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Bioinformatics Resources for Immunologists

Date:

 Monday 4 Friday 8 June 2018

Venue: 

European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom

Application opens: 

Monday December 04 2017

Application deadline: 

Tuesday March 06 2018

Participation: 

Open application with selection

Registration fee: 

£670

Registration closed

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Overview

This course aims to provide an introduction to immunology bioinformatics, offer opportunities to explore key methods, tools and resources that can be applied to research. The course will provide participants with an overview of best-practice methods in applying bioinformatics approaches and enable them to become confident users of their own and public domain data. The resources introduced during the course will cover a variety of data types, from genomic and proteomic data; to computational models, biological pathways and reaction information. Participants will gain experience of the analysis pipelines for NGS experiments relevant to immunology, and will be led through an exploration of this data to identify information of interest. Additionally participants will be introduced to how data from a number of sources can be integrated to provide a wider view of their research.

Audience

This course is aimed at individuals working in immunology research who have minimal experience in bioinformatics. Applicants are expected to be at an early stage of using bioinformatics in their research with the need to develop their skills and knowledge further. Participants will require a basic knowledge of the Unix command line, and the R statistical package. We recommend these free tutorials: introduction to the Unix environment and basic R concepts

Syllabus, tools and resources

The course will explore a number of bioinformatics resources relevant to immunology including:

  • abYsis – antibody discovery system
  • 3i Consortium and immunology databases
  • IntAct database
  • Reactome database
  • BioModels database

Outcomes

After this course participants should be able to:

  • Locate and search publically available bioinformatics data of interest

  • Utilise software and tools to manipulate and analyse immunological data

  • Apply appropriate bioinformatics methodologies to their own research

  • To combine different types of data (eg genomic and structural) to gain further immunological insights

Programme

Time Topic Trainer
Day 1 - Monday 4 June
12:00 - 13:00 Arrival, registration and lunch  
13:00 - 14:00 Welcome, introductions and networking Tom Hancocks 
14:00 - 14:30 Introduction to EMBL-EBI data resources  Tom Hancocks
14:30 - 15:30 Antibody bioinformatics - structure and analysis Andrew Martin 
15:30 - 16:00 Break   
16:00 - 18:00 Antibody bioinformatics - structure and analysis Andrew Martin
18:00 Check-in at Wellcome Conference Centre  
18:30 - 19:30 Welcome drinks Hinxton Hall Lounges 
19:30 Evening meal Hinxton Hall Restaurant 
Day 2 - Tuesday 5 June 
08:45 Arrival  
09:00 - 09:30 Immunology resources: 3i, IMPC and beyond Lucie Abeler-Dörner
09:30 - 10:00 Introduction to advanced analysis of flow data with floSOM Yvan Saeys
10:00 - 11:00 Applying advanced analysis to a 3i data set Adam Laing & Lucie Abeler-Dörner
11:00 - 11:30 Break  
11:30 - 12:15 Comparing advanced analysis to conventional gating Adam Laing & Lucie Abeler-Dörner
12:15 - 13:00 Using advanced analysis in research Yvan Saeys
13:00 - 14:00 Lunch and posters  
14:00 - 15:30 Immunology resources: 3i, IMPC and beyond Anna Lorenc 
15:30 - 16:00 Break   
16:00 - 18:30 Ensembl Regulation resources Ensembl Outreach 
18:30 End of day  
19:00 Evening meal  Hinxton Hall Restaurant
Day 3 - Wednesday 6 June
08:45 Arrival  
09:00 - 10:00 Single-cell RNA sequencing John Marioni 
10:00 - 11:00 scRNA-Seq bioinformatics Aaron Lun, Anna Cuomo & John Marioni 
11:00 - 11:30 Break   
11:30 - 12:30 scRNA-Seq bioinformatics

Aaron Lun, Anna Cuomo & John Marioni

12:30 - 13:30 Lunch and posters  
13:30 - 15:30 High-throughput T-cell receptor repertoires Tomas Pieres de Carvalho Gomes
15:30 - 16:00 Break  
16:00 - 17:30 Immune repertoire sequencing  Velislava Petrova
17:30 - 18:30 Special lecture 1 To be confirmed
19:00 Evening meal Hinxton Hall Restaurant
Day 4 - Thursday 7 June
08:45 Arrival  
09:00 - 11:00 Molecular interaction databases Birgit Meldal & Sandra Orchard 
11:00 - 11:30 Break  
11:30 - 13:00 Molecular interaction databases

Birgit Meldal & Sandra Orchard

13:00 - 14:00 Lunch and posters  
14:00 - 15:30 Identifier mapping  Livia Perfetto
15:30 - 16:00 Break  
16:00 - 18:30 Tools for pathway analysis Thawfeek Varusai
     
19:00 Evening meal Hinxton Hall Restaurant
Day 5 - Friday 8 June
08:30 Check out  
08:45 Arrival  
09:00 - 10:00  Locating models for biological processes Rahuman Sheriff
10:00 - 10:30 Break  
10:30 - 11:15 A Novel T-cell Therapy for Targeting The Achilles Heel of Cancer Fong Chan
11:15 - 12:00 Special lecture To be confirmed
12:00 - 12:45 Special lecture To be confirmed
12:45 - 13:00 Course feedback and wrap up Tom Hancocks
13:00 - 13:45 Lunch  
14:00 Coach to Cambridge Railway Station