Model checking in systems biology: an introduction
Pedro T. Monteiro,
INRIA Rhône-Alpes –
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.
Date: 2009-May-08 Time: 11:00:00 Room: 336
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Workshop “Metabolism and mathematical models: Two for a tango” – 2nd Edition
Title: Workshop Metabolism and mathematical models: Two for a tango – 2nd Edition
Dates: October 25-26, 2022
Location: This workshop will be held in a virtual way
The topic of this workshop is metabolism in general, with a special focus, although not exclusive, on parasitology. Besides an exploration of the biological, biochemical and biomedical aspects, the workshop will also aim at presenting some of the mathematical modelling, algorithmic theory and software development that have become crucial to explore such aspects.
This workshop is being organised in the context of two projects, both with the Inria European Team Erable. One of the projects involves a partnership with the University of São Paulo (USP), in São Paulo, Brazil, more specifically the Institute of Mathematics and Statistics (IME) and the Institute of Biomedical Sciences – Inria Associated Team Capoeira – and the other involves the Inesc-ID/IST in Portugal, ETH in Zürich and EMBL in Heidelberg – H2020 Twinning Project Olissipo.
The workshop is open to all members of these two projects but also, importantly, to the community in general.
The program and more details are available here.