Course at EMBL-EBI

Introduction to multiomics data integration and visualisation

With the increase in the volume of data across the whole spectrum of biology, more opportunities as well as challenges have been created to identify novel perspectives and answer questions in life sciences. This may also include public domain data, which can provide added value to data derived through researcher’s own work and inform experimental design. This introductory course will highlight the challenges that researchers face in integrating multiomics data sets using biological examples. The course will focus on the use of public data resources and open access tools for enabling integrated working, with an emphasis on data visualisation. This course will not include systems biology modelling or machine learning.

A major element of this course is a group project, where participants will be placed in small groups to work together on a challenge set by trainers from EMBL-EBI data resource and research teams. This allows people to explore the bioinformatics tools and resources introduced in the course and to apply these to a set problem, providing hands-on experience of relevance to their own research. The group work will culminate in a presentation session involving all participants on the final day of the course, giving an opportunity for wider discussion on the benefits and challenges of integrating data. You may refer to the previous group projects that were organised for this course in March 2022.

Additional information

The course fee is inclusive of four nights accommodation and catering, including dinner.

We plan to deliver this course in an in-person manner onsite at our training suite at EMBL-EBI, Hinxton.  Hybrid options are not currently available. Please be aware that we are continually evaluating the ongoing pandemic situation and, as such, may need to change the format of courses at short notice. Your safety is paramount to us; you can read our COVID guidance policy for more information. All information is correct at time of publishing.

Please also note that there are delays in the issuing of visas from the UK Government. We encourage you to check if you need a visa and apply in plenty of time before travelling. Current waiting times are more than six weeks. For more information please visit the UK Government website.

Who is this course for?

This introductory course is aimed at biologists who are embarking on multiomics projects and computational biologists/bioinformaticians who wish to gain a better knowledge of the biological challenges presented when working with integrated datasets.

Some practical sessions in the course require a basic understanding of the Unix command line and the R statistics package. If you are not already familiar with these then please ensure that you complete these free tutorials before you attend the course:

What will I learn?

Learning outcomes

After this course you should be able to:

  • Discuss motivations for working in an integrated manner
  • Comprehend the importance of data standards and the collection of metadata
  • Identify challenges for bringing different data types together
  • Use a range of bioinformatics tools to organise and visualise biological data
Course content

During this course you will learn about:

  • Data standards, curation, and ID mapping
  • Quality control for data integration
  • Analysis and visualisation:  Cytoscape, Multiomics factor analysis (MOFA), Reactome, COSMOS
  • Challenges and best practices for working in an integrated manner with biological data

Trainers

Tamás Korcsmáros
Imperial College London
Marton Olbei
Imperial College London
Dezso Modos
Quadram Institute
Aurelien Dugourd
University of Heidelberg
Sandra Orchard
EMBL-EBI
Krishna Kumar Tiwari
EMBL-EBI
Helena Cornu
EMBL-EBI
Ricard Argelaguet
Altos Labs
Charles Barker
EMBL-EBI
Emma Dann
Wellcome Sanger Institute

Programme

The programme below is subjected to minor changes
Day/Time Topic Trainer
Day one – Monday 6 March 2023
10:00 – 10:30 Check-in  
10:30 – 11:00 Welcome and introductions Ajay Mishra
11:00 – 12:00 Keynote: Multiple ways to integrate multi-omics data – case studies from studying human diseases  Tamás Korcsmáros
12:00 – 13:00 Lunch  
13:00 – 14:00 Quality issues – Data standards, curation, ontologies, and metadata Sandra Orchard
14:00 – 14:15 Break  
14:15 – 15:15 Introduction to multiomics integration using COSMOS Aurelien Dugourd
15:15 – 15:30 Break  
15:30 – 17:30 Group project introduction and group discussion Project mentors and all delegates
17:30 End of day  
18:30 Dinner at Hinxton hall  
 
Day 2 – Tuesday 7 March 2023
09:30 – 10:00 Group project plan presentation by groups All delegates
10:00 – 11:15 Multiomics comparative pathway analysis using Reactome analysis tools and pathway browser Krishna Kumar Tiwari
11:15 – 11:30 Break  
11:30 – 12:30 Introductory lecture on stats methods Ricard Argelaguet
12:30 – 13:30 Lunch  
13:30 – 14:30 Multi-Omics Factor Analysis (MOFA) Ricard Argelaguet
14:30 – 15:30 Poster session I  
15:30 – 16:45 Group project  
16:45 – 17:00 Break  
17:00 – 18:00 Group project  
18:00 End of day  
18:30 Dinner at Hinxton hall  
 
Day 3 – Wednesday 8 March 2023
09:00 – 10:15 Introduction to networks and pathways Marton Olbei
10:15 – 10:30 Break  
10:30 – 11:00 ID mapping Dezso Modos
11:00 – 12:00 Hands-on data integration with Cytoscape (Interactive session) Dezso Modos and Marton Olbei
12:00 – 13:00 Lunch  
13:00 – 14:00 Hands-on data integration with Cytoscape (Interactive session) Dezso Modos and Marton Olbei
14:00 – 15:00 Poster session II  
15:00 – 16:30 Group project  
16:30 – 16:45 Break  
16:45 – 18:00 Group project  
18:00 End of day  
18:30 Dinner at Hinxton hall  
 
Day 4 – Thursday 9 March 2023
09:00 – 09:30 Group project update  
09:30 –10:30 Open Targets platform: integrating omics data for drug discovery Helena Cornu
10:30 – 10:45 Break  
10:45 – 12:00 Challenges and opportunities in data integration - Case studies Charles Barker and Emma Dann
12:00 – 13:00 Lunch  
13:00 – 14:00 Poster session III  
14:00 – 15:00 Resource/Tool To be confirmed
15:00 – 15:15 Break  
15:15 – 16:30 Group project  
16:30 – 16:45 Break  
16:45 – 18:15 Group project  
18:15 End of day  
19:00 Dinner (Red lion/Hinxton hall)  
 
Day 5 – Friday 10 March 2023
09:00 – 10:30 Group project wrap up and preparation for short presentation All delegates
10:30 – 10:45 Break  
10:45 – 12:00 Group project wrap up and preparation for short presentation All delegates
12:00 – 13:00 Lunch  
13:00 – 14:00 Presentations and group discussion with the organisers All delegates
14:00 – 14:15 Break  
14:15 – 15:00 Presentations and group discussion with the organisers All delegates
15:00 – 15:30 Feedback and course wrap up Ajay Mishra
15:30 End of course  

Please be advised that the application review process will take longer than planned. All applicants will be informed of the status of their application (successful, waiting list, unsuccessful) by 9 December 2022.

Please read our page on application support before starting your application. In order to be considered for a place on this course, you must do the following:

  • Complete the online application form.
  • Ensure you add relevant information to the ‘submission details’ section where you are asked to provide information on your:
    • pre-requisite skills and knowledge
    • current work and course expectations
    • data availability
  • Upload one letter of support from your supervisor or a senior colleague detailing why you should be selected for the course.

Please submit all documents during the application process by midnight on 18 November 2022. Items marked * in the application are mandatory. Incomplete registrations will not be processed. 

All applicants will be informed of the status of their application (successful, waiting list, unsuccessful) by 2 December 2022. If you have any questions regarding the application process please contact Shereen Pethania

The registration fee of £825.00 includes:

  • Catering as detailed in the course programme
  • Accommodation for 4 nights (6, 7, 8, and 9 March) 
  • Bespoke course handbook with links to all course materials
  • Use of a computer in the EMBL-EBI training suite throughout the course
  • Shuttle bus on the final course day to Cambridge train station 

Accommodation 

Hotel rooms (including breakfast) will be provided onsite at Hinxton Hall Conference Centre. Please contact them directly if you wish to arrange to stay additional nights around the course dates.

Catering

The course includes catering as detailed on the programme tab. Successful applicants will be asked for any dietary requirements and allergies upon registration. 

Course materials

The course materials from the 2022 edition of the course are now live and available for you to use. They provide a mixture of pre-recorded lectures, presentations, and practicals from the course, and will give you a snapshot of what to expect in the 2023 edition.

Posters

All participants are expected to present a poster that will be displayed during the course outside the training room. Successful applicants will be asked to submit their poster upon registration. We will print these for you and have them available when you arrive on site.

All posters should:

•         be A2 in size 420mm x 594 mm
•         be in a portrait orientation
•         include your photograph and contact information

We expect the posters to act as a talking point between you, other participants and the trainers on the course. The posters will be displayed throughout the week so people can view them during breaks and lunch. They should give the reader an idea of the work you are engaged in, what you are planning to do next, and anything of interest that might be useful for sharing with the gathered participants.

 

Applications closed
18 November 2022

06 - 10 March 2023
European Bioinformatics Institute United Kingdom
£825.00 (inclusive of four nights accommodation and catering, including dinner)
Contact
Shereen Pethania
Open application with selection
30 places

Organisers
  • Isidro Cortes Ciriano
    EMBL-EBI
  • Tamás Korcsmáros
    Imperial College London
  • Ajay Mishra
    EMBL-EBI
  • Evangelia Petsalaki
    EMBL-EBI

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