HPCBio

Spatial RNA-Seq Analysis Workshop WHEN: Held over 4 Wednesdays, & an optional 4 Fridays from Oct. 29 – Nov. 21 (See table below). We’ll meet 10am – 3pm w/ an hour break for lunch. Wednesdays will be held online, and Fridays will be held in-person. Dates Wednesday Friday Oct. 29 & 31 Main workshop Advanced workshop Nov. 5 & 7 Main workshop Advanced workshop Nov. 12 & 14 Main workshop Advanced workshop Nov. 19 & 21 Main workshop Advanced workshop Note: We will record the main workshop sessions if you must miss part of a day and make it up later. WHAT:  In addition to our main Spatial RNA-Seq Analysis workshop we are offering advanced Friday sessions. The online main workshop will include an introduction to spatial technology and experimental design, and detailed steps on how to perform bioinformatics and statistical analyses on 10X Genomics’ Visium spatial gene expression data in Linux and R platforms. This includes software like SpaceRanger and Loupe browser, as well as R packages like Seurat. The advanced Friday sessions will include in-person opportunities to apply what we’ve learned in the workshop to your own dataset (or a published dataset) under the guidance of HPCBio staff. What we’ve noticed in the past, is that every dataset is different and there may be several small or large differences between your data and the example dataset provided on Wednesdays that could be tricky to navigate. Due to this, attendees are more likely to achieve their personal research goals by receiving the more individualized guidance offered in these advanced sessions. WHO:  Intended for graduate students, post-docs, research staff, and faculty from any University/organization (different rates apply; see COST section). PREREQUISITES:  A beginner knowledge of bash (a.k.a command line linux), high-performance computing (HPC), and R programming is required to take this workshop. After your registration, we will provide details and materials on how to fulfill these requirements on your own time. This is a fast-paced workshop; while it will reasonable to ask questions about bash, HPC, and R if you forget something, it is not possible for us to catch you up if you haven’t reviewed any prerequisite material. WHERE:  The main workshop on Wednesdays will be held online via Zoom. The Advanced Friday sessions will be held on Fridays in-person at the Institute of Genomic Biology. COST:  See table below.     Main Workshop   Advanced Fridays*  UIUC, UIC, & UIS  $650.00 $600.00 Public Illinois University  $780.00 $720.00 Other  $856.05 $790.20 * Since seats are limited in the advanced Friday sessions, you will only have the opportunity to apply for them when you register for the main workshop. You won’t be charged for them until you are accepted into the advanced Friday sessions. HOW:  Registration has ended.

Microbial Profiling Analysis Workshop WHEN: Held over 3 Fridays from 10am – 2:45pm; Sept. 12, Sept. 19th, & Sept. 26th.   Note: We will record the sessions if you have to miss part of a day and make it up later. WHAT: 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. After a brief introduction to microbial profiling, attendees will be provided a practice data set, and begin processing and filtering the sequenced reads on a high performance computational cluster (Biocluster), and then will cluster these reads into amplicon sequence variants (ASVs). In R, attendees will learn how to perform common statistical analyses and create informative visualizations to investigate abundance and diversity of microorganisms present in the data set. WHO: Intended for graduate students, post-docs, research staff, and faculty from any University/organization (different rates apply; see COST section). PREREQUISITES: A beginner knowledge of bash (a.k.a command line linux), high-performance computing, and R programming is required to take this workshop. After your registration, we will provide details and materials on how to fulfill these requirements on your own time. This is a fast-paced workshop; while it will reasonable to ask questions about bash, HPC, and R if you forget something, it is not possible for us to catch you up if you haven’t reviewed any prerequisite material. WHERE: It will be held online via Zoom. COST: $375 for University of Illinois (UIUC, UIC, & UIS) employees, students, and affiliates. $450 for other State of Illinois Public Universities. $493.88 for all other institutions. HOW:  U of Illinois (UIUC, UIC, UIS) students and employees may register HERE. All others may register HERE. Registration deadline is September 7th!  

WHAT: 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. After a brief introduction to microbial profiling, attendees will be provided a practice data set, and begin processing and filtering the sequenced reads on a high performance computational cluster (Biocluster), and then will cluster these reads into amplicon sequence variants (ASVs). In R, attendees will learn how to perform common statistical analyses and create informative visualizations to investigate abundance and diversity of microorganisms present in the data set. WHO: Intended for graduate students, post-docs, research staff, and faculty. If you are not affiliated with the University of Illinois, you’ll be able to email hpcbio-training@biotech.illinois.edu for alternative sign-up information when registration opens. PRE-REQUISITES: Beginner knowledge of bash (a.k.a command line linux), high-performance computing, and R programming. After registration, we will provide details and optional materials on how to fulfill these requirements. This is a fast-paced workshop; we will not have time to bring you up to speed. WHERE: 241 Wohlers Hall. This is not a computer lab. There will be tables and outlets for your laptops. WHEN: 10am – 3pm (12-1pm will be a lunch break); April 4th, April 11th, and April 18th.    Note: We will record the sessions if you have to miss part of a day and make it up later. COST: $350 for University of Illinois employees, students, and affiliates. Please email if you are outside of the U of I system. HOW: Seats limited to 25 attendees. Registration deadline extended to March 28!  Please register HERE.