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Deep Thinking in Immunology

Hands-on modelling workshop

Modelling, systems biology and bioinformatics are becoming important for every biological field, immunology constituting no exception. Since large data sets are more easily created and the amount of information grows more-or-less exponentially, tools that condense that information into models with major dynamic mechanisms, are more than welcome. At the upcoming European Meeting in Amsterdam, we aim to provide a hands-on workshop on these topics in an integrated manner and enable Immunologists to become inspired into using the new technologies for their own research.

Why Modelling?

Immunology is empowered by lots of data, with deep sequencing or cell population imaging as sources. In the past, one would draw a scheme with perhaps 20 (and usually less) players on the blackboard, with arrows for which influences which, and for up and down regulation. The number of proteins known to be active in every pathway has expanded dramatically as have their ways of regulation in time and space. With the advent of deep data, our traditional way of thinking falters. Yet we are faced with these enormous data sets and the question is how to use them for better understanding and manipulation of immunological processes. We may need something called ‘deep thinking’.

But what is deep thinking? The human brain is not fit for thinking rationally about thousands of molecules at the same time. But it can invoke a little help from its friends. It is wise to befriend computers handling virtually unlimited numbers of data. They can empower mathematical models that simulate immunological reality. For a long time already, mathematical modelling has played a significant role in biology. It has helped appreciate the role of self-organization in developmental biology, synchronization of cellular oscillations, and fragilities in the performance of metabolic and signal transduction pathways. That modelling however, has not been ‘deep’ modelling. Most of those mathematical models focused on concept rather than realism, and were small rather than ‘deep’.

With systems biology and functional genomics a new type of modelling is developing, i.e. one that aims to integrate ‘all’ the relevant data into mathematical models of reality. Married to the deep data, these models enhance understanding of reality rather than potentiality. They help forming and testing hypotheses in hard rather than soft ways. Assisted by computers and systems biology, the models upgrade the human mind, from traditional to ‘deep’ thinking.

This ‘deep thinking’ is not easy. It constitutes a challenge. First, one has to befriend computers and systems biology. And then one has to converse with them patiently, so as to ensure that computer programs make sense immunologically.



This workshop is for the brave immunologists, i.e. for those that accept the challenge. But they will obtain unique qualities that will foster their research in return. In this workshop, we will do the following:

  • Acquaint immunologists with some of the easy-to-use modelling software, which requires very little mathematics
  • Make immunologists use existing systems biology models to address some paradoxes in cell biology and to experience how modelling can fortify the mind and help it to resolve such paradoxes.
  • Enable immunologists to access existing model repositories and interrogate many  more existing models
  • Enable immunologists to integrate deep data into such models
  • Show immunologists how they could make and run their first model
  • Befriend immunologists with some modelers.

The workshop will provide the programs and a number of models to play with under the guidance of an expert systems biologist with the help of a number of expert PhD students. After an introduction, every participant with his/her computer will work out some of the questions related to the different modelling questions provided and is expected to transfer this knowledge to his/her lab and to immunological questions at hand. This will be an exciting challenge to improve and train the next generation immunologists with challenges that result from today’s big data generation.


  1. Laptop with USB port (apple or ear (=PC)).
  2. Good mood.  
  3. Profound interest in immunology and its complexities.

How to register?

You can add a ticket for the hands-on workshop during the regular registration process. We will charge 15€ per workshop/ticket.