Shell for Bioinformatics

Note: Some HBC workshops are taught in person and others online via Zoom. Please take note for scheduling purposes!

ONLINE Workshop dates and times:

Tuesday, January 21, 2025: 9:30 AM - 12 PM

Friday, January 24, 2025: 9:30 AM - 12 PM

Tuesday, January 28, 2025: 9:30 AM - 12 PM <!– Tuesday, April 22, 2025: 9:30 AM - 12 PM

Friday, April 25, 2025: 9:30 AM - 12 PM

Tuesday, April 29, 2025: 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!

Description:

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:

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) - guest logins are provided

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

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.