Introduction to the Command-Line Interface (Shell, Bash, Unix, Linux) (2023)

Note: In 2023, some HBC workshops will be taught in person and others will be online via Zoom.

ONLINE Workshop dates and times:

Tuesday, November 14th 2023: 9:30 AM - 12 PM

Friday, November 17th 2023: 9:30 AM - 12 PM

Tuesday, November 21st 2023: 9:30 AM - 12 PM

Instruction will be mostly learner-centric, requiring a time commitment between the workshop sessions!

Description:

Access to tools and computational resources for large-scale data analysis often require knowledge of the command-line interface (also referred to as Unix or Linux or bash or shell). In this 3-day hands-on workshop participants will learn the following:

basic shell commands for navigating the file system, exploring file contents, performing basic operations, such as moving, copying, and renaming
how to write shell scripts and use “for” loops for efficiently running the same commands on multiple files
how to use HMS-RC’s O2 cluster for high-performance computing (HPC)

Together, this knowledge is critical for researchers looking to improve efficiency when performing computational tasks and it forms the foundation needed to analyze high-throughput sequencing data.

Prerequisites:

This is one of our basic workshops, and has NO prerequisites and no prior programming experience is required.

This workshop is a prerequisite for advanced workshops introducing the analysis of RNA-seq, ChIP-seq and Introduction to Chromatin biology.

Who should attend?

Eligible* Harvard researchers who:

want to learn how and why to use the command line interface (Unix/Linux Shell) to efficiently manage and analyze data
want to use local clusters/high-performance computing environments for analyzing data (e.g. HMS-RC’s O2 cluster, or FASRC cluster)
are interested in taking an advanced workshop with us on analysis of sequencing data within the next 6 - 8 months

Cost:

There is a non-refundable and non-transferable $50 registration fee for this workshop.

We will be accepting 25 participants on a first-come, first-served basis:

If you are one of the first 25 eligible* registrants, you will receive an email within 1 week with a link to pay the (non-refundable & non-transferable) $50 registration fee.
If you are not among the first 25 eligible* registrants, you will be added to the waitlist and notified when we open registration for the next iteration of this workshop.

NOTE: You will not have a reserved seat for this workshop until you pay the registration fee. Please make sure you pay within the time stated in that email, else you will lose your spot to someone on the waitlist.

*NOTE: HMS Graduate Students may receive waivers on registration fees. Please register and we’ll followup with you.

Registration:

Please make sure you take the following into account when signing up for the workshop:

Mandatory attendance for all three classes.
2-3 hours of reading and exercises from selected lessons before each workshop session.
Active paricipation during discussion sessions.

(Registration opens 2 weeks before the start of basic workshops.)

Eligibility requirements:

^*To be eligible to attend this workshop you should fulfill at least one of the following criteria:

Harvard Medical School researcher in a lab on the Quad, with grants administered by HMS Gordon Hall
Harvard School of Dental Medicine researcher, with grants administered by HMS Gordon Hall
Graduate student at the Harvard Medical School
Researcher affiliated with the Dana-Farber / Harvard Cancer Center (DF/HCC).
Researcher at a Harvard affiliated institution participating in HIV related research.

If you are unsure of your eligibility, please register anyway and we will get back to you.

(Please check the eligibility requirements prior to registering)

NOTE: We do not record our training sessions.

Questions?

Please email us at hbctraining@hsph.harvard.edu with any questions.