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  • Created 08 Sep 2021

Update on 9/29/21:

Please note that this is an interactive workshop and that we strongly recommend that participants use the provided “virtual machine” (VM), to which all registrants will be granted access. This will ensure that all participants will see the exact same environment, the course setup procedure is automatically and correctly completed ahead of time, and we will be able to provide IT support if necessary.

The VM will only be available on the NIH network. So if you cannot participate on an NIH campus nor access the virtual private network (VPN), you will need to set up for the workshop yourself, and we will likely be unable to help you with your local environment. However, the setup procedure is not terribly involved, particularly for Mac and Linux users; the steps can be followed here.

Otherwise, if you will have access to the NIH network, all you need to do to prepare for the workshop is check you are able to SSH into the provided VM (while connected to the network). Please follow the “SSH” subsections in either the “Connecting from Windows,” “Connecting from Macs,” or “Connecting from Linux” sections at this link, replacing “biowulf.nih.gov” or “helix.nih.gov” with the VM address that will be provided to registrants on or after 9/29/21. You will be notified via email once your account on the VM is ready; simply use your NIH username and password as your credentials for the VM. (For Windows’ PuTTY setup instructions, there is no need to change any of the configuration options.)

Regardless, all workshop sessions will be recorded and will be posted on this page.

Please reach out to NCIDataScienceLearningExchange@mail.nih.gov if you have any questions or concerns.


Join the Software Carpentry Series of Hands-on Workshops to learn how to use the Linux Shell for Data Science!

The Linux “shell” is the command-line interface to the Linux operating system. It is built in to all Linux systems, from Android devices to the world’s largest supercomputers, including NIH’s Biowulf cluster.

In this four-week series of two-hour workshops, we will introduce Bash, by far the most popular version of the Linux shell and a useful scripting language for Linux. Instructors will use the Linux terminal and you will follow along on a remote Linux system accessible by all course registrants, allowing you to gain a strong foundation in the fundamentals of and best practices for using Linux.

NOTE: This is a four-part course, held weekly for four weeks from 11 am – 1 pm, with a 20-minute lunch break. When you register, you are registering for all four weeks. Please make sure you have time in your schedule to commit to all four sessions!

Registration is required; please register here.

Dates, Topics, and Recordings:

  • Week 1, Oct 5, 11 a.m. – 1 p.m. ET:Introducing the shell, navigating files and directories; Working with files and directories (Part I) (WebEx link; meeting number: 2316 376 5365, password: October5@11am) (Recording)
  • Week 2, Oct 12, 11 a.m. – 1 p.m. ET: Working with files and directories (Part II); Pipes and filters (WebEx link; meeting number: 2305 771 0695, password: October12@11am) (Recording)
  • Week 3, Oct 19, 11 a.m. – 1 p.m. ET: Loops; Shell scripts (Part I) (WebEx link; meeting number: 2303 882 4082, password: October19@11am) (Recording)
  • Week 4, Oct 26, 11 a.m. – 1 p.m. ET: Shell scripts (Part II); Finding things (WebEx link; meeting number: 2317 368 0772, password: October26@11am) (Recordings of Shell scripts (Part II) and Finding things)

Workshop Materials:

Before the workshop: We will use a Linux virtual machine (VM) for this workshop. All registrants will receive access to this VM for the duration of each workshop. Instructions will be sent out for participants to test out logging in to the VM before 9/21 so that we can jump right in to the course material.

Presenters: Amy Stonelake, PhD, BTEP Program Manager; George Zaki, PhD, Bioinformatics Manager; Andrew Weisman, PhD, HPC Analyst, Frederick National Lab

Questions? Contact the NCI Data Science Learning Exchange

Created by Clint Malone Last Modified Thu January 13, 2022 11:36 pm by Clint Malone