Course at EMBL-EBI
Systems biology: from large datasets to biological insight
This course covers the use of computational tools to extract biological insight from omics datasets. The content will explore a range of approaches – ranging from network inference and data integration to machine learning and logic modelling – that can be used to extract biological insights from varied data types. Together these techniques will provide participants with a useful toolkit for designing new strategies to extract relevant information and understanding from large-scale biological data.
The motivation for running this course is a result of advances in computer science and high-performance computing that have led to groundbreaking developments in systems biology model inference. With the comparable increase of publicly-available, large-scale biological data, the challenge now lies in interpreting them in a biologically valuable manner. Likewise, machine learning approaches are making a significant impact in our analysis of large omics datasets and the extraction of useful biological knowledge.
Who is this course for?
This course is aimed at advanced PhD students, post-doctoral researchers, and non-academic scientists who are currently working with large-scale omics datasets with the aim of discerning biological function and processes. Ideal applicants should already have some experience (ideally one to two years) working with systems biology or related large-scale (multi-)omics data analyses.
Applicants are expected to have a working knowledge of the Linux operating system and the ability to use the command line. Experience of using a programming language (i.e. Python) is highly desirable, and while the course will make use of simple coding or streamlined approaches such as Python notebooks, higher levels of competency will allow participants to focus on the scientific methodologies rather than the practical aspects of coding and how they can be applied in their own research.
We recommend these free tutorials:
Basic introduction to the Unix environment: https://swcarpentry.github.io/shell-novice/
Introduction and exercises for Linux: https://training.linuxfoundation.org/free-linux-training
Python tutorial: https://www.w3schools.com/python/
R tutorial: https://www.datacamp.com/courses/free-introduction-to-r
Regardless of your current knowledge we encourage successful participants to use these to prepare for attending the course and future work in this area. Selected participants will also be sent materials prior to the course. These might include pre-recorded talks and required reading that will be essential to fully understand the course.
What will I learn?
Learning outcomes
After the course you should be able to:
- Discuss and apply a range of data integration and reduction approaches for large-scale omics data
- Apply different approaches to explore omics data at the network level
- Describe principles behind different machine learning methods and apply them on omics datasets to extract biological knowledge
- Infer biological models using statistical methods
- Identify strengths and weaknesses of different inference approaches
- Compare signal propagation through logic modelling vs diffusion-based approaches
Course content
The course will include lectures, discussions, and practical computational exercises covering the following topics:
- Machine and deep learning – practical exercises on supervised machine learning, including classification and regression, graph neural network, and deep learning
- Bulk and single-cell multiomics data integration – introduction and practical on using methods for integrative analysis of multiomics data
- Functional inference from omics data – approaches to extract signatures of cell state from omics data including transcription factor activation and kinase activity states. Extraction of upstream signalling pathways from transcriptomics datasets
- Network inference and signal propagation – network inference approaches from omics data, including cell cell communication networks from scRNAseq data
- Introduction to executable modelling – including how to fit omics data to executable and predictive logic models
Trainers
Federica Eduati
Eindhoven University of Technology Konrad Förstner
ZB MED – Information for Life Sciences Manik Garg
AstraZeneca Till Sauerwein
ZB MED Cologne Mike van Santvoort
Eindhoven University of Technology Roser Vento-Tormo
Wellcome Sanger Institute Judith Zaugg
EMBL Heidelberg
Programme
The programme is subject to minor changes.
Time
Topic
Trainer
Day one – Monday 10 June 2024
10:30 – 10:45
Arrival and registration
10:45 – 11:15
Introduction to the course and EMBL-EBI
Marta Lloret Llinares
11:15 – 12:00
Keynote lecture: Generative modelling for cellular biology
Mohammad Lotfollahi
12:00 - 13:00
Machine learning
Konrad Förstner and Till Sauerwein
13:00 – 14:00
Lunch
14:00 – 15:30
Machine learning
Konrad Förstner and Till Sauerwein
15:30 – 16:00
Break
16:00 - 17:00
Machine learning
Konrad Förstner and Till Sauerwein
17:00 - 17:45
Flash talks I
18:30
Dinner in Hinxton Hall
Day two – Tuesday 11 June 2024
09:00 – 10:30
Deep learning
Konrad Förstner and Till Sauerwein
10:30 – 11:00
Break
11:00 – 13:00
Deep learning
Konrad Förstner and Till Sauerwein
13:00 – 14:00
Lunch Break
14:00 – 15:30
Inference and evaluation of enhancer‐mediated gene regulatory networks with GRaNIE and GRaNPA
Judith Zaugg, Christian Arnold and Aryan Kamal
15:30 – 16:00
Break
16:00 – 16:45
Inference and evaluation of enhancer‐mediated gene regulatory networks with GRaNIE and GRaNPA
Judith Zaugg, Christian Arnold and Aryan Kamal
16:45 – 17:30
Flash talks II
17:30 – 18:30
Poster session I
19:00
Dinner in Hinxton Hall
Day three – Wednesday 12 June 2024
09:00 – 10:30
Data integration using MOFA
Manik Garg
10:30 – 11:00
Break
11:00 – 12:30
Data integration using MOFA
Manik Garg
12:30 – 13:30
Lunch
13:30 – 15:00
Single-cell multiomics data integration
Valentina Lorenzi
15:00 – 15:30
Break
15:30 – 17:00
Single-cell multiomics data integration
Valentina Lorenzi
17:00 – 18:00
Poster session II
19:00
Dinner in Hinxton Hall
Day four – Thursday 13 June 2024
09:00 – 10:15
PhuEGO and network propagation
Haoqi Chen and Thodoris Koutsandreas 10:15 – 10:45
Break
10:45 – 11:30
PhuEGO and network propagation
Haoqi Chen and Thodoris Koutsandreas 11:30 – 12:15
Multi-omics data integration with prior knowledge to decipher signaling and metabolic deregulation in complex diseases
Aurelien Dugourd
12:15 – 13:15
Lunch break
13:15 – 15:00
Multi-omics data integration with prior knowledge to decipher signaling and metabolic deregulation in complex diseases
Aurelien Dugourd
15:00 – 15:30
Break
15:30 – 17:30
Project work
18:30
Dinner
Day five – Friday 14 June 2024
09:00 – 10:30
Cell-cell communication
Federica Eduati and Mike van Santvoort
10:30 – 11:00
Break
11:00 – 11:45 Keynote lecture: Gene regulation of human cell systems
Roser Vento-Tormo
11:45 – 12:30
Project work
12:30 – 13:30
Lunch
13:30 - 14:30
Presentation of project work
14:30 – 15:00
Final discussion session
All
15:00 – 15:15
Course wrap-up and feedback
Marta Lloret Llinares
15:15
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 3 March 2024. 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 17 March 2024. If you have any questions regarding the application process please contact Juanita Riveros.
The registration fee of £850.00 includes:
- Catering as detailed on the course programme
- Accommodation for four nights (10, 11, 12, and 13 June ) at Hinxton Hall Conference Centre.
- 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 presentations and practicals from the course, and will give you a snapshot of what to expect in the 2024 edition.
Flash talks
All participants will be asked to give a short presentation about their research work as part of the course. These provide an opportunity to share their research with the other participants and provide a forum for discussion. Successful applicants will be required to submit their talks upon registration.
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.
Eindhoven University of Technology
ZB MED – Information for Life Sciences
AstraZeneca
ZB MED Cologne
Eindhoven University of Technology
Wellcome Sanger Institute
EMBL Heidelberg
Programme
The programme is subject to minor changes.
Time | Topic | Trainer |
Day one – Monday 10 June 2024 | ||
10:30 – 10:45 | Arrival and registration |
|
10:45 – 11:15 | Introduction to the course and EMBL-EBI | Marta Lloret Llinares |
11:15 – 12:00 | Keynote lecture: Generative modelling for cellular biology | Mohammad Lotfollahi |
12:00 - 13:00 | Machine learning
| Konrad Förstner and Till Sauerwein |
13:00 – 14:00 | Lunch |
|
14:00 – 15:30 | Machine learning | Konrad Förstner and Till Sauerwein |
15:30 – 16:00 | Break | |
16:00 - 17:00 | Machine learning | Konrad Förstner and Till Sauerwein |
17:00 - 17:45 | Flash talks I | |
18:30 | Dinner in Hinxton Hall |
|
Day two – Tuesday 11 June 2024 | ||
09:00 – 10:30 | Deep learning | Konrad Förstner and Till Sauerwein |
10:30 – 11:00 | Break |
|
11:00 – 13:00 | Deep learning | Konrad Förstner and Till Sauerwein |
13:00 – 14:00 | Lunch Break |
|
14:00 – 15:30 | Inference and evaluation of enhancer‐mediated gene regulatory networks with GRaNIE and GRaNPA | Judith Zaugg, Christian Arnold and Aryan Kamal |
15:30 – 16:00 | Break |
|
16:00 – 16:45 | Inference and evaluation of enhancer‐mediated gene regulatory networks with GRaNIE and GRaNPA | Judith Zaugg, Christian Arnold and Aryan Kamal |
16:45 – 17:30 | Flash talks II |
|
17:30 – 18:30 | Poster session I |
|
19:00 | Dinner in Hinxton Hall |
|
Day three – Wednesday 12 June 2024 | ||
09:00 – 10:30 | Data integration using MOFA
| Manik Garg |
10:30 – 11:00 | Break |
|
11:00 – 12:30 | Data integration using MOFA | Manik Garg |
12:30 – 13:30 | Lunch | |
13:30 – 15:00 | Single-cell multiomics data integration | Valentina Lorenzi |
15:00 – 15:30 | Break | |
15:30 – 17:00 | Single-cell multiomics data integration | Valentina Lorenzi |
17:00 – 18:00 | Poster session II |
|
19:00 | Dinner in Hinxton Hall |
|
Day four – Thursday 13 June 2024 | ||
09:00 – 10:15 | PhuEGO and network propagation
| Haoqi Chen and Thodoris Koutsandreas |
10:15 – 10:45 | Break |
|
10:45 – 11:30 | PhuEGO and network propagation | Haoqi Chen and Thodoris Koutsandreas |
11:30 – 12:15 | Multi-omics data integration with prior knowledge to decipher signaling and metabolic deregulation in complex diseases | Aurelien Dugourd |
12:15 – 13:15 | Lunch break |
|
13:15 – 15:00 | Multi-omics data integration with prior knowledge to decipher signaling and metabolic deregulation in complex diseases | Aurelien Dugourd |
15:00 – 15:30 | Break | |
15:30 – 17:30 | Project work | |
18:30 | Dinner | |
Day five – Friday 14 June 2024 | ||
09:00 – 10:30 | Cell-cell communication
| Federica Eduati and Mike van Santvoort |
10:30 – 11:00 | Break |
|
11:00 – 11:45 | Keynote lecture: Gene regulation of human cell systems | Roser Vento-Tormo |
11:45 – 12:30 | Project work | |
12:30 – 13:30 | Lunch |
|
13:30 - 14:30 | Presentation of project work | |
14:30 – 15:00 | Final discussion session | All |
15:00 – 15:15 | Course wrap-up and feedback | Marta Lloret Llinares |
15:15 | 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 3 March 2024. 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 17 March 2024. If you have any questions regarding the application process please contact Juanita Riveros.
The registration fee of £850.00 includes:
- Catering as detailed on the course programme
- Accommodation for four nights (10, 11, 12, and 13 June ) at Hinxton Hall Conference Centre.
- 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 presentations and practicals from the course, and will give you a snapshot of what to expect in the 2024 edition.
Flash talks
All participants will be asked to give a short presentation about their research work as part of the course. These provide an opportunity to share their research with the other participants and provide a forum for discussion. Successful applicants will be required to submit their talks upon registration.
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.