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Shell on HPC for Bioinformatics (2024)

Note: In 2024, some HBC workshops will be taught in person and others will be online via Zoom.

IN-PERSON Workshop dates and times:

Location: Longwood Medical Area

Tuesday, September 3, 2024: 9:30 AM - 12 PM

Friday, September 6, 2024: 9:30 AM - 12 PM

Tuesday, September 10, 2024: 9:30 AM - 12 PM

NOTE: Workshop dates are subject to change

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


Large-scale data analysis often requires use of high-performance computing (HPC) resources and knowledge of tools available via 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:

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.


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 including the upcoming Variant Calling and Understanding Chromatin biology (ChIP-seq/ATAC-seq) workshops as well as Introduction to bulk RNA-seq I.

Who should attend?

Eligible* Harvard researchers who:


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:

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.


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

  1. Mandatory attendance for all three classes.
  2. 2-3 hours of reading and exercises from selected lessons before each workshop session.
  3. 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:

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.


Please email us at with any questions.