Virtual course

Mathematics of life: Modelling molecular mechanisms

This course will provide participants with an introduction and hands-on training on modelling approaches, tools and resources used in systems biology as well as touch on network analysis.

Computer models are increasingly used to understand the essential processes of biology. Researchers in academic institutions as well as the pharmaceutical industry use mathematical models to generate hypotheses on how complex biomolecular systems work. Modelling of biochemical pathways deregulated in disease conditions can offer mechanistic insights into the pathology, help to elucidate mechanisms behind drug action, and predict the dose required for treatment thus facilitating fundamental research and drug discovery. This course will provide a helpful introduction to tools and resources used in this scientific field.

The course will involve participants learning via pre-recorded lectures, live presentations, trainer Q&A sessions and hands-on tutorials. The content will be delivered over Zoom, with additional text communication over Slack.  In order to make the most out of the course, you should make sure to have a stable internet connection throughout the week.

Computational practicals will be run on EMBL-EBI's virtual training infrastructure; this means there is no need to have a powerful computer to run exercises or a requirement to install complex software before the course. Trainers will be available to provide support, answer questions, and further explain the analysis during these practicals.

Selected participants will 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.

Participants will need to be available between the hours of 09:30-17:15 BST each day of the course.

Who is this course for?

This course is aimed at experimental biologists, bioinformaticians and mathematicians who have just started in systems biology, are familiar with the basic terminology in this field and who are now keen on gaining a better knowledge of systems biology modelling approaches to understand biological and biomedical problems.

An experience of using a programming language (e.g Python, R, Matlab) would be a benefit but is not mandatory.

An undergraduate knowledge of molecular and cellular biology or some background in mathematics is highly beneficial. 

What will I learn?

Learning outcomes

After the course, participants should be able to:

  • Identify the strength and weakness of systems qualitative and quantitative modelling approaches
  • Access, query and retrieve data/ models from public repositories for systems biology modelling
  • Use modelling software to develop reproducible systems biology models
  • Discuss the real-life application of models in fundamental and industrial research

Course content

During this course you will learn about: 

  • Network Analysis and Pathway Enrichment
  • Qualitative (e.g. logic) modelling and quantitative (e.g. chemical kinetics, constraint based) modelling
  • Data resources for modelling, pathways and molecular interaction: BioModels, Reactome, IntAct, ComplexPortal etc.
  • Model sharing: how to encode, annotate and distribute models
  • Several tools will be used during the course, including accessing IntAct data from Cytoscape, COPASI, MORPHEUS and CellCollective
  • Group challenge on model curation


Rahuman Sheriff
Alexandra Holinski
Birgit Meldal
Kalpana Panneerselvam
Thawfeek Varusai
Alfonso Martinez-Arias
Universidad Pompeu Fabra
Tomas Helikar
University of Nebraska-Lincoln
Lutz Brusch
Technische Universität Dresden
Eva Geissen
Kausthubh Ramachandran
Carmen Pin
Elisa Passini
Universty of Oxford
Andreas Dräger
University of Tübingen
Eliot Rageneau
Jörn Starruß
Technische Universität Dresden
Diego Jahn
Technische Universität Dresden
Robert Mueller
Technische Universität Dresden


Times in BST

Monday 27 September 2021
09.30-10.00 Introduction to EMBL-EBI and the course Alex Holinski
10.00-10.30 Get to know each other - icebreaker Jane Reynolds, Alex Holinski
10.30-10.45 Course overview Rahuman Sheriff
10.45-11.00 Break  
11.00-13.00 An Introduction to Network Analysis using the Cytoscape IntAct App - Q&A and Practical Birgit Meldal, Kalpana Panneerselvam, Eliot Rageneau
13:00 - 14:00 Break  
14.00-15.30 Introduction to Reactome Pathway Analysis and tutorial Thawfeek Varusai
15.30-16.00 Break  
16.00-17.00 Scientific networking - flash talks  
17.00-17.15 Introduction to Wonder Jane Reynolds
17.15-17.45 Optional networking and social time - Wonder  
Tuesday 28 September 2021
09.30-09.45 Morning quiz  
09.45-10.45 Keynote lecture and Q&A - "A matter of genes, cells and numbers" Alfonso Martinez Arias
10.45-11.15 Break  
11.15-12.15 Scientific networking - flash talks  
12.15-13.15 Break  
13.15-14.15 Introduction to kinetic modelling and COPASI Rahuman Sheriff
14.15-14.45 Introduction to group challenge Rahuman Sheriff, Alex Holinski
14.45-15.15 Break  
15.15-17.15 COPASI tutorial - start of group challenge Rahuman Sheriff, Kausthubh Ramachandran, Eva Geissen
Wednesday 29 September 2021
09.30-09.45 Morning quiz  
09.45-11.15 Scientific talks and Q&A Elisa Passini, Andreas Dräger
11.15-11.30 Break  
11.30-12.30 Scientific networking - flash talks  
12.30-13.30 Break  
13.30-14.00 Introduction to logic modelling and available tools Tomas Helikar
14.00-14.30 Overview of Cell Collective Tomas Helikar
14.30-15.00 Break  
15.00-15.30 Breaking down the process of modelling: A practical guide Tomas Helikar
15.30-17.15 Building, simulating and analysing your model in Cell Collective Tomas Helikar
Thursday 30 September 2021
09.30-09.45 Morning quiz  
09.45-10.45 Introduction to spatial modelling (Morpheus) Lutz Brusch
10.45-11.15 Break  
11.15-12.30 Tutorial on spatial modelling Lutz Brusch, Jörn Starruß, Diego Jahn, Robert Mueller
12.30-13.15 Scientific networking - flash talks  
13.15-14.00 Break  
14.00-14.30 BioModels and standards for reproducible modelling Rahuman Sheriff
14.30-15.30 Group challenge on model curation Rahuman Sheriff, Kausthubh Ramachandran, Eva Geissen
15.30-15.45 Break  
15.45-17.00 Group challenge Rahuman Sheriff, Kausthubh Ramachandran, Eva Geissen
Friday 1 October 2021
09.30-09.45 Morning challenge  
09.45-10.45 Keynote lecture and Q&A - "Quantitative systems models to address drug safety challenges in the pharmaceutical industry" Carmen Pin
10.45-11.00 Break  
11.00-13.00 Group challenge on model curation Rahuman Sheriff, Kausthubh Ramachandran, Eva Geissen
13.00-13.30 Break  
13.30-15.00 Group challenge on model curation Rahuman Sheriff, Kausthubh Ramachandran, Eva Geissen
15.00-15.45 Group challenge wrap-up  
15.45-16.00 Group photo, course wrap-up and feedback  







Please read our page on application advice 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 "application submission" section where you are asked to provide three 100-word paragraphs that cover your:
    • scientific biography
    • work history
    • current research interests
  • Upload a letter of support from your supervisor or a senior colleague detailing reasons why you should be selected for this course; and also that you can dedicate your time to this virtual course.

Please submit all documents during the application process by midnight on Friday 2 July 2021.

Incomplete applications will not be considered.

All applicants will be informed of the status of their application (successful, waiting list, rejected) by Friday 16 July 2021. If you have any questions regarding the application process please contact Jane Reynolds

Participant 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. Further details will be provided for selected applicants.

This course has ended

27 September - 01 October 2021
Jane Reynolds

  • Rahuman Sheriff
  • Alexandra Holinski

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