Consistency and Sensitivity Analysis of Multi-level Petri Net Models of Biological Systems

Consistency and Sensitivity Analysis of Multi-level Petri Net Models of Biological Systems Shauheen Zahirazami Doctor of Philosophy Concordia University 2013 The recent developments in biological experiments have awarded the research community with valuable information, which describe finely regulated systems that govern the cell dynamics. One of the greatest challenges, however, remains to represent this extensive amount of knowledge in a proper way that can be used in simulations, and validated automatically, in order to understand the dynamics and ultimately achieve a desired behaviour for the system (cell) under control. Many tools and techniques have been proposed in the literature to address this important problem. In this research, the use of Petri nets for knowledge representation is investigated. The initial focus of this research is then to introduce a concept of consistency between Petri nets obtained from various knowledge sources. Two algorithms are provided to construct Petri net models for cell dynamics using data available in public domain biological database. The first algorithm generates a low-level model capturing proteinprotein interactions and the second, produces a high-level model which describes pathway sequences and is considerably easier to analyze. Appropriate tests are developed to study