T4: Logical modelling of regulatory networks


Claudine Chaouiya (Instituto Gulbenkian de Ciência, Oeiras, Portugal) and Aurelien Naldi (University of Montpellier, France )

Tutorial website

Tutorial Summary:

The identification of large regulatory and signalling networks involved in the control of crucial cellular processes calls for proper modelling approaches. Indeed, models can help elucidate properties of these networks, understand their behaviours, and provide (testable) predictions by performing in silico experiments.

In this context, qualitative, logical frameworks have emerged as relevant approaches, as demonstrated by a growing number of published models, along with new methodologies and software tools. This productive activity led to the establishment of CoLoMoTo (the Consortium for Logical Modelling and Tools) as a concerted effort to ensure model reusability and interoperability between tools.

This tutorial aims at providing an introduction to the field and an overview of the diverse formalisations covering “logical modelling” (Boolean, multilevel, deterministic, stochastic, etc.). This diversity is illustrated by the development of different computational tools, which can be used in a complementary fashion thanks to the exchange format --Systems Biology Markup Language Qualitative Models (SBML qual).

Taking the case of T lymphocyte differentiation, published logical models will be discussed and analysed using a range of tools: GINsim, SQUAD, BoolSim and the Cell Collective.

Specifically, the tutorial will cover the following topics:

  1. Brief introduction to the logical modelling;
  2. Existing software tools and their specificities: from model generation to model analysis;
  3. SBML qual package, a standard format for model exchange;
  4. CoLoMoTo, activities and goals;
  5. Logical models of T lymphocyte differentiation;
  6. Using these models, demos and hands-on with

a. GINsim (http://www.ginsim.org/),
b. The Cell Collective (http://www.thecellcollective.org/),
c. SQUAD & BoolSim (http://www.vital-it.ch/software/genYsis/).

Material or infrastructure required. Attendees may come with their laptop.

Target audience Students and researchers interested in learning a modelling approach to tackle the complexity of regulatory and signalling networks. This tutorial should interest not only new-comers to the field of network modelling, but also those already familiar with a particular tool, willing to learn about complementary approaches. No prior modelling experience is necessary.


Tutorial speakers:

Claudine Chaouiya (IGC, Oeiras PT)

Isaac Crespo (Vital-IT, SIB Lausanne CH)

Julien Dorier (Vital-IT, SIB Lausanne CH)

Aurélien Naldi (UM2, Montpellier FR)

Tutorial Agenda



Introduction to logical modelling



Software tools, and overview, SBML & CoLoMoTo



Logical models of T lymphocyte activation and differentiation



The Cell Collective – short demo



Coffee Break



SQUAD & BoolSim – hands on



GINsim & Model checking – hands on