Workshops

The UW-Madison Biotechnology Center is currently open and following the UW-Madison Covid-19 Response regarding campus operations.

workshop shared screen imac

Upcoming Workshops

REGISTRATION: Within the calendar below click on the selected workshop for the chosen date. Then click the “Registration” link. (If calendar below does not work click this calendar link – opens in a new window.)

Note: It is necessary to register for each workshop separately.
A confirmation email and later a reminder email will be sent.
Due to the covid-19 situation, workshops are currently only taught by video conference.

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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.

Due to the covid-19 situation, workshops are currently only 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.

Workshop details and pricing

Each workshop requires a separate registration and fee. During Covid-19 fees are reduced as material is provided electronically rather than in print.

Linux-based workshops

These workshops require access to a Linux server. As of now, this is ony possible for UW-Madison personel (see above) but may become again available to external users in the future.

The following workshops are offered on a regular basis as an all day(9am ~ 4pm) session. Only reduced online fees are shown.

Title Short description Online Fee Remarks
Linux Essentials Essential command line (bash shell) for navigating a remote Linux server and running software successfully without a mouse. $75 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) $125 All day.
bash skills required. Recommended before attending mRNAseq or ChIP workshops.
mRNAseq Workshop Principles of mRNA-Seq analysis pipelines, high level analysis, differential gene expression. $170 All day.
Recommended workshop for Advanced mRNAseq.

These workshops are not presented regularly:

Title Short description Online Fee Remarks
Survival Bash Shorter, alternate replacement of Linux Essentials $35 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. all day

R-based workshops

See also microbiota entries below.

Title Short description Online Fee Remarks
Introduction to R / Rstudio / bioconductor Preparation for Next-Generation Sequencing Data Analysis using R. Includes methods for reproducible research and markdown language. TBD All day.
Preparation to all other R-based workshops. Provides insights to essential Rcommands.
Introduction to R / Rstudio Cover classic R and elements of Tidyverse and reproducible research (dynamic documents.) TBD ½ day.
Preparation to other R-based workshops. Insights to essential Rcommands.
mRNA-Seq Analysis with R Focused on differential gene expression analysis (DEG) with alternate, R-based methods TBD All day.
Prerequisites: prior experience with R
ChIP-Seq Analysis with R R-based methods to analyze ChIP-Seq data TBD 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 visualsing and interpreting DEG results. TBD All day.
Prerequisites: bash, R, mRNA-Seq analysis.
Single-cell RNA-seq TBD TBD TBD

Microbiota workshops

Workshops based on mothur:

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

Workshops based on QIIME2:

Title Short description Online Fee Remarks
Microbiome analysis using QIIME2 Amplicon-based microbiome analysis using the QIIME2 vialine command methods TBD 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. TBD All day.
Prerequisites: familiarity with R and basic understanding of statistical method and QIIME2

Get yourself and your laptop ready for data analysis

There is a minimal set of software that should be installed on laptops BEFORE attending a workshop. Instructions will be provided to attendees prior to the workshop and can also be found within the following PDF documents. 

– One for open-source, Linux-based workshops
– One for R-based analysis workshops

Preparation for Linux-based workshops
Preparation for R-based workshops

There are numerous online resources that can help you get started learning Linux and NGS analysis. Here is a list of some useful websites:

Linux:

General Data Analysis:

  • Harvard CS109 Data Science: cs109.github.io/2015 (contains  CS 109 taught from 2013 to present)

 


Previous workshop Dates

Advanced mRNA-seq (part I):
2018 July 30

mRNA-seq Data Analysis:
2021 April 26 (online), July 21 (online)
2020 May 7 (online pilot), Aug 14 (online), Oct 26 (online), Dec 14 (online)
2020 Feb 28
2019 Feb 25, Apr 22, July 12, Nov 11
2018 Feb 21, Apr 18, May 16, July 23, Oct 3, Dec 5
2017 Mar 3, Apr 7, May 12, June 2, July 19, Sep 20, Oct 13, Dec 8
2016 Mar 11, Apr 29, July 20, Oct 31
2015 Mar 12, Apr 24, May 29, Nov 6, Dec 15
2014 Dec 9, Oct 28, May 12, Mar 18
2013 Dec 2, Oct 28

Introductory NGS Data Analysis:
2021 April 19 (online), July 19 (online)
2020 Feb 14, Oct 19 (online), Dec 7 (online)
2019 Feb 18, Apr 15, July 11, Nov 4
2018 Feb 14, Apr 11, May 9, July 16, Sep 26, Nov 28
2017 Feb 24, Mar 31, May 5, June 21, Sep 15, Dec 6
2016 Mar 4, Apr 22, July 15, Oct 24
2015 Mar 11, Apr 23, May 27, Oct 30, Dec 11
2014 Dec 5*, Oct 10*, May 9*, Mar 4*
2013 Oct 14*, Sep 30*, May 6*

Survival Bash
2020 April 29 (online Pilot), August 13 (online)
2019 Sep 27

Linux Essentials (Stand alone classes)
2021 April 5 (online), July 12 (online)
2020 Feb 7, Oct 12 (online), Nov 23 (online)
2019 Feb 11, Apr 8, July 9, Oct 28, Oct 28
2018 Feb 7, Mar 24, Apr 4, May 2, July 9, Sep 19, Nov 19
2017 Jan 27, Feb 3, Mar 24, Apr 28, May 31, June 19, July 12, Sep 13, Oct 4, Nov 1, Dec 1
2016 Mar 2, Apr 20, July 6, July 13, Oct 17
2015 Mar 11, Apr 23, May 28, Oct 23, Dec 4

ChIP-seq Data Analysis:
2017 July 17, Sep 29
2015 Mar 13, June 1, Nov 13
2014 Dec 18

Single Cell RNA-Seq Analysis:
2016 July 27

Microbiota Processing with mothur:
2019 Oct 7
2018 May 7, Oct 10
2017 Mar 30, Nov 3
2016 Nov 4

Microbiota Analysis in R (of mothur files)
2019 Oct 14
2018 May 14, Oct 17
2017 Apr 13, Nov 17
2016 Nov 11

Microbiome Analysis: QIIME2
2021 March 22 (online)
2020 Feb 19, Nov 9 (online)
2019 May 8, Oct 21

Analysis of microbiome data with R (after QIIME2)

2021 March 19 (online)
2020 Feb 26, Nov 16 (online)

Introduction to R/RStudio + bioconductor
2019 July 23

Introduction to R/RStudio 1/2 day
2021 March 08 (online)
2020 Nov 2 (online)

mRNA-Seq analysis with R
2019 July 26

(*) Combined with Linux Essentials