Linux for Biologists (WCMC)  
April 14-28 2020

NOTE: This workshop is now open both to Ithaca Campus and WCMC.

This workshop is designed to prepare biologists to work in the interactive Linux environment of our BioHPC Cloud servers.  We will cover basics of Linux operating system, needed to operate the servers. In particular the topics will include:
  • Navigating a Linux workstation: logging in and out of a Linux 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 Cloud. The workstations will be accessed using the Secure SHell (ssh) protocol. To participate in the exercises you will need to use your own laptop or desktop with an ssh client installed. MACs and Linux laptops come with native ssh clients and no extra installation 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 client, 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 how to access BioHPC machines, please refer to the following document:, especially points 1 and 2.2-2.4.

This workshop is divided into paired sessions: a lecture/presentation session (Tuesday) followed by a hands-on session (Thursday), allowing for plenty of time for hands-on training.

Access to BioHPC Cloud workstations requires a BioHPC Cloud account. If you did not already have such account, you were asked to create one at the time you registered for the workshop. It you need to re-set your BioHPC password, you can do it at If you do not know your BioHPC user ID, contact us at

Since the BioHPC resources are behind the Cornell firewall, the easiest way to access them is from Ithaca campus network (not possible at present) or from any other location while using the Cornell VPN. The latter is avaliable to all users having the Cornell NetID. Please check the relevant CIT website to see if you are elligible for a NetID and obtain one if possible. While out-of-campus access to BioHPC Cloud without the VPN is still possible, it is somewhat more complicated.

A Linux machine for hands-on exercises will be assigned to you automatically (you do not have to make your own reservation). You will have access to your machine for the entire three weeks of the workshop.

Machine allocations are posted here.

This workshop will be conducted remotely via Zoom. The link to the workshop Zoom session will be sent in advance to all participants via e-mail.

Lecture slides for Part 1&2   (may be udated during workshop)

Lecture slides for Part 3       (may be updated during workshop)

Exercise handouts: Part 1 PDF Part 1 HTML   Part 2 PDF   Part 2 HML  Part 3 PDF Part 3 HTML (content may change slightly during workshop)


Workshop Outline  
Session 1 Apr 14 2020 3:00PM - 4:30PM Zoom
Lecture - Part 1
Session 2 Apr 16 2020 3:00PM - 4:30PM Zoom
Hands-on session - Part 1
Session 3 Apr 21 2020 3:00PM - 4:30PM Zoom
Lecture - Part 2
Session 4 Apr 23 2020 3:00PM - 4:30PM Zoom
Hands-on session - Part 2
Session 5 Apr 28 2020 3:00PM - 4:30PM Zoom
Lecture - Part 3
Session 6 Apr 30 2020 3:00PM - 4:30PM Zoom
Hands-on session - Part 3
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