Development of advanced techniques for biological network visualisation is crucial for successful progress in the areas of systems-level biology and data-intensive bioinformatics. However, current techniques for biological network visualisation fall short of expectations for representing extensive biological networks. In order to provide really useful network visualisation tools, new approaches have to be proposed and applied alongside with those most powerful features of current visualisation systems. The resulting representation techniques have to be tested by applying to large-scale examples that would include metabolic, signaling and gene expression events. User survey should also be carried out to further prove the advantages of the new techniques. The present thesis describes an attempt to achieve the above objectives, by performing the following steps: 1) existing approaches in the area of network representation were analyzed and their shortcomings and advantages were defined; 2) new notation has been developed, in which, the defined best features of the existing systems were integrated with newly introduced potent features such as compact visualization, ‘functional gate’ and ‘identity gate’, 4) new framework was developed that allows managing large-scale networks that are represented on different levels of details and different levels of constrains, while keeping each diagram semantically unambiguous, 5) extensive examples, including genome-scaled human metabolic network and TNF-alpha receptor signalling network, were used to prove that the designed notation and the framework can be applied efficiently, and, finally, 6) a notation survey has been carried out to validate the advantages of the newly developed notation over the existing ones.

This thesis describe two graphical modeling languages that can be used for specifying the access control setup in most systems that store information in a tree based structure. The Tree-based Access control Modeling Language (TACOMA) is the simplest language that is defined. It is easy to learn and use as it has only 8 symbols and two relations. With this language it is possible to define the exact access control rules for users using a graphical notation. The simplicity of the language do however come at a cost: it is best suited for small or medium sized tasks where the number of users and objects being controlled are limited. To solve the scalability problem a second language is also presented. The Policy Tree-based Access control Modeling Language (PTACOMA) is a policy based version of TACOMA that doubles the number of symbols and relations. While it is harder to learn it scales better to larger tasks. It also allows for distributed specification of access rules where administrators of different domains can be responsible for specifying their own access control rules. Domains can be organized in a hierarchical manner so that administrators on a higher level can create policies that have higher priority and therefor limits what administrators at lower levels can do. The thesis describes the two languages in detail and provides a comparison between them to show the strong and weak points of each language. There is also a detailed case study that shows how the two languages can be used for specifying access control in SNMPv3.

This study investigates the possibility of applying Hatten’s theory of musical gesture to a formal system of musical analysis. Using historical antecedents and established musicological practice as a guide, a range of musical parameters in a motive length span of music are incorporated into a single gesture. This gesture forms the basic semantic unit upon which an analytical tableau structure is built, and a syntax is developed to allow derivations of new gestures; a large scale structure displaying fractal-like self-similarity is then proposed. The completed system is applied to the analysis of the ‘Adagio’ of Mozart’s Flute Quartet K.285 to test whether it can consistently be implemented and whether it produces falsifiable results while maintaining predictive power. It is found that these requirements are indeed met and that a set of inference rules can be derived suggesting that the proposed system has ample scope for further development. / Art History, Visual Arts & Musicology / M. Mus.

This study investigates the possibility of applying Hatten’s theory of musical gesture to a formal system of musical analysis. Using historical antecedents and established musicological practice as a guide, a range of musical parameters in a motive length span of music are incorporated into a single gesture. This gesture forms the basic semantic unit upon which an analytical tableau structure is built, and a syntax is developed to allow derivations of new gestures; a large scale structure displaying fractal-like self-similarity is then proposed. The completed system is applied to the analysis of the ‘Adagio’ of Mozart’s Flute Quartet K.285 to test whether it can consistently be implemented and whether it produces falsifiable results while maintaining predictive power. It is found that these requirements are indeed met and that a set of inference rules can be derived suggesting that the proposed system has ample scope for further development. / Art History, Visual Arts and Musicology / M. Mus.