Data resources and bioinformatics tools for immunologists
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Date:
Monday 12 - Friday 16 June 2017Venue:
European Bioinformatics Institute (EMBL-EBI) - Training Room 2 - Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United KingdomApplication opens:
Friday 10 February 2017Application deadline:
Friday 17 March 2017Participation:
Open application with selectionContact:
Frank O’DonnellRegistration fee:
£625 (includes food and accommodation)Registration closed
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 |
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