Bioinformatics Resources for Immunologists
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Date:
Monday 4 - Friday 8 June 2018Venue:
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United KingdomApplication opens:
Monday 04 December 2017Application deadline:
Tuesday 06 March 2018Participation:
Open application with selectionContact:
EMBL-EBI Training TeamRegistration fee:
£670Registration closed
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
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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 | Introduction to 3i and flow data in 3i | 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 | Erin Haskell |
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 | Free time | |
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 - 17:00 | Locating models for biological processes | Rahuman Sheriff |
17:00 - 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 | Tools for pathway analysis | Thawfeek Varusai |
10:00 - 10:30 | Break | |
10:30 - 11:15 | Immunotherapeutic Approaches for Targeting The Achilles Heel of Cancer | Fong Chan |
11:15 - 12:00 | IBDomics | Tim Raine |
12:00 - 12:30 | Course feedback and wrap up | Tom Hancocks |
12:30 - 13:30 | Lunch | |
14:00 | Coach to Cambridge Railway Station |