Wim J. Bos - Interactive Signaling Network Analysis Tool

author:Wim J. Bos
title:Interactive Signaling Network Analysis Tool
keywords:biology, kinase signaling pathways, timed automata, UPPAAL
committee:dr. P.E. van der Vet
dr.ir. R. Langerak
ir. Jetse Scholma
graduation date:August 2009 (mark: 8/10)


Abstract

When researching kinase signaling pathways in cells, molecular biologists are confronted with large experimental data sets. Evaluation of these data sets, together with the fitting of these data on possible pathway models, is a highly nontrivial task. The aim of this research is to support biologists in exploring the space of networks inferred from experimental data by means of software that is both interactive and visual, thereby considerably alleviating this task. At the basis of the software lies a quantitative modeling technique that makes use of a computer science model called timed automata. Timed automata models can be created, simulated, and analyzed with UPPAAL, which is a state-of-the-art tool for analysis and design of real-time systems. Modeling a pathway with timed automata makes it possible to decide, using UPPAAL, whether experimental data fits a specific model, or whether such a model should somehow be updated. In order to hide the technical intricacies of timed automata and UPPAAL from the molecular biologist, a prototype interface tool has been built. This interface tool lets users draw a network and add experimental data to it, and then exports this information to a timed automata model to be verified by UPPAAL. Finally, the results from this verification process are translated back to the interface and presented in a graphical manner.