Course at EMBL-EBI

Systems biology: From large datasets to biological insight

Welcome to the new EMBL-EBI Training site. Please tell us what you think!

For some time, advances in computer science and high performance computing have led to ground-breaking developments in systems biology model inference. However, only now has there been sufficient large-scale data available to parameterise these models and use them usefully. Similarly, machine learning approaches have recently started having a significant impact in our analysis of large omics datasets and extraction of useful biological knowledge.

Therefore this course, run in collaboration with the Wellcome Genome Campus Advanced Courses and Scientific Conferences Team, will provide timely advanced-level training in using large-scale multi-omics data and machine learning to infer biological models.

Who is this course for?

Applicants should be researchers who are using large multi-omics datasets to infer systems biology models. This is an advanced-level course, and so we will select applicants who already have some experience (ideally 1-2 years) of working with systems biology modelling or related large-scale multi-omics data analysis. Additionally, applicants will be expected to have a working knowledge of using Linux commands, and experience of using a programming language (e.g. Python or Perl).

What will I learn?

Learning outcomes

After the course the participants should be able to:

  • Discuss and apply a range of data integration and reduction approaches for large scale omics data
  • Describe principles behind different machine learning methods and apply them on omics datasets to extract biological knowledge
  • Infer biological models using machine learning and statistical methods
  • Identify strengths and weaknesses of different inference approaches
  • Compare signal propagation through logic modelling vs diffusion-based approaches
  • Access, query and retrieve models from public repositories for systems biology
Course content

The programme will include, lectures, discussions and practical computational exercises covering the following topics:

  • Introductory session
  • Omics data integration / reduction and interpretation
  • Protein-protein interaction, gene regulatory and signalling network inference
  • Logic modelling
  • Machine learning / deep learning for model inference


Rahuman Sheriff
Girolamo Giudice
Ricard Argelaguet
Leopold Parts
Welcome Sanger Institute, UK
Javier De Las Rivas
University of Salamanca, Spain
Evangelia Petsalaki
Julio Saez-Rodriguez
Jasmin Fisher
UCL Cancer Institute, UK
Jan Hasenauer
University of Bonn, Germany
Konrad Förstner
German National Library of Medicine, Germany
Eva-Maria Geissen
EMBL Heidelberg, Germany
Nicolas Rodriguez
Babraham Institute, UK
Dmytro Fishman
University of Tartu, Estonia
Emanuel Goncalves
Wellcome Sanger Institute, UK
Yu Fu
Pablo Porras Millan
Daniel Seaton


Day 1 - Monday 8th July

Introduction & Overview and Data reduction/integration session

08:00 - 08:30 Registration  
08:30 - 08:45 Transfer to EMBL-EBI training rooms  
08:45 - 09:00 An introduction to EMBL-EBI Alexandra Holinski
09:00 - 09:15 Overview of course content Evangelia Petsalaki
09:15 - 10:15 Introduction to data reduction methods and practical exercises Evangelia Petsalaki
10:15 - 10:45 Tea/coffee break  
10:45 - 12:15 Introduction to data reduction methods and practical exercises (continued) Evangelia Petsalaki
12:15 - 12:45 Introdctuion to data integration Pablo Porras
12:45 - 13:45 Lunch  
13:45 - 14:00 Matrix factorization approaches for data integration Ricard Argelaguet
14:00 - 15:45 Practical exercise using MOFA for data integration Ricard Argelaguet
15:45 - 16:15 Tea/coffee break  
16:15 - 17:15 Keynote lecture: Data integration Daniel Seaton
17:15 - 18:30 Data integration practical Pablo Porras
19:00 Dinner  

Day 2 - Tuesday 9th July

Network Inference

09:00 - 09:30 Introduction to network inference Evangelia Petsalaki
09:30 - 11:00 Protein interactions network inference Javier De Las Rivas
11:00 - 11:30 Tea/coffee break   
11:30 - 12:00

Introduction to team work projects

2 teams gene expression to gene regulatory networks

2 teams phosphoproteomics to signalling networks

12:00 - 13:00 Start of team work projects  
13:00 - 14:00 Lunch  
14:00 - 16:00 Continue team work projects and prepare presentations (including tea/coffee break)  
16:00 - 17:00 Keynote lecture: network inference and model parametrization Jan Hasenauer
17:00 - 18:30 Poster session with cheese and wine  
19:00 Dinner  

Day 3 - Wednesday 10th July

Signal propagation/modelling

09:00 - 09:30 Standards in Systems Biology Nicolas Rodriguez
09:30 - 10:00 Introduction to chemical kinetics, simulation, parameter estimation / COPASI Eva-Maria Geissen
10:00 - 10:30 BioModels Rahuman Sheriff
10:30 - 11:00 Tea/coffee break  
11:00 - 13:00 Practical All
13:00 - 14:00 Lunch  
14:00 - 16:15 From data analysis to logic modelling (theory & practical) Julio Saez-Rodriguez, Emanuel Goncalves
16:15 - 16:45 Tea/coffee break   
16:45 - 18:15 15 minute presentations from projects and discussions  
19:00 Dinner  

Day 4 - Thursday 11th July

Signal propagation modelling ctnd & machine learning

09:00 - 11:30 Diffusion based approaches for signal propagation, Introduction and practical exercise Evangelia Petsalaki
11:30 - 12:00 Tea/coffee break  
12:00 - 13:00 Keynote: mechanistic modelling Jasmin Fisher
13:00 - 14:15 Lunch  
14:15 - 15:15 Introduction to supervised machine learning Konrad Förstner
15:15 - 16:00 Introduction & practical exercise: classification and regression Konrad Förstner
16:00 - 16:30 Tea/coffee break  
16:30 - 18:30 Practical exercise continued Konrad Förstner
19:00 Dinner  

Day 5 - Friday 12th July

Deep learning

08:00 - 08:30 Check-out  
08:45 - 11:00 Introduction to deep learning & Practical exercise Leo Parts, Dmytro Fishman
11:00 - 11:30 Tea/coffee break  
11:30 - 12:30 Practical exercise continued Leo Parts, Dmytro Fishman
12:30 - 13:15 Keynote lecture: deep learning Yu Fu
13:15 - 13:45 Q&A, course wrap-up and feedback  
13:45 - 14:30 Lunch  
14:30 End of course  

Registration is handled through the Wellcome Genome Campus Connecting Science Advanced Courses and Scientific Conferences website.

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This course has ended

08 - 10 July 2019
European Bioinformatics Institute United Kingdom
Yvonne Thornton

  • Evangelia Petsalaki
  • Alexandra Holinski
  • Julio Saez Rodriguez
    University of Heidelberg, Germany

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