Glasgow Bioinformatics Summer School 2022

Please look at the change of date... We are aiming to do the workshop in person in Glasgow!

 

 

 

When: Monday 29/08/2022 - Friday 02/09/2022.

Application opening: 01/03/2022

Application Deadline: 07/07/2022

Topics: (see below for more details):

  •      Basics of Linux
  •      Introduction to R
  •      Introduction to next-generation sequencing
  •      Data visualization
  •      SNP analysis
  •      Transcriptomics: bulk RNA-Seq and single-cell RNA-Seq
  •      Databases
  •      Data processing

Keynote speaker: To be confirmed

Cost:  £600 for academics / £1000 commercial

How to apply: Places are assigned on the first-come to the first-served basis upon receipt of the fee. Please contact iii-informatics@glasgow.ac.uk for the booking.

Cancellation Policy: Cancellations more than 30 days before the start date will incur a 30% cancellation fee. Cancellations less than 30 days before the start date cannot be refunded

Participants are encouraged to attend the full course, daily, core hours 9:00-17:00h.

 

COVID-19 mitigation

We will be running the bioinformatics summer school in person this year.

We will adhere to local restrictions, which might involve face masks and hand hygiene, which we will ask the participants to follow.

 

Full description

Next generation sequencing (NGS) and bioinformatics has become an essential tool in genetic and genomic analysis. It is increasingly important for experimental scientists to gain the bioinformatics skills required to assess and analyse the large volumes of sequencing data produced by next generation sequencers. With the ongoing omics initiatives, we would like to give PhD students and postdocs the opportunity to learn about NGS and bioinformatics.

This week-long course aims to provide experimental biologists working with omics data with (i) a comprehension of “bioinformatics” language and terminology, (ii) an understanding of  the underlying concepts (iii) hands-on experience in genomic-scale data analysis for

-          Linux: The operating system for most bioinformatics software. This part will also explain how to process data on the Glasgow high performance compute cluster (HPCC each participant will need an account, information to follow). This will allow participants to apply the knowledge they have gained in the future.

-          NGS mapping and variant calling: Learn how to map sequencing reads and visualize the data. Find copy number and sequence variants and understand the different types of variation.

-          Transcriptomics:

  • Analyse a dataset by comparing the transcriptome of a knock-out versus a wildtype parasite - from the mapping of short reads, visualization, differential expression up to GO enrichment!
  • Single cell RNA-Seq

-          R is a statistical package based on a Linux like syntax. Many tools for genomics and transcriptomics analysis are written in R.  We will explore using some of these tools and creating publication-ready figures in R

-          Databases: Get an overview of the most common databases and learn how to download published data or perform simple analysis on them.

The data used during the workshop will be derived from bacteria, single celled parasites and human or mouse, but the learning outcomes can be applied to other organisms.

At the end of the course you will have the opportunity to work on a larger task with a group to gain experience of applying the learning outcomes of the course independently.  If you wish to bring your own data for the group task, please contact the course organisers in advance.

Initially, participants will work from a virtual machine, which will be provided on a USB hard disc,  and can be taken away at the end of the course at no additional cost. Some exercises will be taught on the Glasgow high performance compute cluster.

Learning outcomes

After attending this course, participants should be able to:

  • Comfortably work with state-of-the-art bioinformatics software in a Linux-like environment
  • Have a good understanding of the application, opportunities, visualization and analysis of next-generation sequencing datasets
  • Integrate and query large-scale genomic and functional genomic databases to answer biology-related research questions and develop testable hypotheses
  • Experience analysing RNA-Seq and scRNA-Seq data
  • Ideas around integrative analysis and how to run basic analysis in R

Please note: The practical sessions will be taught exclusively through Unix/Linux. Knowledge in Linux is helpful, but not required. The course aims to provide a hands-on introduction to bioinformatics for next-generation sequencing and should not be considered a complete education in the theoretical and mathematical foundations of the topics. This course is aimed at applicants solely interested in the analysis of NGS data and bioinformatics.

About the organisers

Thomas Otto is a Senior lecturer for Bioinformatics at the University of Glasgow. He has a vast experience in NGS genomics, from the basics of sequencing technologies, quality control of data, genome and transcriptomic projects and genotype to phenotype projects.

Through his career, he taught many workshops on NGS genomics, including de novo assembly, Introduction to bioinformatics (Wellcome Trust advanced courses (WTAC)), more applied workshops like working with pathogen genomes or working with parasite databases. He also teaches at the University of Glasgow data analysis, R and transcriptomics for undergraduate and masters students.

Kathryn Crouch is a team leader for the bioinformatics team at the Wellcome Centre for  Integrative Parasitology, University of Glasgow. Her background is in comparative immunology and she worked in the pharmaceutical industry for several years before taking up her current position. 

In her current role, she manages a team providing advice and computational analysis to Wellcome Centre members working with NGS and other high throughput data in eukaryotic pathogens. She also develops software for the VEuPathDB suite of databases (https://veupathdb.org/). Teaching experience includes running an applied bioinformatics module on the MSc Bioinformatics at the University of Glasgow for the last three years, and contributing to applied courses including the Wellcome Trust Advanced Courses Working with Parasite Database Resources workshop for the last six years.

The pair have run the annual Bioinformatics summer school together since 2018.