Workshop on Computational Tools to Define and Analyse Logical Models of Cellular Networks

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 “logical modelling” (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.

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.

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.

Instructors

1. Claudine Chaouiya (Instituto Gulbenkian de Ciência, Oeiras Portugal)
2. Thomas Cokelaer (EMBL-EBI, UK)
3. Tomas Helikar (University of Nebraska-Lincoln, USA)
4. Julio Saez-Rodriguez (EMBL-EBI, UK)

Note that this workshop is coupled with the workshop "Logical Modelling and Analysis of Cellular Networks", on the previous day (Saturday, September 6th, 2014, http://www.eccb14.org/program/workshops/lmacn).

Read more

http://www.embnet.org/events