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Digital archive of theses discussed at the University of Pisa

 

Thesis etd-12162010-120629


Thesis type
Tesi di dottorato di ricerca
Author
BASUKI, THOMAS ANUNG
URN
etd-12162010-120629
Thesis title
Modelling Biological Systems From Molecular Interactions to Population Dynamics
Academic discipline
INF/01
Course of study
INFORMATICA
Supervisors
tutor Prof. Maggiolo Schettini, Andrea
relatore Cerone, Antonio
Keywords
  • rewriting systems
  • stocastic models
  • Systems biology
Graduation session start date
17/12/2010
Availability
Full
Summary
Biological systems are examples of complex systems, which consist of several interacting components. Understanding the behaviour of such systems requires a multidisciplinary approach that encompasses biology, mathematics, computer science, physiscs and chemistry. New research areas are emerging as the result of this multidisciplinarity, such as bioinformatics, systems biology and computational biology. Computer science plays an important role in the newly emerging research areas by offerring techniques, algorithms, languages and software to solve research problems efficiently. On the other hand, the efforts to solve these research problems stimulate the development of new and better computer science techniques, algorithms, languages and software.
This thesis describes our approach in modelling biological systems as a way to better understand their complex behaviours. Our approach is based on the Calculi of Looping Sequences, a class of formalisms originally developed to model biological systems involving cells and their membrane-based structures. We choose Stochastic CLS and Spatial CLS, two variants of the calculi that support quantitative analysis of the model, and define an approach that support simulation, statistical model-checking and visualisation as analysis techniques. Moreover, we found out that this class of formalisms can be easily extended to model population dynamics of animals, a kind of biological systems that does not involve membrane-based structures.
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