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Workshops

Linux for Biologists  
February 11-27 2019

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 http://the.earth.li/~sgtatham/putty/latest/x86/putty.exe 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 https://www.realvnc.com/download/viewer/). 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: http://cbsu.tc.cornell.edu/lab/doc/Remote_access.pdf, 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

Exercise slides: Part 1  Part 2 Part 3

 

Workshop Outline  
Session 1 Feb 11 2019 3:30PM - 5:00PM 655 Rhodes Hall
Part 1 lecture and presentation.
Session 2 Feb 13 2019 3:30PM - 5:00PM 655 Rhodes Hall
Part 1 hands-on session
Session 3 Feb 18 2019 3:30PM - 5:00PM 655 Rhodes Hall
Part 2 lecture and presentation
Session 4 Feb 20 2019 3:30PM - 5:00PM 655 Rhodes Hall
Part 2 hands-on session
Session 5 Feb 25 2019 3:30PM - 5:00PM 655 Rhodes Hall
Part 3 lecture and presentation
Session 6 Feb 27 2019 3:30PM - 5:00PM 655 Rhodes Hall
Part 3 hands-on session
 
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