Course at EMBL-EBI
Introduction to multi-omics 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 multi-omics 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 2023.
Who is this course for?
This course is aimed at biologists who are beginning to work on multi-omics data integration 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:
- Introduction and exercises for Linux: https://training.linuxfoundation.org/free-linux-training
- Basic R concept tutorials: www.r-tutor.com/r-introduction
What will I learn?
Learning outcomes
After this course you should be able to:
- Discuss motivations for working in an integrated manner
- Identify challenges for bringing different data types together
- Use a range of bioinformatics tools to analyse and visualise biological data
Course content
During this course you will learn about:
- Data curation, and ID mapping
- Quality control for data integration
- Analysis and visualisation: Cytoscape, Multi-omics factor analysis (MOFA), Reactome, COSMOS
- Challenges and best practices for working in an integrated manner with biological data
Trainers
Ricard Argelaguet
Altos Labs Aurelien Dugourd
Heidelberg University Tamas Korcsmaros
Imperial College London Theodoros Koutsandreas
EMBL-EBI Dezso Modos
Imperial College London Marton L Olbei
Imperial College London Chenqu Suo
Wellcome Sanger Institute Umran Yaman
UCL Pau Badia i Mompel
Heidelberg University Iguaracy Pinheiro de Sousa
EMBL-EBI Ajay Mishra
EMBL-EBI
Programme
Day/Time Topic Trainer Day one – Monday 4 March 2024 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 Introduction to network propagation Thodoris Koutsandreas 14:00 – 14:30 Break 14:30 – 15:30 Introduction to multi-omics integration using COSMOS Aurelien Dugourd 15:30 – 15:45 Break 15:45 – 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 5 March 2024 09:30 – 10:00 Group project plan reporting by groups All delegates 10:00 – 11:15 Introductory lecture on stats methods Ricard Argelaguet 11:15 – 11:30 Break 11:30 – 12:30 Multi-Omics Factor Analysis (MOFA) Ricard Argelaguet 12:30 – 13:30 Lunch 13:30 – 14:30 Poster session one 14:30 – 16:00 Group project 16:00 – 16:30 Break 16:30 – 18:00 Group project 18:00 End of day 18:30 Dinner at Hinxton hall Day 3 – Wednesday 6 March 2024 09:30 – 10:00 Group project reporting by groups All delegates 10:00 – 11:00 Introduction to networks and pathways Marton Olbei 11:00 – 11:15 Break 11:15 – 12:30 ID mapping and hands-on data integration with Cytoscape (Interactive session) Dezso Modos and Marton Olbei 12:30 – 13:30 Lunch 13:30 – 14:30 Poster session two 14:30 – 16:00 Hands-on data integration with Cytoscape (Interactive session) Dezso Modos and Marton Olbei 16:00 – 16:30 Break 16:30 – 18:00 Group project 18:00 End of day 18:30 Dinner at Hinxton hall Day 4 – Thursday 7 March 2024 09:00 – 09:30 Group project update 09:30 – 10:45 Challenges and opportunities in data integration – Case studies Chenqu Suo and Valentina Lorenzi 10:45 – 11:00 Break 11:00 – 12:30 Multiomics comparative pathway analysis using Reactome analysis tools and pathway browser Eliot Ragueneau 12:30 – 13:30 Lunch 13:30 – 14:30 Poster session three 14:30 – 16:00 Group project 16:00 – 16:30 Break 16:30 – 18:00 Group project 18:00 End of day 19:00 Dinner at the Red lion Day 5 – Friday 8 March 2024 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 All delegates 14:00 – 14:15 Break 14:15 – 15:00 Presentations and group discussion All delegates 15:00 – 15:30 Feedback and course wrap up Ajay Mishra 15:30 End of course
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 reasons why you should be selected for the course.
Please submit all documents during the application process by midnight on 26 November 2023. 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 Friday 8 December. If you have any questions regarding the application process please contact Meredith Willmott.
The registration fee of £850.00 includes:
- Catering as detailed on the course programme
- Accommodation for 4 nights (4, 5, 6 and 7 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 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 2023 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 2024 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.
Altos Labs
Heidelberg University
Imperial College London
EMBL-EBI
Imperial College London
Imperial College London
Wellcome Sanger Institute
UCL
Heidelberg University
EMBL-EBI
EMBL-EBI
Programme
Day/Time | Topic | Trainer |
Day one – Monday 4 March 2024 | ||
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 | Introduction to network propagation | Thodoris Koutsandreas |
14:00 – 14:30 | Break | |
14:30 – 15:30 | Introduction to multi-omics integration using COSMOS | Aurelien Dugourd |
15:30 – 15:45 | Break | |
15:45 – 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 5 March 2024 | ||
09:30 – 10:00 | Group project plan reporting by groups | All delegates |
10:00 – 11:15 | Introductory lecture on stats methods | Ricard Argelaguet |
11:15 – 11:30 | Break | |
11:30 – 12:30 | Multi-Omics Factor Analysis (MOFA) | Ricard Argelaguet |
12:30 – 13:30 | Lunch | |
13:30 – 14:30 | Poster session one | |
14:30 – 16:00 | Group project | |
16:00 – 16:30 | Break | |
16:30 – 18:00 | Group project | |
18:00 | End of day | |
18:30 | Dinner at Hinxton hall | |
Day 3 – Wednesday 6 March 2024 | ||
09:30 – 10:00 | Group project reporting by groups | All delegates |
10:00 – 11:00 | Introduction to networks and pathways | Marton Olbei |
11:00 – 11:15 | Break | |
11:15 – 12:30 | ID mapping and hands-on data integration with Cytoscape (Interactive session) | Dezso Modos and Marton Olbei |
12:30 – 13:30 | Lunch | |
13:30 – 14:30 | Poster session two | |
14:30 – 16:00 | Hands-on data integration with Cytoscape (Interactive session) | Dezso Modos and Marton Olbei |
16:00 – 16:30 | Break | |
16:30 – 18:00 | Group project | |
18:00 | End of day | |
18:30 | Dinner at Hinxton hall | |
Day 4 – Thursday 7 March 2024 | ||
09:00 – 09:30 | Group project update | |
09:30 – 10:45 | Challenges and opportunities in data integration – Case studies | Chenqu Suo and Valentina Lorenzi |
10:45 – 11:00 | Break | |
11:00 – 12:30 | Multiomics comparative pathway analysis using Reactome analysis tools and pathway browser | Eliot Ragueneau |
12:30 – 13:30 | Lunch | |
13:30 – 14:30 | Poster session three | |
14:30 – 16:00 | Group project | |
16:00 – 16:30 | Break | |
16:30 – 18:00 | Group project | |
18:00 | End of day | |
19:00 | Dinner at the Red lion | |
Day 5 – Friday 8 March 2024 | ||
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 | All delegates |
14:00 – 14:15 | Break | |
14:15 – 15:00 | Presentations and group discussion | All delegates |
15:00 – 15:30 | Feedback and course wrap up | Ajay Mishra |
15:30 | End of course |
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 reasons why you should be selected for the course.
Please submit all documents during the application process by midnight on 26 November 2023. 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 Friday 8 December. If you have any questions regarding the application process please contact Meredith Willmott.
The registration fee of £850.00 includes:
- Catering as detailed on the course programme
- Accommodation for 4 nights (4, 5, 6 and 7 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 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 2023 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 2024 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.