Biologists need tools to see the structural relationships encoded in biological sequences (strings). The Walking Tree heuristics calculate some of these relationships. I have designed and implemented graphic presentations which allow the biologist (user) to see these relations. This thesis contains background information on the biological sequences and some background on the Walking Tree heuristics. I demonstrate my methods by showing a visual matching of mitochondrial genomes. I also show matchings based on amino acids and on hydrophobicity. I also show how the parameters of the visualization can be varied to produce more useful pictures. I implemented a parallel version of the Walking Tree heuristic and used it to produce a phylogenetic tree for picornaviruses. I also implemented several user interfaces. These programs are available on my WWW page which allows a user to produce a picture of a matching by giving the sequences in Gen Bank format and by making a few mouse clicks. / Graduation date: 1998

Thesis (Ph. D.)--University of Washington, 2001. / Vita. Includes bibliographical references (p. 155-162).

Although metaphors are common in computing, particularly in human-computer interfaces, opinion is divided on their usefulness to users and little evidence is available to help the designer in choosing or implementing them. Effective use of metaphors depends on understanding their role in the computer interface, which in tum means building a model of the metaphor process. This thesis examines some of the approaches which might be taken in constructing such a model before choosing one and testing its applicability to interface design. Earlier research into interface metaphors used experimental psychology techniques which proved useful in showing the benefits or drawbacks of specific metaphors, but did not give a general model of the metaphor process. A cognitive approach based on mental models has proved more successful in offering an overall model of the process, although this thesis questions whether the researchers tested it adequately. Other approaches which have examined the metaphor process (though not in the context of human-computer interaction) have come from linguistic fields, most notably semiotics, which extends linguistics to non-verbal communication and thus could cover graphical user interfaces (GUls). The main work described in this thesis was the construction of a semiotic model of human-computer interaction. The basic principle of this is that even the simplest element of the user interface will signify many simultaneous meanings to the user. Before building the model, a set of assertions and questions was developed to check the validity of the principles on which the model was based. Each of these was then tested by a technique appropriate to the type of issue raised. Rhetorical analysis was used to establish that metaphor is commonplace in command-line languages, in addition to its more obvious use in GUIs. A simple semiotic analysis, or deconstruction, of the Macintosh user interface was then used to establish the validity of viewing user interfaces as semiotic systems. Finally, an experiment was carried out to test a mental model approach proposed by previous researchers. By extending their original experiment to more realistically complex interfaces and tasks and using a more typical user population, it was shown that users do not always develop mental models of the type proposed in the original research. The experiment also provided evidence to support the existence of multiple layers of signification. Based on the results of the preliminary studies, a simple means of testing the semiotic model's relevance to interface design was developed, using an interview technique. The proposed interview technique was then used to question two groups of users about a simple interface element. Two independent researchers then carried out a content analysis of the responses. The mean number of significations in each interview, as categorised by the researchers, was 15. The levels of signification were rapidly revealed, with the mean time for each interview being under two minutes, providing effective evidence that interfaces signify many meanings to users, a substantial number of which are easily retrievable. It is proposed that the interview technique could provide a practical and valuable tool for systems analysis and interface designers. Finally, areas for further research are proposed, in particular to ascertain how the model and the interview technique could be integrated with other design methods.

Thesis (M.S.)--Brigham Young University. Dept. of Mechanical Engineering, 2006. / Includes bibliographical references (p. 91-93).

Thesis (M.S.)--Ohio University, March, 2000. / Title from PDF t.p.

Thesis (M.S.)--Ohio University, June, 2004. / Title from PDF t.p. Includes bibliographical references (leaves 96-99).

Thesis (M.S.)--Ohio University, June, 1997. / Title from PDF t.p.

Thesis (Ph. D.)--University of Missouri-Columbia, 1997. / Typescript. Vita. Includes bibliographical references (leaves 280-283). Also available on the Internet.

Thesis (Ph. D.)--Auburn University, 2008. / Abstract. Includes bibliographical references (p. 119-122).

Thesis (Ph. D.)--University of Missouri-Columbia, 1997. / Typescript. Vita. Includes bibliographical references (leaves 280-283). Also available on the Internet.