Mathematical Modelling Series I – Models of signal transduction networks and CellNOpt software

This course will briefly describe different approaches to model signal transduction networks. It will focus on ‘causal’ methods, in particular logic-based formalisms, that do not get into biochemical details. These methods scale up better to large networks and require less knowledge of the system, at the price of providing less detailed insight. We will then discuss how these models can be fitted to experimental data, typically phosphoproteomics, and finally illustrate the insight that can be gained with these models, in particular in the context of understanding the deregulation of signal transduction in human disease.

In the practical part we will use the tool CellNOpt (www.cellnopt.org), via the Cytoscape plug-in CytoCopter, to illustrate some of these concepts. We will finally discuss with the attendees that wish to do so which modelling approach and tool is best suited to their own data and question.

The course does not require any previous programming experience. We will provide you with computers, but you can also install the software on your personal machine, from the following website: https://github.com/saezlab/cellnopt.

The course is free for all members of EMBL.

Tutors: Prof. Julio Saez Rodriguez (EBI and RWTH Aachen University), his postdoc Attila Gábor and Dr. Karin Sasaki (EMBL-CBM)