Object Orientated Computational Models of Prion Propagation

Biological systems such as cells are overwhelmingly complex, the work undertaken in the lab to further our understanding can take months, years or even decades to complete. Using computer simulations (a ''Virtual lab'') allows scientists to carry out experiments in hours rather than decades. This thesis describes the development of just such a system. An application that computationally models the propagation of yeast prion, in Saccharomyces cerevisiae employing an Object Orientated approach and a graphical user interface in Java. Chapter One: introduces the reader to the biological backgorund of the project. This is necessary in order to establish an understanding of and the requirements of the system. This is followed by a literature survey of similar work in computer simulations. Chapter Two: addresses the issue surrounding traditional software engineering approaches and a suitable development life cycle is established in order to implement this unconventional type of application. Additionally, the question of how to most efficiently and accurately represent the real system is discussed. Chapter Three: details the development and implementation of the simulation. Chapter Four: covers how the testing of the application was carried out including a critical analysis of this process, and final stage scientific testing and results. Chapter Five: analyses the end product and proposes potential avneues for future research and development.