T02 - Computational Tools to Define and Analyse Logical Models of Cellular Networks

Short description

The logical framework is being increasingly used to model the dynamical behaviour of biological regulatory networks. In this context, a range of computational tools have been developed to support model definition and analysis. These tools reflect the diversity of formalisations covering ‚Äúlogical modelling‚ÄĚ (Boolean, multilevel, deterministic, stochastic, etc.). This tutorial aims at providing an overview of this diversity, demonstrating the complementarity between existing computational tools made possible by a novel exchange format --Systems Biology Markup Language¬† Qualitative Models (SBML qual). Instructors will provide an overview of existing technology powering efficient qualitative modelling of regulatory and signalling networks. Real biological examples will be used in the proposed tutorial session. Specifically, presentations will cover the following topics:

  1. Brief introduction to logical modelling;
  2. Existing software tools and their specificities;
  3. SBML qual package, a standard format for model exchange;
  4. CellNOpt: a toolbox for creating logic-based models of signal transduction networks, and training them against high-throughput biochemical data (http://www.cellnopt.org/), overview and short demo;
  5. GINsim, a software tool for the definition simulation and analysis of regulatory and signalling networks (http://www.ginsim.org/), overview and short demo;
  6. The Cell Collective, a platform for collaborative creation and simulation of large-scale Boolean models (http://www.thecellcollective.org/), overview and short demo.

Attendees will have access to all the material necessary in order to follow/reproduce the various short demonstrations. Speed dating will be organised along the main conference, for one-on-one hands-on training with attendees' custom data. 

Latest information:

The tutorial is mainly based on the following paper:  C. Chaouiya et al (2013) BMC Systems Biology, 7:135

1/ CellNOpt: you would need to install Cytoscape v3.1 and R v3.x

Detailed information here: http://www.cellnopt.org/cytocopter/index.html

The tutorial is here:  http://www.cellnopt.org/cytocopter/resources/CytocopterManual.pdf

2/ GINsim can be download at http://ginsim.org. Please choose the latest version (File with dependencies included: GINsim-2.9.3-with-deps.jar). In order to run this version of GINsim, JAVA version 1.6 or higher is required. It comes as a .JAR file which can be launched directly if your system is properly configured, or with the command:   java -jar GINsim-2.9.3-with-deps.jar

3/ Cell Collective can be accessed online at htttp://www.thecellcollective.org. Recommended browsers to use are Chrome and Firefox.

Download the model (SBML qual and GINsim formats) and C. Chaouiya's slides here. J. Saez Rodriguez' slides are here


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.


This tutorial will be held on Sunday, 7 september 2014 afternoon. Note that it will follow the workshop Logical modelling and analysis  of cellular networks scheduled the day before.


Schedule and venue:

  • 13:30-14:20 Introduction and overview
  • 14:20-15:10 CellNOpt
  • 15:10:16:00 GINsim
  • 16:00-16:20 Coffee break
  • 16:20-17:10 The Cell Collective
  • 17:10-18:00 Conclusions - discussions

The tutorial will be held in the "Palais de la Musique et des Congrès", Place de Bordeaux,  67082 Strasbourg (see location on google map). 






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