Thesis (Master)--İzmir Institute of Technology, İzmir, 2005 / Keywords: Interface, graphical user interface design, interaction, human-computer interaction. Includes bibliographical references (leaves. 95).

Thesis (Ph. D.)--University of Washington, 2004. / Vita. Includes bibliographical references (p. 71-78).

Thesis (M.S.S.I.S.)--Regis University, Denver, Colo., 2009. / Title from PDF title page (viewed on Jun. 25, 2010). Includes bibliographical references.

Thesis (Ph. D.)--University of Washington, 2005. / Vita. Includes bibliographical references (p. 94-95).

Thesis (M. S. in Systems Technology (Command, Control and Communications)) Naval Postgraduate School, June 1997. / Thesis advisors, Gary R. Porter and Tim L. Phillips. Includes bibliographical references (p. 27). Also available online.

Complying with a security policy often requires users to create long and complex passwords to protect their accounts. However, remembering such passwords appears difficult for many and may lead to insecure practices, such as choosing weak passwords or writing them down. One-Time Passwords (OTPs) aim to overcome such problems; however, most implemented OTP techniques require special hardware, which not only adds costs, but also raises issues regarding availability. This type of authentication mechanism is mostly adopted by online banking systems to secure their clients’ accounts. However, carrying around authentication tokens was found to be an inconvenient experience for many customers. Not only the inconvenience, but if the token was unavailable, for any reason, this would prevent customers from accessing their accounts securely. In contrast, there is the potential to use graphical passwords as an alternative authentication mechanism designed to aid memorability and ease of use. The idea of this research is to combine the usability of recognition-based and draw-based graphical passwords with the security of OTP. A new multi-level user-authentication solution known as: Graphical One-Time Password (GOTPass) was proposed and empirically evaluated in terms of usability and security aspects. The usability experiment was conducted during three separate sessions, which took place over five weeks, to assess the efficiency, effectiveness, memorability and user satisfaction of the new scheme. The results showed that users were able to easily create and enter their credentials as well as remember them over time. Eighty-one participants carried out a total of 1,302 login attempts with a 93% success rate and an average login time of 24.5 seconds. With regard to the security evaluation, the research simulated three common types of graphical password attacks (guessing, intersection, and shoulder-surfing). The participants’ task was to act as attackers to try to break into the system. The GOTPass scheme showed a high resistance capability against the attacks, as only 3.3% of the 690 total attempts succeeded in compromising the system.

Thesis (M.S.)--Boston University / The Earlab Project at Boston University Hearing Research Center (HRC), http://earlab.bu.edu, is a computational simulation system created by the HRC to allow researchers to run simulations efficiently, using software representations of physiological pathways. The existing complexity of Earlab presents difficulty for users who may wish to adjust the parameters necessary to change from models of the ear to models that simulate other physiological pathways. To address this difficulty, several approaches were explored to assist in formulating a new framework for editing files associated with Earlab. XML, a mark-up language, was used to derive a series of prototype XML based documents as replacements for existing Earlab files. Microsoft Visual Studio and C# was then used to create a prototype of a graphical user interface that is capable of displaying an XML based document in a visual manner. The resulting framework shows the process of the intake of an XML document of an sample Earlab model, the presentation of the model in a graphical framework and the ability to edit the model and receive feedback on the suitability of values in the model.

Modelling interactions between genes and their regulators is fundamental to understanding how, for example a disease progresses, or the impact of inserting a synthetic circuit into a cell. We use an existing method to infer regulatory networks under multiple conditions: the Joint Graphical Lasso (JGL), a shrinkage based Gaussian graphical model. We apply this method to two data sets: one, a publicly available set of microarray experiments perturbing the gram-positive bacteria Bacillus subtilis under multiple experimental conditions; the second, a set of RNA-seq samples of Mouse (Mus musculus) embryonic fibroblasts (MEFs) infected with different strains of the parasite Toxoplasma gondii. In both cases we infer a subset of the regulatory networks using relatively small sample sizes. For the Bacillus subtilis analysis we focused on the use of these regulatory networks in synthetic biology and found examples of transcriptional units active only under a subset of conditions, this information can be useful when designing circuits to have condition dependent behaviour. We developed methods for large network decomposition that made use of the condition information and showed a greater specificity of identifying single transcriptional units from the larger network using our method. Through annotating these results with known information we were able to identify novel connections and found supporting evidence for a selection of these from publicly available experimental results. Biological data collection is typically expensive and due to the relatively small sample sizes of our MEF data set we developed a novel empirical Bayes method for reducing the false discovery rate when estimating block diagonal covariance matrices. Using these methods we were able to infer regulatory networks for the host infected with either the ME49 or RH strain of the parasite. This enabled the identification of known and novel regulatory mechanisms. The Toxoplasma gondii parasite has shown to subvert host function using similar mechanisms as cancers and through our analysis we were able to identify genes, networks and ontologies associated with cancer, including connections that have not previously been associated with T. gondii infection. Finally a Shiny application was developed as an online resource giving access to the Bacillus subtilis inferred networks with interactive methods for exploring the networks including expansion of sub networks and large network decomposition.

Neste trabalho e apresentada uma nova abordagem para a representação gráfica de intervalos. Segundo esta abordagem é possível realizar a análise visual de intervalos a partir da associação entre propriedades geométricas do piano cartesiano e de conjuntos de intervalos representados como pontos desse piano. Esta nova abordagem possibilita a representação da interpretação dual de intervalos, assim como a analise visual de relacionamentos em (IR, <=) e (IR, C). Neste contexto, a representação gráfica do conjunto de intervalos degenerados, representado pela reta y = x, constitui um caso especial desta representação,"o. Por sua vez, a relação (IR, representada pelo semiplano superior a reta y = x, denotado piano IR. A interpretação visual de operações intervalares é obtida diretamente através da aplicação da representação gráfica proposta. Além disto, operandos e operadores podem ser estudados diretamente a partir desta representação. Foram desenvolvidos experimentos de analise visual de intervalos utilizando a abordagem proposta e resultados bastante promissores foram obtidos. Estes experimentos possibilitaram a identificação de novas propriedades de intervalos assim como interpretações não usuais para operações intervalares. Esta representação pode ser utilizada também para observar o comportamento de seqüências de intervalos gerados a partir de programas baseado na aplicação da aritmética intervalar. Nesta caso, pode ser observado como os intervalos desta seqüência variam com relação ao seu ponto médio e o raio, assim como a relação entre eles. Esta representação foi utilizada com sucesso para obter a solução geométrica da equação intervalar afim e efetuando sua validação. Finalmente, analisamos a contribuição efetiva deste trabalho no contexto da aritmética intervalar. / This thesis presents a framework enabling the visual analysis of intervals, obtained by mapping geometric properties of the cartesian plane into interval sets to obtain a graphical representation. This new approach makes possible a dual interval representation and the immediate visual analysis of several relationships in (IR, <=) and (IR, C). In this sense, the set of degenerated intervals is a special case of this approach as they are represented by the straight line y=x. In turn, the order relation in (IR, C) is represented through the half-plane above the straight line y = x, denoted IR plane. Applying this framework, the visual interpretation of most interval operations is obtained directly from the graphical representation of the operands and the operations being studied. On the other hand, some experiments on interval visual analysis were developed with good final results. Thus, new properties and unusual interpretations for known operations can be developed with rather small effort. Moreover, this representation can be easily embedded into a running algorithm, to observe convergence and behavior of interval iterations, as one can easily see how intervals change with respect to midpoint and radius, as well as with respect to each other. The validation of this new approach was carried through the geometric solution of linear interval equations. This result was analyzed in order to verify the effective contribution of this geometrical representation in the context of interval arithmetic.

Neste trabalho e apresentada uma nova abordagem para a representação gráfica de intervalos. Segundo esta abordagem é possível realizar a análise visual de intervalos a partir da associação entre propriedades geométricas do piano cartesiano e de conjuntos de intervalos representados como pontos desse piano. Esta nova abordagem possibilita a representação da interpretação dual de intervalos, assim como a analise visual de relacionamentos em (IR, <=) e (IR, C). Neste contexto, a representação gráfica do conjunto de intervalos degenerados, representado pela reta y = x, constitui um caso especial desta representação,"o. Por sua vez, a relação (IR, representada pelo semiplano superior a reta y = x, denotado piano IR. A interpretação visual de operações intervalares é obtida diretamente através da aplicação da representação gráfica proposta. Além disto, operandos e operadores podem ser estudados diretamente a partir desta representação. Foram desenvolvidos experimentos de analise visual de intervalos utilizando a abordagem proposta e resultados bastante promissores foram obtidos. Estes experimentos possibilitaram a identificação de novas propriedades de intervalos assim como interpretações não usuais para operações intervalares. Esta representação pode ser utilizada também para observar o comportamento de seqüências de intervalos gerados a partir de programas baseado na aplicação da aritmética intervalar. Nesta caso, pode ser observado como os intervalos desta seqüência variam com relação ao seu ponto médio e o raio, assim como a relação entre eles. Esta representação foi utilizada com sucesso para obter a solução geométrica da equação intervalar afim e efetuando sua validação. Finalmente, analisamos a contribuição efetiva deste trabalho no contexto da aritmética intervalar. / This thesis presents a framework enabling the visual analysis of intervals, obtained by mapping geometric properties of the cartesian plane into interval sets to obtain a graphical representation. This new approach makes possible a dual interval representation and the immediate visual analysis of several relationships in (IR, <=) and (IR, C). In this sense, the set of degenerated intervals is a special case of this approach as they are represented by the straight line y=x. In turn, the order relation in (IR, C) is represented through the half-plane above the straight line y = x, denoted IR plane. Applying this framework, the visual interpretation of most interval operations is obtained directly from the graphical representation of the operands and the operations being studied. On the other hand, some experiments on interval visual analysis were developed with good final results. Thus, new properties and unusual interpretations for known operations can be developed with rather small effort. Moreover, this representation can be easily embedded into a running algorithm, to observe convergence and behavior of interval iterations, as one can easily see how intervals change with respect to midpoint and radius, as well as with respect to each other. The validation of this new approach was carried through the geometric solution of linear interval equations. This result was analyzed in order to verify the effective contribution of this geometrical representation in the context of interval arithmetic.