Course at EMBL-EBI
Bioinformatics for immunologists
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.
Who is this course for?
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:
- Introduction to the Unix environment – http://www.ee.surrey.ac.uk/Teaching/Unix/
- Basic R concepts – http://www.r-tutor.com/r-introduction
What will I learn?
Learning 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
Course content
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
Trainers
Tom Hancocks
EMBL-EBI, UK Yvan Saeys
University of Ghent, Belgium Anna Lorenc
King's College London, UK Niels Vandamme
University of Ghent, UK Andrew Martin
University College London, UK Benjamin Moore
EMBL-EBI, UK Birgit Meldal
EMBL-EBI, UK James Lee
University of Cambridge, UK Bruck Taddese
MedImmune, UK Livia Perfetto
EMBL-EBI, UK Pablo Porras Millan
EMBL-EBI, UK Krishna Kumar Tiwari
EMBL-EBI, UK
EMBL-EBI, UK
University of Ghent, Belgium
King's College London, UK
University of Ghent, UK
University College London, UK
EMBL-EBI, UK
EMBL-EBI, UK
University of Cambridge, UK
MedImmune, UK
EMBL-EBI, UK
EMBL-EBI, UK
EMBL-EBI, UK
Programme
Day 1 – Monday 15 July 2019 |
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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 |
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08:45 | Arrival | |
09:00-11:00 | Handling cytometry data in R and quality control | Yvan Sayes, Sofie Van Gassen & Anna Lorenc |
11:00-11:30 | Break | |
11:00-13:00 | Visualising cytometry data in R | Yvan Sayes, Sofie Van Gassen, & 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 |
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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 |
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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 |
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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 | Krishna Tiwari |
15:00-15:15 | Feedback and survey | Tom Hancocks |
15:15 | End of course | |
15:30 | Shuttle to Cambridge Station |
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Registration is handled through the Wellcome Genome Campus Connecting Science Advanced Courses and Scientific Conferences website.