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Upcoming Workshops

Below are our plans for the upcoming semester. This semester we will be offering all of our workshops online, but they will be live on Zoom at scheduled times. Due to staff time constraints we will be teaching for 2-hour sessions on Wednesday and Friday afternoons. See the table below for an idea of what to expect this semester. Below this table are more details and links for each workshop.

HPCBio Fall 2020 Workshop Schedule

      DAY OF THE WEEK
Week Date(s) Time Wednesday Friday
3 Sept. 9 & 11 1-3pm Intro to Linux & Biocluster (pt. 1) Intro to Linux & Biocluster (pt. 2)
4 Sept. 16 & 18 1-3pm Intro to Linux & Biocluster (pt. 3) Intro to Linux & Biocluster (pt. 4)
5 Sept. 23 & 25 1-3pm Microbial Profiling (pt. 1) Microbial Profiling (pt. 2)
6 Sept. 30 & Oct. 2 1-3pm Microbial Profiling (pt. 3) Microbial Profiling (pt. 4)
7 Oct. 7 & 9 1-3pm Microbial Profiling (pt. 5) Microbial Profiling (pt. 6)
8 Oct. 14 & 16 1-3pm Intro to R & Bioconductor (pt. 1) Intro to R & Bioconductor (pt. 2)
9 Oct. 21 & 23 1-3pm Intro to R & Bioconductor (pt. 3) Intro to R & Bioconductor (pt. 4)
10 Oct. 28 & 30 1-3pm 10X Single Cell RNA-Seq Analysis (pt. 1) 10X Single Cell RNA-Seq Analysis (pt. 2)
11 Nov. 4 & 6 1-3pm 10X Single Cell RNA-Seq Analysis (pt. 3) 10X Single Cell RNA-Seq Analysis (pt. 4)
12 Nov. 11 & 13 1-3pm 10X Single Cell RNA-Seq Analysis (pt. 5) 10X Single Cell RNA-Seq Analysis (pt. 6)
13 Nov. 18 & 20 1-3pm 10X Single Cell RNA-Seq Analysis (pt. 7) 10X Single Cell RNA-Seq Analysis (pt. 8)
14 Nov. 23-27 NA FALL BREAK FALL BREAK
15 Dec. 2 & 4 1-3pm Advanced R: Variant Analysis (pt. 1) Advanced R: Variant Analysis (pt. 2)

The above outlines the schedule for all of HPCBio's Fall 2020 workshops. See below for more details and sign-up links.


WORKSHOP DETAILS

Please read all details on each Eventbrite page before purchasing a ticket!

 

INTRO TO LINUX & BIOCLUSTER

Prerequisites: None

This four-part workshop taught by HPCBio (with the support of the OVCR) & CNRG will be held September 9, 11, 16, & 18 from 1-3pm each day. This workshop fulfills a pre-requisite needed to attend the following Microbial Profiling and 10X Single Cell RNA-Seq Analysis 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 (a set of written instructions for the cluster to execute). 

More info & sign up: Closed

 

MICROBIAL PROFILING ANALYSIS

Prerequisites: Intro to Linux & Biocluster or pre-existing knowledge/experience with bash and Biocluster. Email us at hpcbiotraining@igb.illinois.edu for alternatives.

This six-part workshop held from September 23 to October 9 (see calendar for exact dates) from 1-3pm each day, 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.

More info & sign up: Closed

 

INTRO TO R & BIOCONDUCTOR

Prerequisites: None

This two-day workshop will be held on Oct. 14, 16, 21, & 23 from 1pm - 3pm each day, and is a pre-requisite to the following 10X Single Cell RNA-Seq Analysis 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: Closed

 

10X SINGLE CELL RNA-SEQ ANALYSIS

Prerequisites: Intro to Linux & Biocluster and Intro to R & Bioconductor; Or pre-existing knowledge/experience with bash, HPC on Biocluster, R, and Bioconductor. Email us at hpcbiotraining@igb.illinois.edu for alternatives.

This workshop will be held over 8 sessions from Oct. 28 - Nov. 20 (see calendar above for exact days) from 1pm - 3pm each day. The aim of this workshop is to expose attendees to 10X Single Cell technology from a data analysis perspective rather than a wet-lab perspective. Attendees will be introduced to single cell applications and experimental design considerations. Additionally, attendees will learn how to analyze, explore, and visualize an RNA-Seq example dataset through hands-on exercises covering command line software and R packages.

More info & sign up: Closed

 

ADVANCED R: Variant Analysis

Prerequisites: Intro to R & Bioconductor or knowledge and pre-existing knowledge of  R and Bioconductor. Email us at hpcbiotraining@igb.illinois.edu for alternatives.

This two-part workshop will be held on Dec. 2 & 4 from 1pm - 3pm each day. Attendees will learn how to read, filter, and interrogate variant calls that are in VCF (Variant Call Format) format with Bioconductor packages in R. Analyses may include some or all of the following topics: assessing minor allele frequency, missing data rate, heterozygosity, and/or linkage disequilibrium; working with genome annotations as TxDb objects; discovering what genes are near SNPs of interest; identifying functional consequences of variants.

More info & sign up: https://www.eventbrite.com/e/advanced-r-variant-analysis-fall-2020-regi…