INESC-ID   Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa
technology from seed


Knowledge Discovery and Bioinformatics
Inesc-ID Lisboa

Model checking in systems biology: an introduction

05/08/2009 - 11:00
05/08/2009 - 12:00

The study of gene regulatory networks, as well as other biological networks, have recently yield an increase on the number and detail of available models describing specific intracellular processes. The study of these models by means of analysis and simulation tools leads to innumerous predictions representing the possible behaviours of the system. In order to validate these predictions one must confront them with experimental data. Performed manually, this comparison may prove to be impracticable and prone to errors, leading to a growing need for an automatic and scalable method to perform this task. The formal verification field provides powerful methods to deal with the analysis of large models. Some issues still need to be addressed tough, in order to achieve a good integration of formal verification tools in the modeling practice in systems biology. We present the CTRL temporal logic which is powerful enough to express biological properties (multistability and oscillations), as well as an implementation of a set of temporal logic patterns for systems biology, and its integration with the GNA modeling tool. We also propose a web-server based architecture to integrate modeling and simulation tools with model-checking tools and its application to the analysis of the carbon starvation response model in E. coli.