Mathematics of life: Modelling molecular mechanisms (Virtual)


 Monday 28 September Friday 2 October 2020


Virtual - EMBL-EBI, Hinxton,  CB10 1SD, United Kingdom

Application opens: 

Monday 22 June 2020

Application deadline: 

Friday 14 August 2020


Open application with selection


Rebecca Nicholl

Registration fee: 


Registration closed

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Computer models are increasingly used to understand 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 participants with an introduction to modelling resources, tools and approaches used in systems biology as well as touch on network analysis.

This course will be a virtual event delivered via a mixture of live-streamed sessions, pre-recorded lectures and tutorials with live support. We will be using Zoom to run the live stream sessions (all fully password protected) with support provided by Slack. In order to make most out of the course you should make sure to have a stable internet connection throughout the week.

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.


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.

A working knowledge of the Linux operating system and ability to use the command line or experience of using a programming language (e.g Python) would be a benefit but is not mandatory.

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

Syllabus, tools and resources

The programme will cover the following syllabus, tools and resources:

  • Network Analysis and Pathway Enrichment
  • Qualitative (e.g. logic) modelling and quantitative (e.g. chemical kinetic) 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 and CellCollective
  • Group challenge on model curation


After the course, participants should be able to:

  • Identify 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


This course will be delivered as a mixture of live-streamed sessions, pre-recorded lectures and tutorials which you will work through at your pace with live trainer support. A preliminary programme is given below. In order to make most out of this virtual course we recommend you to carve out full days as if you were attending an onsite course. The given time is BST (GMT+1).

Day 1 – Monday 28th September 2020
Networks and pathways
09:30 - 10:00 Introduction to EMBL-EBI and the course Alexandra Holinski
10:00 - 10:30 Get to know each other - icebreaker Rebecca Nicholl, Alex Holinski
10:30 - 10:45 Course overview Rahuman Sheriff

10:45 - 11:00



11:00 - 11:45

Intro to network analysis and molecular interaction database

Pablo Porras and Molecular Interaction Team
11:45 - 12:00 How to build your own networks: Accessing IntAct data from Cytoscape Pablo Porras and Molecular Interaction Team
12:00 - 13:00 Tutorial Pablo Porras and Molecular Interaction Team
13:00 - 14:00 Lunch 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  
Day 2 – Tuesday 29th September 2020
Kinetic modelling
09:30 - 10:00 Morning challenge (focusing on EuropePMC) Dayane Araujo
10:00 - 11:00 Keynote lecture: "A matter of genes, cells and numbers" Alfonso Martinez Arias
11:00 - 11:15 Questions and Answers session for keynote lecture Alfonso Martinez Arias
11:15 - 11:30 Break  
11:30 - 12:30 Scientific networking - Flash talks  
12:30 - 13:30 Lunch break  
13:30 - 14:30 Introduction to kinetic modelling and COPASI Rahuman Sheriff (BioModels team)
14:30 - 14:45 Break  
14:45 - 15:15 Introdcution to group challenge

Rahuman Sheriff, Krishna Tiwari, Alex Holinski

15:15 - 17:00 COPASI tutorial Rahuman Sheriff, Krishna Tiwari (BioModels team)
Day 3 – Wednesday 30th September 2020
Logic modelling
09:30 - 10:00 Morning challenge (focusing on BioStudies) Ugis Sarkans
10:00 - 10:45 Science talk 1:  "Automated Synthesis and Analysis of Logical Network Models to Study Pluripotency"   +  Q&A Sara-Jane Dunn
10:45 - 11:30 Science talk 2: "Modelling temperature-dependent epigenetic regulation" + Q&A Rea Antoniou - Kourounioti
11:30 - 11:45 Break  
11:45 - 12:45 Scientific networking - Flash talks  
12:45 - 13:45 Lunch break and meet the speaker Rea Antoniou - Kourounioti  
13:45 - 14:15 Introduction to logic modelling and available tools Tomas Helikar
14:15 - 14:45 Overview of Cell Collective Tomas Helikar
14:45 - 15:00 Break  
15:00 - 15:30 Breaking down the process of modelling: A practical guide Tomas Helikar
15:30 - 17:00 Building, simulating and analysing your model in Cell Collective Tomas Helikar
Day 4 – Thursday 1st October 2020
Spatial modelling and group challenge
09:30 - 10:00 Interactive morning challenge (focusing on OmicsDI) Gaurhari Dass
10:00 - 11:00 Introduction to spatial modelling (Morpheus) Lutz Brusch
11:00 - 11:15 Break  
11:15 - 12:30 Tutorial on spatial modelling Lutz Brusch
12:30 - 13:15 Scientific networking - Flash talks  
13:15 - 14:00 Lunch break and meet the speaker Sara-Jane Dunn  
14:00 - 14:30 BioModels and standards for reproducible modelling Rahuman Sheriff (BioModels team)
14:30 - 15:30 Group challenge on model curation  
15:30 - 15:45 Break  
15:45 - 17:00 Group challenge on model curation  
Day 4 – Friday 2nd October 2020
Group challenge
09:30 - 10:30 Keynote lecture: "Mathematical modelling for drug discovery" - time to watch the pre-recording James Yates
10:30 - 11:00 Questions and Answers session for keynote lecture James Yates
11:00 - 11:15 Break  
11:15 - 13:00 Group challenge on model curation  
13:00 - 13:30 Lunch break  
13:30 - 15:00 Group challenge on model curation  
15:00 - 15:45 Group challenge wrap-up  
15:45 - 16:00 Course wrap-up and feedback Alexandra Holinski