Linux for Biologists  
March 2-18 2020

This workshop is designed to prepare a biologist to work in an interactive Linux environment of our BioHPC Lab workstations.  We will then cover basics of Linux operating system, needed to operate the workstations. In particular the topics will include: 

  • Navigating a Linux workstation: logging in and out of a Linuix machine, directory structure, basic commands for dealing with files and directories
  • Working with text files
  • Transfer of files to and from a Linux workstation
  • Basics of running applications on Linux
  • Using multiple CPUs/cores: parallel applications
  • Basics of shell scripting

The presented material will be illustrated by hands-on exercises hosted on dedicated workstations of the BioHPC Lab. The workstations will be accessed using the Secure SHell (ssh) protocol. To participate in the exercises, please bring your own laptop with an ssh client installed. MACs and Linux laptops come with native ssh clients and no extra installtion is needed. For windows, the recommended ssh client is PuTTy - please install it prior to the workshop(just download the executable file and put it anywhere on your hard drive; double-click to launch) . To be able to run Linux programs with graphical inerface displaying on your laptop, you should also install RealVNC viewer (download one appropriate for your laptop from To transfer files between your laptop and a Linux machine, you will need an sftp clinet, such as FileZilla (although MAC and Linux laptops come with native sftp clients and no extra installation is necessary, FileZilla would be helpful on these platforms as well). For detailed instructions and more information on access to BioHPC machines, please refer to the following document:, especially points 1 and 2.2-2.4.


This workshop is divided into paired sessions: lecture/presentation session (Mondays) followed by hands-on session (Wednesdays), this arrangement will allow for plenty of time for hands-on training.

Access to BioHPC Lab workstations requires a Lab account. If you do not yet have an account on BioHPC Lab system, we will create one for you. Also, we will assign a machine for you to work on during and after the workshop (you do not have to make your own reservation).

Machine allocations are posted here.

Lecture slides (likely to be updated as the workshop proceeds - please fetch a fresh copy)

Lecture slides for Part 3  Part3_extra

Exercise handouts: Part 1 PDF Part 1 HTML   Part 2 PDF   Part 2 HML Part3 PDF Part 3 HTML


Workshop Outline  
Session 1 Mar 2 2020 3:30PM - 5:00PM 655 Rhodes Hall
Part 1 lecture and presentation.
Session 2 Mar 4 2020 3:30PM - 5:00PM 655 Rhodes Hall
Part 1 hands-on session
Session 3 Mar 9 2020 3:30PM - 5:00PM 655 Rhodes Hall
Part 2 lecture and presentation
Session 4 Mar 11 2020 3:30PM - 5:00PM 655 Rhodes Hall
Part 2 hands-on session
Session 5 Mar 16 2020 3:30PM - 5:00PM Zoom
Part 3 lecture and presentation. Download Slides 
Session 6 Mar 18 2020 3:30PM - 5:00PM Zoom
Part 3 hands-on session. Download handouts. HTML formated; PDF formated.
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