Intro to Linux & Biocluster (Spring 2019)

Workshop Description

This workshop will:

• Teach the basics of command line Linux, necessary to run most bioinformatics software
• Explain how to interact with Biocluster2, log onto a compute node, and submit job scripts (using a SLURM scheduler)
• Fulfill part of the pre-requisites needed for the upcoming RNA-Seq workshop. The other pre-requisite is a basic understanding of R.

This two-part workshop being taught by HPCBio (with the support of the OVCR) & CNRG will be held February 13th & 15th from 9am - 12:30pm. This workshop fulfills part of the pre-requisites needed to attend the following RNA-Seq workshop. The other pre-requisite is a basic understanding of R programming.

This workshop will familiarize attendees with basic Linux CLI commands that enable one to move around a linux directory, and create, investigate and manipulate files. Students will be introduced to the structure of IGB's computational cluster, Biocluster, and will learn how to interact with the cluster both interactively and via job scripts (a set of written instructions for the cluster to execute). Biocluster uses a SLURM scheduler, which is software that allows one to interact with computational clusters.

This workshop is appropriate for all graduate students, post-docs, and researchers. No prior knowledge of Linux or R are required.

FAQs

Is this a pre-requisite for the RNA-Seq workshop?

Yes! This workshop fulfills part of the pre-requisites needed to attend the following RNA-Seq workshop. The other pre-requisite is a basic understanding of R programming. The only reason you would not need to take this before the RNA-seq workshop, is if you feel very confident with basic linux CLI, and using SLURM commands on Biocluster.

What are the dates and times of this workshop?

The workshop falls on February 13 & 15th. It will run from 9am to 12:30pm each day.

How do I pay using a C-FOPAL account number?

Please register as a "Participant (Pay $20 via UIUC account)". During checkout, please provide us with the account number you wish to use for payment. Please note that we are not able to accept grant accounts (those starting with 1-4 and 1-5). If you want to use a grant account, we suggest paying by card and then providing the receipt to your department's business office for reimbursement.

What if I do not work at or attend UIUC?

We ask that non-UI (University of Illinois) attendees email us at hpcbiotraining@igb.illinois.edu to sign-up for a workshop rather than using the Eventbrite links.

Do I need to bring my own computer?

Dell desktops will be available for every attendee. You may bring your own laptop, but make sure to have the necessary software installed (you will be emailed these details before the workshop starts).

What if I need to miss a day of the workshop?

All of the sessions will be recorded (assuming no technical difficulties arise), and necessary materials and slides will be posted on a workshop webpage.

What if I can't attend this workshop at all, but would like to attend the RNA-Seq workshop?

Please contact us at hpcbiotraining@igb.illinois.edu to explore alternatives.

When do ticket sales end?

We will stop selling tickets on February 13th at 9am.

Why have the workshop fees changed?

Thanks to the generosity of the OVCR (Office of the Vice Chancellor for Research) we are able to offer our workshops for a nominal fee. Without this support, the true cost to run such workshops could be hundreds to over a thousand dollars per attendee.

How can I contact the organizer with any questions?

You may email us at hpcbiotraining@igb.illinois.edu for any questions pertaining to training.