN active:
ssh student50@gsafcomp02.ccbb.utexas.edu

# The common password for these accounts is posted in the Zoom chat.

Tip

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 (and put it in your ~/.profile login script)

export LS_COLORS=$LS_COLORS:'di=1;33:'