Bioinformatics for Immunologists

Date:

 Monday 15 Friday 19 July 2019

Venue: 

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

Application opens: 

Monday 14 January 2019

Application deadline: 

Tuesday 23 April 2019

Participation: 

Open application with selection

Registration fee: 

£680

Registration closed

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Overview

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

  • Computation approaches for flow cytometry
  • abYsis – antibody discovery system
  • Single-cell RNA sequencing and databases of regulatory information
  • Immunology databases
  • EMBL-EBI data resources: IntAct, Reactome, BioModels

Audience

The 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:

Syllabus, tools and resources

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

  • Computation approaches for flow cytometry
  • abYsis – antibody discovery system
  • Single-cell RNA sequencing and databases of regulatory information
  • Immunology databases
  • EMBL-EBI data resources: IntAct, Reactome, BioModels

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

Day 1 – Monday 15 July 2019
10:00-11:00 Arrival and registration EMBL-EBI South Building
11:00-12:00 Welcome, introductions and networking Tom Hancocks
12:00-12:30 Introduction to EMBL-EBI data resources Tom Hancocks
12:30-13:30 Lunch  
13:30-15:30 Computational flow cytometry Yvan Saeys
15:30-16:00 Break  
16:00-18:30 R for immunology bioinformatics Yvan Saeys & Sofie Van Gassen
18:45 Check into Conference Centre  
19:00 Welcome drinks Hinxton Hall Lounges
20:00 Evening meal Hinxton Hall Restaurant
Day 2 – Tuesday 16 July 2019
08:45 Arrival  
09:00-11:00 Handling cytometry data in R and quality control Yvan Sayes, Sofie Van Gassen, Adam Laing & Anna Lorenc
11:00-11:30 Break  
11:00-13:00 Visualising cytometry data in R Yvan Sayes, Sofie Van Gassen, Adam Laing & Anna Lorenc
13:00-14:00 Lunch and posters  
14:00-16:00 Detecting differential patterns in cytometry data Yvan Sayes, Sofie Van Gassen, Adam Laing & Anna Lorenc
16:00-16:30 Break  
16:30-18:30 B/T-cell receptor analysis Anna Lorenc
19:00 Evening meal  Hinxton Hall Restaurant
Day 3 – Wednesday 17 July 2019
08:45 Arrival  
09:00-11:00 Single-cell RNA sequencing Niels Vandamme
11:00-11:30 Break  
11:30-12:30 Single-cell RNA sequencing Niels Vandamme
12:30-13:30 Lunch and posters  
13:30-14:30 Single-cell RNA sequencing Niels Vandamme
14:30-16:00 Antibody bioinformatics - structure and analysis Andrew Martin
16:00-16:30 Break  
16:30-18:30 Antibody bioinformatics - structure and analysis Andrew Martin
19:00 Evening meal  Hinxton Hall Restaurant
Day 4 – Thursday 18 July 2019
08:45 Arrival  
09:00-10:30 Ensembl Regulation Ben Moore
10:30-11:00 Break  
11:00-12:00 Ensembl Regulation Ben Moore
12:00-13:00 Protein interactions Birgit Meldal
13:00-14:00 Lunch and posters  
14:00-16:30 Protein interactions Birgit Meldal
16:30-17:00 Break  
17:00-17:45 From the bedside to the bench and back again James Lee
17:45-18:30 Computational structural biology for antibody development Bruck Taddese
18:45 Drinks reception Hinxton Hall Lounges
19:30 prompt Silver service dinner Hinxton Hall Restaurant
Day 5 – Friday 19 July 2019
08:30 Checkout of accommodation  
08:45 Arrival  
09:00-10:30 Identifier mapping Livia Perfetto
10:30-11:00  Break  
11:00-12:30 Tools for pathway analysis Pablo Porras
12:30-13:30 Lunch and posters  
13:30-15:00 Locating models for biological processes Rahuman Sherrif
15:00-15:15 Feedback and survey Tom Hancocks
15:15 End of course  
15:30 Shuttle to Cambridge Station