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HPCBIO WORKSHOPS

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ABOUT HPCBIO WORKSHOPS
 

Our Training Mission

We recognize that there are many researchers on (and off) the UIUC campus that need help analyzing their genetic data computationally and statistically. Our goal, in addition to offering consultation services, is to offer hands-on and practical bioinformatics workshops that are relevant and up-to-date. We hope these workshops will enhance graduate students, post-docs, and faculty's understanding of popular bioinformatics topics and skills such as Linux, R, RNA-Seq, ChIP-Seq, 16S micrombiome analysis, and more!
 

Explanation of workshop fees

The true cost to run bioinformatics-based workshops can range from hundreds to over a thousand dollars per attendee, but we strive to keep these costs low so that all UIUC students, post-docs and faculty can benefit from hands-on bioinformatics workshops to enhance their research. And thanks to the support of the OVCR (Office of the Vice Chancellor for Research) are now able to offer HPCBio workshops for nominal fees. If you have trouble with paying for the workshops due to unexpected circumstances, please let us know and we may be able to waive the fees. We also welcome attendees from outside of UIUC, but please keep in mind that there are additional charges for external attendees. We ask that non-UIUC attendees email us at hpcbiotraining@igb.illinois.edu to sign-up for a workshop rather than using the Eventbrite links.
 

 

UPCOMING WORKSHOPS

HPCBio Spring 2019 Workshop Schedule

  Day of the week
Semester Week Date(s) Time Wednesday Thursday Friday
3 Jan. 31 & Feb. 1 9am-4:30pm   DC for Genomics (pt. 1) DC for Genomics (pt. 2)
4 Feb. 4-8        
5 Feb. 13 & 15 9am-12:30pm Intro to Linux & Biocluster (pt. 1)   Intro to Linux & Biocluster (pt. 2)
6 Feb. 22 9am-12:30pm     RNA-Seq Analysis (pt. 1)
7 Mar. 1 9am-12:30pm     RNA-Seq Analysis (pt. 2)
8 Mar. 8 9am-12:30pm     RNA-Seq Analysis (pt. 3)
9 Mar. 15 9am-12:30pm     RNA-Seq Analysis (pt. 4)
10 Mar. 18-22   Spring Break Spring Break Spring Break
11 Mar. 27 & 29 9am-12:30pm Intro to R & Bioconductor (pt. 1)   Intro to R & Bioconductor (pt. 2)
12 Apr. 5 9am-12:30pm     RNA-Seq Analysis (pt. 5)
13 Apr. 12 9am-12:30pm     RNA-Seq Analysis (pt. 6)
14 Apr. 19 9am-12:30pm     RNA-Seq Analysis (pt. 7)
15 Apr. 26 9am-12:30pm     RNA-Seq Analysis (pt. 8)

The above outlines the schedule for all of HPCBio's Spring workshops. Note that the introductory workshops have been scheduled around the longer RNA-Seq workshop in a way that works best with the topics covered. 


Workshop Details

DC (Data Carpentry) for Genomics

A two full-day (Jan. 31 & Feb 1) workshop jointly conducted by CSE and HPCBio, that allows attendees to learn basic skills necessary to get started working on genomic data. This includes hands-on introductions to linux command line, R programming and Bioconductor packages, as well as running through a basic bioinformatics workflow.

More info & sign up: eventually will be listed here -> https://cse.illinois.edu/cse-training/

Intro to Linux & Biocluster

This two-part workshop being taught by HPCBio & 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. 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. 

More info & sign up: https://hpcbio-linux-hpc-sp2019.eventbrite.com

Intro to R & Bioconductor

This two-day workshop will be held from 9am - 12:30pm (Mar 27 & 29), and is a pre-requisite to the Spring 2019 RNA-Seq workshop. The aim of this workshop is to introduce attendees to basic R commands, functions, and jargon needed to transform a novice into a beginning R/Bioconductor user. Additionally, we will give an overview of the Bioconductor project, common object structures and manipulation, tips on finding particular packages and how to start learning to use a package.

More info & sign up: https://hpcbio-r-sp2019.eventbrite.com

RNA-Seq Analysis

This workshop will be held on 8 Friday mornings from 9am - 12:30pm. Please see calendar below for exact dates. This workshop will cover experimental design, evaluation of sequencing quality, genome alignment, gene count extraction, differential gene expression analysis and downstream data mining. This requires a background knowledge of basic R, Linux, and Biocluster usage.

More info & sign up: https://hpcbio-rnaseq-sp2019.eventbrite.com

What workshops do you want to be offered?

We would love your input as to what kind of topics you'd like to see covered in a HPCBio workshop for the future, so please let us know in this 2 question survey: https://goo.gl/forms/CcjDRONHByeoX2KY2.


 

PREVIOUS WORKSHOP MATERIALS
 
Creative Commons License
HPCBio Workshop materials are licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.
 
 
Microbiome rRNA Analysis (+ Intro to Linux)

Description: This workshop will teach attendees how to analyze rRNA amplicon (e.g. 16S, 18S, ITS...) microbiome datasets for the purpose of investigating the presence and diversity of microorganisms. This workshop first aims to familiarize attendees with basic Linux commands necessary to run microbiome analysis programs, and to give an introduction to amplicon design and sequencing. Attendees will be provided a practice dataset, and begin analysis by properly processing and filtering the sequenced reads, followed by clustering these reads into operational taxonomic units (OTUs). Following this, attendees will learn how to perform common statistical analysis and create informative visualizations to investigate abundance and diversity of microorganisms present in the dataset.

Link to Materials:

October 2018 (QIIME2)

August 2017 (QIIME2)

July 2016 (QIIME)

August 2015 (QIIME)

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Introduction to R

Description: R is a free, open-source software environment and programming language for statistical computing and graphics. It is available for all computer platforms and is widely used, and many packages have been developed in the Bioconductor project for analysis of genomic data, including Next Generation Sequencing (NGS) data. This workshop aims to take the novice and turn them into a beginning R user. We will describe the R environment and programming language structure so that students can start to read and write code and know where to get additional help.

Links to Materials:

Fall 2017

Fall 2016

Fall 2015

Spring 2015

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Introduction to R and Bioconductor

Description: R is a free, open-source software environment and programming language for statistical computing and graphics. It is available for all computer platforms and is widely used, and many packages have been developed in the Bioconductor project for analysis of genomic data, including Next Generation Sequencing (NGS) data. This workshop aims to take the novice and turn them into a beginning R/Bioconductor user. We will describe the R environment and programming language structure so that students can start to read and write code and know where to get help. Additonally, we will give an overview of the Bioconductor project, common object structures and manipulation, tips on finding particular packages and how to start learning to use a package.

Links to Materials:

Fall 2018

Spring 2018

Spring 2016

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Introduction to Linux and Biocluster

Description: The Linux command line interface is a text-based way of interacting with a computer, particularly high performance computer systems that are capable of analyzing NGS data. The most common and cutting-edge bioinformatics tools are best run via the command line. This is a workshop for biologists who want to get acquainted with using the Linux command line interface. Additionally, the workshop will cover the basics of cluster computing and how to navigate and submit jobs to IGB’s Biocluster high performance computing environment.

Links to Materials:

Fall 2018

Spring 2018

Fall 2017

Fall 2016

Spring 2016

Fall 2015 

Spring 2015

Fall 2014

 
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RNA-Seq analysis with Biocluster and R

Prerequisite: R, Linux, & Biocluster knowledge

Description: Sequencing of RNA (RNA-Seq) is the latest method to assess global gene expression because it can be done on any species.  This is a 4-day workshop for biologists who are doing or plan on doing RNA-Seq experiments and would like to learn how to analyze their data. It will cover experimental design, evaluation of sequencing quality, genome alignment, gene count extraction, differential gene expression analysis and downstream data mining. It will also include discussions of what to do if your species lacks gene models and/or a genome.

Links to Materials:

Spring 2018

Spring 2017

Fall 2016

Spring 2016

Fall 2015 

Spring 2015

 
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Description: This workshop is geared towards biologists who would like to learn the tools for graphical representation and visualization of genomics data. The focus will be on two genome browsers, Integrative Genomics Viewer (IGV) and the Ensembl browser, and Ensembl's BioMartThis workshop will cover how to use each browser, including the use of pre-generated datasets and custom datasets.

Link to Materials:

Spring 2016

Spring 2014 

 

Computational Skills for Genomics Workshop

Description: This hands-on workshop, jointly taught by HPCBio and CNRG, aims to introduce you to high performance cluster computing, linux command line, R programming and Bioconductor packages. In addition, attendees will learn how to move data to a computational cluster, and perform initial quality control steps on sequence reads using FASTQC. Knowledge of Linux and R can be very useful for analyzing genomics and many other -omics data. At the end of this workshop you will gain a familiarity with Linux and R commands. You will not become an expert in genomics analysis techniques, but you will get an idea of where to start when given raw sequence data.

Link to Materials:

November 2018

March 2017

 

Data Carpentry Genomics Workshop

Description: Join this workshop being conducted by HPCBio, CSE, and KnowEng to learn basic skills necessary to get you started working on genomic data. This includes hands-on introductions to high performance cluster computing, linux command line, best data tidiness practices, R programming and Bioconductor packages. In addition, attendees will learn how to move sequencing data to a computational cluster, and perform initial quality control steps.

Link to Materials:

Fall 2018

Spring 2018

Summer 2016

Summer 2015

 

ChIP-Seq analysis

Description:  ChIP-Seq is a sequencing method used to investigate protein binding sites in DNA. This three half-day workshop will introduce you to this method of sequencing as well as teach you how to process the sequences, align sequences to a reference, and call peaks by following a bioinformatics pipeline used by HPCBio staff. Additional topics such as normalization, visualization,  will be explored as time allows.

Link to Materials:

Fall 2017