Data resources and bioinformatics tools for immunologists

Date:

 Monday 12 Friday 16 June 2017

Venue: 

European Bioinformatics Institute (EMBL-EBI) - Training Room 2 - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom

Application opens: 

Friday February 10 2017

Application deadline: 

Friday March 17 2017

Participation: 

Open application with selection

Contact: 

Frank O’Donnell

Registration fee: 

£625 (includes food and accommodation)

Registration closed

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Overview

This course will introduce and explore a number of key bioinformatics tools and resources that can be applied to immunological research, with a particular focus on T-cell biology. Targeted at life scientists with a wet-lab focus, it 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 ChIP-Seq and RNA-Seq experiments, and will be led through an exploration of this data to identify regulatory regions, changes in gene expression and T-cell receptor sequences.

This course has been developed in collaboration with the ENLIGHT-TEN project, a consortium focused on developing early-stage research expertise in T-cell immunology and big data analysis.

Audience

The course is aimed at wet-lab scientists working in the field of immunology who wish to learn more about available data and tools that can help them in their research.

13 places are reserved for early-stage researchers from the ENLIGHT-TEN project.

Syllabus, tools and resources

During this course you will learn about:

  • Bioinformatics experiments, data submission and approaches
  • Databases relevant to immunology research
  • Ensembl genome browser and Ensembl Regulation
  • scRNA-Seq data analysis and the TraCeR tool
  • IntAct, Reactome, BioModels databases
  • Example use cases of bioinformatics used in immunology

Outcomes

After this course, you should be able to:

  • Locate and search bioinformatics resources for data of interest
  • Utilise software and tools to manipulate and analyse immunology data
  • Use experience in NGS workflows for analysis of ChIP-Seq and RNA-Seq datasets
  • Apply bioinformatics methodologies to your own research

Additional information

All participants are invited to produce an A2 (420mm x 594mm) portrait poster for display during the course. Postersshould include current research interests, the relevance the course has to your work, and potential areas you will be able to explore in the future.

Programme

Time Title Trainer
Day 1 - Monday 12 June
12:00 - 13:00 Arrival, registration and lunch  
13:00 - 14:00

State-of-the-art in T-cell immunology

Sarah Teichmann
14:00 - 15:00

Welcome, introductions and networking

All
15:00 - 15:30

Introduction to EMBL-EBI

Tom Hancocks
15:30 - 16:00 Break  
16:00 - 17:00

Immunology bioinformatics: history and use

Lee Larcombe
17:20 - 17:20

Immunology resources: 3i consortium

Lucie Abeler-Dorner
17:20 - 18:30 Immunology resources: 3i, IMPC and beyond Anna Lorenc
18:30 End of day  
19:00 Welcome drinks Hinxton Hall Bar
19:30 Evening meal Hinxton Hall Restaurant
Day 2 - Tuesday 13 June
08:45 Arrival  
09:00 - 09:30

Introduction to flow cytometry analysis

Adam Laing
09:30 - 10:30

Gating of immune populations

Adam Laing & Lucie Abeler-Dorner

10:30 - 10:45 Break  
10:45 - 11:15 Introduction to data analysis and statistics Lucie Abeler-Dorner
11;15 - 12:45 Data analysis and discussion

Adam Laing & Lucie Abeler-Dorner

12:45 - 13:30 Lunch and posters  
13:30 - 14:30 Introduction to high-throughput sequencing Myrto Kostadima
14:30 - 15:15 Introduction to ChIP-Seq Myrto Kostadima
15:15 - 15:45 Break  
15:45 - 17:30 Analysis of ChIP-seq data and visualisation in Ensembl Myrto Kostadima
17:45 - 18:30

Ensembl Regulation resources

Myrto Kostadima 
18:30

End of day

 
19:30 Evening meal  Hinxton Hall Restaurant
Day 3 - Wednesday 14 June
08:45 Arrival  
09:00 - 10:00

Single-cell RNA sequencing

John Marioni 
10:00 - 10:45

scRNA-Seq bioinformatics

John Marioni & Aaron Lun
10:45 - 11:15 Break  
11:15 - 12:30 scRNA-Seq bioinformatics John Marioni & Aaron Lun
12:30 - 13:30 Lunch and posters  
13:30 - 15:30 Using the TraCeR tool Mike Stubbington
15:30 - 16:00 Break  
16:00 - 17:30 Data reproducibility Amy Tang
17:30 - 18:30 Cellular States, Differentiation Trajectories and Regulatory Networks of Blood Cell Development  Bertie Gottgens
19:00 Evening meal  Hinxton Hall Restaurant
Day 4 - Thursday 15 June
08:45 Arrival  
09:00 - 10:45 Molecular interaction databases Sandra Orchard
10:45 - 11:15 Break  
11:15 - 12:30 Identifier mapping Pablo Porras
12:30 - 13:30 Lunch and posters  
13:30 - 14:00 Introduction to data integration – why, how, promise and pitfalls

Lee Larcombe

14:00 - 14:45 Industry use cases - Achilles Therapeutics Katy Newton 
14:45-15:30 Industry use cases -   
15:30 - 16:00 Break  
16:00 - 16:30 Introduction to Reactome

Steve Jupe

16:30-17:30 Tools for pathway analysis Steve Jupe
17:30 - 18:00 BraCeR: Clonal inference of B cells from scRNA-seq data

Ida Linderman

18:00 End of day  
19:00 Evening meal Hinxton Hall Restaurant
Day 5 - Friday 16 June
08:45 Arrival  
09:00 - 09:30

Industry use case

Edgardo Ferran
09:30 - 11:00

Tools for pathway analysis

Steve Jupe
11:00 - 11:30 Break  
11:30 - 12:30

Locating models of biological processes

Vijayalakshmi Chelliah 
12:30 - 12:45 Course feedback  
12:45 - 13:15 Lunch  
13:15 End of course  
13:30 Coach to Cambridge Railway Station