Linux for Biologists  
November 2, 9 and 16 2016

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. To be able to run Linux programs with graphical inerface displaying on your Windows laptop, you should also install MobaXterm (this is not essential for the workshop). To transfer files between your laptop and a Linux machine, you will need an sftp clinet, such as FileZilla on Windows (MAC and Linux laptops come with native sfpt clients and no extra installation is needed). For links to client software mentioned above, instructions, and more information on access to BioHPC machines, please refer to the following document:, especially points 1 and 2.2-2.4.

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.

The machine allocations are posted here.

Workshop Outline
Session 1 11/2/2016 3:30:00 PM 655 Rhodes Hall
Session 2 11/9/2016 3:30:00 PM 655 Rhodes Hall
Session 3 11/16/2016 3:30:00 PM 655 Rhodes Hall
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