Workshops

Upcoming Workshops

Workshops are offered at least once every semester. Registration opens about 3 weeks before the actual workshop dates or series. Dates will appear in Calendar below when scheduled.
(The Agenda list format may help find future dates.)

Workshops are heavily based on direct hands-on experience.

REGISTRATION: Within the calendar click on the selected workshop on the chosen date. Then click the “Registration” link. (Alternatively open calendar link in a new window.)
Use links Look for earlier events and Look for more to navigate calendar dates.

Note: It is necessary to register for each workshop separately. A confirmation email and later a reminder email will be sent.

Workshop details and pricing

The workshop series are categorized by the underlying supporting software, primarily Linux-based open-source software and R-based software. Another category is specific for Microbiota analysis. Each workshop requires a separate registration and fee.

Linux-based workshops

These workshops use “open source” software and require access to a Linux server. As of now, this is only possible for UW-Madison personnel (see below “Who can attend”) but may become again available to external users in the future. External users with their own server might qualify.
Current offerings are “in person.”

R-based workshops

These workshop only require a personal computer with R and RStudio software installed.

Microbiota workshops

Microbiota workshops are offered for either mothur or QIIME2 depending on the availability of instructors.

Flow Cytometry

These workshop only require a personal computer with FloJow software installed. Installation/License provided

Descriptions and fees

Find more details on the description and associated fees for the workshops within the accordion links below.

Linux-based workshops

The following workshops are offered on a regular basis as an <q>all day</q> (9am ~ 4pm) session.

Title	Short description	In Person Fee	Remarks
Linux Essentials	Essential command line (`bash` shell) for navigating a remote Linux server and running software successfully without a mouse.	$145	All day. Required before other workshops. Declaration of proficiency is accepted.
Intro to NGS Data Analysis	Practice hands-on analysis of Next Generation DNA Sequencing data to identify single nucleotide polymorphisms (SNP)	$210	All day. `bash` skills required. Recommended before attending mRNAseq or ChIP workshops.
mRNAseq Workshop (Tuxedo Suite 1)	Principles of mRNA-Seq analysis pipelines, high level analysis, differential gene expression.	$290	All day. Recommended workshop for Advanced mRNAseq.
mRNA-seq (Tuxedo Suite 2)	Set-up of an mRNA-Seq analysis pipelines analysis with differential gene expression on a laptop leveraging “container” software technology.	$375	All day. Recommended workshop for Advanced mRNAseq and scRNAseq.

The workshops below are not presented regularly:

Title	Short description	Online Fee	Remarks
Survival Bash	Shorter, alternate replacement of Linux Essentials	$85	only 2 hours.
ChIPseq	Covers major aspects of ChIP-seq data analysis: quality control, mapping, normalization, peak calling, peak annotation, analysis of motifs, visualization of results.	$210	all day

R-based workshops

Title	Short description	Fee	Remarks
Introduction to R / Rstudio / bioconductor	Preparation for Next-Generation Sequencing Data Analysis using `R`. Includes methods for reproducible research and markdown language.	$195	All day. Preparation to all other `R`-based workshops. Provides insights to essential `R`commands.
Introduction to R / Rstudio	Cover classic R and elements of Tidyverse and reproducible research (dynamic documents.)	$145	½ day. Preparation to other `R`-based workshops. Insights to essential `R`commands.
mRNA-Seq Analysis with `R`	Focused on differential gene expression analysis (DEG) with alternate, `R`-based methods	$190	All day. Prerequisites: prior experience with `R`
ChIP-Seq Analysis with R	`R`-based methods to analyze ChIP-Seq data	$190	All day. Prerequisites: prior experience with `R`
Advanced mRNAseq differential gene expression	Differential gene expression analysis (DEG) in more depth (statistical methods and normalization.) Focus on visualzing and interpreting DEG results.	$275	All day. Prerequisites: `bash`, `R`, mRNA-Seq analysis.
New for Fall 2024. Single-cell RNA-seq	Cover fundamentals of single-cell technologies and Sc-RNA-seq data analysis including tips for experimental design. Learn how to turn raw data into biological insight with hands-on analysis of real datasets. Focus on `Seurat` R package, and overview of other software.	$650	Workshop spans 2 full days. Prerequisites: prior experience with `R` strongly encouraged.

The following workshop uses R for differential gene expression. It should be noted that the mapping of “reads” from fastq files (to create Sam/Bam files) is never done within R.

Transcript-level mRNAseq on the desktop with Docker”

Set-up of an mRNA-Seq analysis pipelines analysis with differential gene expression on a laptop leveraging “container” software technology.

$375

All day.
Recommended workshop for Advanced mRNAseq and scRNAseq.

Microbiota workshops

Workshops based on mothur:

Title	Short description	in person Fee	Remarks
Microbiota Processing in mothur	Identification of operational taxonomic units (OTUs) with `mothur` from Illumina data covering 16S rRNA gene sequences.	$275	All day. Prerequisites: `bash`
Microbiota Analysis in `R`	Statistical analysis of `mothur` results with `R`.	$275	All day. Prerequisites: Microbiota Processing in mothur or prior knowledge.

Workshops based on QIIME2:

Title	Short description	in person Fee	Remarks
Microbiome analysis using QIIME2	Amplicon-based microbiome analysis using the QIIME2 vialine command methods	$275	All day. Prerequisites: `bash`
Analysis of microbiome data using `R`	Result from previous workshop to determine if and how communities differ by variables of interest using `R`.	$275	All day. Prerequisites: familiarity with `R` and basic understanding of statistical method and QIIME2

Flow Cytometry

Workshops based on FlowJo:

Title	Short description	in person Fee	Remarks
FlowJo Analysis for High-Parameter Data Sets	Intended Audience: Researchers currently using FlowJo to analyze flow & spectral cytometry data sets containing a minimum of 8 colors […] data quality control, clean up, normalization, and dimensionality reduction algorithms […]	$195	All day. Access to FlowJo will be provided.

Note: participants can obtain a Free 30-day FlowJo trial.

FlowJo full License can be obtained at UW: The Flow Lab hosts a site license for FlowJo Single Cell Data Analysis Software available to anyone with an “@wisc.edu” email account. The cost of the license is about $220 per registration, per year.

Who can attend

Workshops are primary organized for UW-Madison personnel using the services of the DNA-sequencing facility and are taught on Linux server with access to the same software utilized by the Biotechnology Center Bioinformaticians. All UW-Madison personnel is welcome to attend.

Recent changes in the overall UW-Madison Campus network now prevents non-UW-Madison users to access the Linux servers. We are working on ways to address this issue for the future.

Note: some workshops are held in person while others may be taught by video conference.

Workshop design

The workshops are designed to learn by doing and are therefore very hands-on in practice. The successive workshops provide incremental learning. There are no prior requirements to attend, but a knowledge of bash is essential to navigate a remote Linux computer. Therefore the first workshop titled Linux Essentials is required unless proficiency is declared.

There are many analysis methods and the workshop presentation is just an example of data analysis that may need to be adapted for user’s own research.

The workshops are based on open source software that users can access and download on their own systems.

Suggestions to prepare for workshops.

List of previous workshop dates