Survival Bash

Survival bash : A short version of Linux Essentials for Next-Generation Sequencing Data Analysis

Note: required before taking any other workshop. Statement of proficiency in bash shell accepted to attend other workshops; check dates. 

2020 dates(s):
29 April – Pilot online
13 August – online 

: Online during COVID19
Genetics/Biotech Center
425 Henry Mall Madison, WI 53706

LIMITED to 8 participants – (2 minimum)

REGISTER: use Google Calendar link on chosen date to register (opens in new TAB or new window.)

It is necessary to register for each workshop separately.
– Printed original exercise book: 
if registration is less than 1 week a photocopy version may be substituted. During COVID19 material is provided as PDF and HTML

This workshop is meant to learn and understand basic command lines as they are typed on a text terminal for a Unix-style operating system (Linux or Macintosh, or Windows with added software) to reach  minimal proficiency.

Students will learn the essential techniques to interact with the powerful Linux operating system via the bash shell commands that are necessary to leverage the capabilities of many of the latest, most popular bioinformatics tools used in NGS analysis but applies to other situations as well.

A central goal of the workshop is to make users more comfortable with what is likely an unfamiliar computing environment so that they can more confidently understand and employ these methods in the context of their independent research projects.

Learning Objectives:

• Connect to a remote Linux system
•  Understand the computer organization (file structure and path)
• Create, delete and navigate directories
• Create, delete, explore and edit text files
• Download Internet data files directly into the remote computer
• Understand compressed and archived files (zip and tar.gz)
• Apply key concepts (standards and streams, piping and redirecting) that make Linux very powerful

This workshop is a preparation to all other workshops and provides insights to essential Linux commands, and for most applicants is a required session. (Statement of proficiency might be acceptable – enquire by email)

The workshop is mostly active hands-on directed exercises and examples

The computer laboratory exercises require that students bring a laptop* to connect to the Linux system in the Biotechnology Center.

A fee ($35 online during COVID19)  is required for each student and includes costs for a printed manual workbook of about 115 pages or more. (Note: during COVID19 – book provided as PDF.)

* There is a minimal set of software that should be installed on laptops BEFORE attending the workshop. Instructions will be provided to attendees prior to the workshop and can be found within the PDF document: Preparation for Linux-based workshop  (Opens in new TAB or new window.)

Dr. Jean-Yves Sgro,  Ph.D., Biotechnology Center –

*No-show Policy*
All cancellations need to be notified 72 hours in advance.