Featured Workshop: Command Line for Biologists

Join us on Wednesday, April 19, from 1 to 3 p.m., for an online workshop, Command Line for Biologists*.

This workshop is based on the Software Carpentry Lesson on the Unix Shell. The Unix shell is a powerful tool that allows users to perform simple tasks, including managing data. In recent years, basic programming skills such as Unix shell have become vital for biomedical research. Learning how to use the shell is still relevant, as the instructor notes explain:

  • Because so much else depends on it. Installing software, configuring your default editor, and controlling remote machines frequently assume a basic familiarity with the shell, and with related ideas like standard input and output.
  • Because it’s an easy way to introduce some fundamental ideas about how to use computers.
  • Because it enables use of many domain-specific tools and compute resources researchers cannot access otherwise.

We are pleased to be offering this workshop for the first time, tailored to Pitt researchers. In this workshop, you will learn how to:

  • Access a remote Unix machine through the Center for Research Computing – HTC Cluster
  • Use basic Unix commands for navigating and working with files and directories
  • Generate MD5SUMs for data upload to NCBI GEO
  • Transfer files using FTP client software
  • Access HTC Cluster-installed open-source bioinformatics software packages

You must sign up for a Center for Research Computing HPC allocation prior to attending this workshop.

If you are unable to attend this scheduled class, consider requesting a customized instruction session for your course, group, or department.

*HSLS classes are open to University of Pittsburgh faculty, staff, and students, as well as UPMC residents and fellows. A valid email address is required to register.