<p>In the post-genomics era, the sheer volume of data is overwhelming without appropriate tools for data integration and analysis. Studying genomic sequences in the context of other related genomic sequences, i.e. comparative genomics, is a powerful technique enabling the identification of functionally interesting sequence regions based on the principal that similar sequences tend to be either homologous or provide similar functionality.</p> <p>Costs associated with full genome sequencing make it infeasible to sequence every genome of interest. Consequently, simple, smaller genomes are used as model organisms for more complex organisms, for instance, Mouse/Human. An annotated model organism provides a source of annotation for transcribed sequences and other gene regions of the more complex organism based on sequence homology. For example, the gene annotations from the model organism aid interpretation of expression studies in more complex organisms.</p> <p>To assist with comparative genomics research in the Arabidopsis/Brassica (Thale-cress/Canola) model-crop pair, a web-based, graphical genome browser (BioViz) was developed to display short Brassica genomic sequences in the context of the Arabidopsis model organism genome. This involved the development of graphical representations to integrate data from multiple sources and tools, and a novel user interface to provide the user with a more interactive web-based browsing experience. While BioViz was developed for the Arabidopsis/Brassica comparative genomics context, it could be applied to comparative browsing relative to other reference genomes.</p> <p>BioViz proved to be an valuable research support tool for Brassica / Arabidopsis comparative genomics. It provided convenient access to the underlying Arabidopsis annotation, allowed the user to view specific EST sequences in the context of the Arabidopsis genome and other related EST sequences. In addition, the limits to which the project pushed the SVG specification proved influential in the SVG community. The work done for BioViz inspired the definition of an opensource project to define standards for SVG based web applications and a standard framework for SVG based widget sets.</p>

<p>Among the various physical systems considered for scalable quantum information processing (QIP), individually trapped ions or neutral atoms have emerged as promising candidates. Recent experiments using these systems have demonstrated the basic building blocks required for a useful quantum computer. In many of these experiments, precisely tuned lasers control and manipulate the quantum bit (qubit) represented in the electronic energy levels of the ion or atom. Scaling these systems to the necessary number of qubits needed for meaningful calculations, requires the development of scalable optical technology capable of delivering laser resources across an array of ions or atoms. That scalable technology is currently not available.</p><p>In this dissertation, I will report on the development, design, characterization, and implementation of an optical beam steering system utilizing microelectromechanical systems (MEMS) technology. Highly optimized micromirrors enable fast reconfiguration of multiple laser beam paths which can accommodate a range of wavelengths. Employing micromirrors with a broadband metallic coating, our system has the flexibility to simultaneously control multiple beams covering a wide range of wavelengths. </p><p>The reconfiguration of two independent beams at different wavelengths (780 and 635 nm) across a common 5x5 array of target sites is reported along with micromirror switching times as fast as 4 us. The optical design of the system minimizes residual intensity at neighboring sites to less than 40 dB below the peak intensity. Integration of a similar system into a neutral atom QIP experiment is reported where 5 individually trapped atoms are selectively manipulated through single qubit rotations with a single laser source. This demonstration represents the first application of MEMS technology in scalable QIP laser addressing.</p> / Dissertation

This dissertation presents a wide-band lumped element equivalent circuit model and a building block-based scalable circuit model for multiple quantum well laser diodes. The wide-band multiple-resonance model expresses two important laser diode characteristics such as input reflection and electrical-to-optical transmission together. Additionally, it demonstrates good agreements with the measurement results of the selected commercial discrete laser diodes. The proposed building block-based modeling approach proves its validity using a numerically derived scalable rate equation. Since success in a circuit design depends largely on the availability of accurate device models, the practical application of the proposed models provides improved accuracy, simple implementation and a short design time.

Based on the fast evolution of wireless networks and multimedia compression technologies in recent years, real-time multimedia transmission over wireless networks will be the next step for the implementation of contemporary communication system. Lower bandwidth and higher loss rate make wireless networks hard to transmit multimedia content than its wired counterpart. In addition, the common delay constraint from real-time multimedia transmission raises the challenges for the design of wireless communication system. This dissertation proposes an adaptive unequal error protection (UEP) and packet size assignment scheme for scalable video transmission over a burst error channel. An analytic model is developed to evaluate the impact of channel bit-error-rate on the quality of streaming scalable video. A video transmission scheme, which combines the adaptive assignment of packet size with unequal error protection to increase the end-to-end video quality is proposed. Several distinct scalable video transmission schemes over burst-error channel have been compared, and the simulation results reveal that the proposed transmission schemes can react to varying channel conditions with less and smoother quality degradation. Furthermore, in order to meet the real time need in many video transmission applications, this dissertation has proposed low time-complexity packet size assignment schemes. Meanwhile, from the test result, it can be seen that although this method has sacrificed a little bit video quality as compared to optimized method, yet it can adapt to all kinds of network situations and display smoother quality and performance. Moreover, as compared to optimized method, this strategy greatly reduces the calculation time-complexity.

A common feature of emerging future Internet architectures is the ability for applications to select the path, or paths, their packets take between a source and destination. Unlike the current Internet architecture where routing protocols find a single (best) path between a source and destination, future Internet routing protocols will present applications with a set of paths and allow them to select the most appropriate path. Although this enables applications to be actively involved in the selection of the paths their packets travel, the huge number of potential paths and the need to know the current network conditions of each of the proposed paths will make it virtually impossible for applications to select the best set of paths, or just the best path. To tackle this problem, we introduce a new Network Path Advising Service (NPAS) that helps future applications choose network paths. Given a set of possible paths, the NPAS service helps applications select appropriate paths based on both recent path measurements and end-to-end feedback collected from other applications. We describe the NPAS service abstraction, API calls, and a distributed architecture that achieves scalability by determining the most important things to monitor based on actual usage. By analyzing existing traffic patterns, we will demonstrate it is feasible for NPAS to monitor only a few nodes and links and yet be able to offer advice about the most important paths used by a high percentage of traffic. Finally, we describe a prototype implementation of the NPAS components as well as a simulation model used to evaluate the NPAS architecture.

In cooperative networked haptic systems, some distributed distant users may decide to leave or join the cooperation while other users continue to manipulate the shared virtual object (SVO). Cooperative haptic systems that support interaction among a variable number of users, called scalable haptic cooperation systems herein, are the focus of this research. In this thesis, we develop distributed control strategies that provide stable and realistic force feedback to a varying number of users manipulating a SVO when connected across a computer network with imperfections (such as limited packet update rate, delay, jitter, and packet-loss). We fi rst propose the average position (AP) scheme to upper bound the effective stiff ness of the SVO coordination and thus, to enhance the stability of the distributed multi-user haptic cooperation. For constant and small communication delays and over power-domain communications, the effectiveness of the proposed AP paradigm is compared with the traditional proportional-derivative (PD) scheme via multi-rate stability and performance analyses supported with experimental verif cations. Next, in a passivity-based approach, the scalability is pursued by implementing the AP scheme over wave-domain communication channels along with passive simulation of the dynamics. By constructing a passive distributed SVO in closed-loop with passive human users and haptic devices, we guarantee the stability of the distributed haptic cooperation system. However, energy leak at joining/leaving instances may compromise the passivity of the SVO. We examine the preservation of passivity of the proposed SVO scheme for such situations. A switching algorithm is then introduced in order to improve the performance of the cooperative haptic system. Experiments in which three users take turn in leaving or joining the cooperation over a network with varying delay and packet-loss will support the theoretical results. / Graduate / 0771 / 0548 / 0537 / 0544 / rrakhsha@uvic.ca

Multiple Description Coding (MDC) was fi rst formulated by A. Gersho and H. Witsenhausen as a way to improve the robustness of telephony links to outages. Lots of studies have been done in this area up to now. Another application of MDC is the transmission of an image in diff erent descriptions. If because of the link outage during transmission, any one of the descriptions fails, the image could still be reconstructed with some quality at the decoder side. In video coding, inter prediction is a way to reduce temporal redundancy. From an information theoretical point of view, one can model inter prediction with Causal Video Coding (CVC). If because of link outage, we lose any I-frame, how can we reconstruct the corresponding P- or B-frames at the decoder? In this thesis, we are interested in answering this question and we call this scenario as causal video coding with possible loss of the fi rst encoded frame and we denote it by CVC-PL as PL stands for possible loss. In this thesis for the fi rst time, CVC-PL is investigated. Although, due to lack of time, we mostly study two-frame CVC-PL, we extend the problem to M-frame CVC-PL as well. To provide more insight into two-frame CVC-PL, we derive an outer-bound to the achievable rate-distortion sets to show that CVC-PL is a subset of the region combining CVC and peer-to-peer coding. In addition, we propose and prove a new achievable region to highlight the fact that two-frame CVC-PL could be viewed as MDC followed by CVC. Afterwards, we present the main theorem of this thesis, which is the minimum total rate of CVC-PL with two jointly Gaussian distributed sources, i.e. X1 and X2 with normalized correlation coeffi cient r, for di fferent distortion pro files (D1,D2,D3). Defi ning Dr = r^2(D1 -1) + 1, we show that for small D3, i.e. D3 < Dr +D2 -1, CVC-PL could be treated as CVC with two jointly Gaussian distributed sources; for large D3, i.e. D3 > DrD2/(Dr+D2-DrD2), CVC-PL could be treated as two parallel peer-to-peer networks with distortion constraints D1 and D2; and for the other cases of D3, the minimum total rate is 0.5 log (1+ ??)(D3+??)/ (Dr+?? )(D2+?? ) + 0.5 log Dr/(D1D3) where ??=D3-DrD2+r[(1-D1)(1-D2)(D3-Dr)(D3-D2)]^0.5/[Dr+D2-(D3+1) ] We also determine the optimal coding scheme which achieves the minimum total rate. We conclude the thesis by comparing the scenario of CVC-PL with two frames with a coding scheme, in which both of the sources are available at the encoders, i.e. distributed source coding versus centralized source coding. We show that for small D2 or large D3, the distributed source coding can perform as good as the centralized source coding. Finally, we talk about future work and extend and formulate the problem for M sources.

There is an increasing demand from businesses and industries to make the best use of their data. Clustering is a powerful tool for discovering natural groupings in data. The k-means algorithm is the most commonly-used data clustering method, having gained popularity for its effectiveness on various data sets and ease of implementation on different computing architectures. It assumes, however, that data are available in an attribute-value format, and that each data instance can be represented as a vector in a feature space where the algorithm can be applied. These assumptions are impractical for real data, and they hinder the use of complex data structures in real-world clustering applications. The kernel k-means is an effective method for data clustering which extends the k-means algorithm to work on a similarity matrix over complex data structures. The kernel k-means algorithm is however computationally very complex as it requires the complete data matrix to be calculated and stored. Further, the kernelized nature of the kernel k-means algorithm hinders the parallelization of its computations on modern infrastructures for distributed computing. This thesis defines a family of kernel-based low-dimensional embeddings that allows for scaling kernel k-means on MapReduce via an efficient and unified parallelization strategy. Then, three practical methods for low-dimensional embedding that adhere to our definition of the embedding family are proposed. Combining the proposed parallelization strategy with any of the three embedding methods constitutes a complete scalable and efficient MapReduce algorithm for kernel k-means. The efficiency and the scalability of the presented algorithms are demonstrated analytically and empirically.

Networking multiple "smart" displays together is an affordable way of creating large high-resolution display systems. In this work I propose a new structure and data distribution paradigm for displays of this nature. I model my work on the peer-to-peer style of content distribution, as opposed to the traditional client-server model for this kind of system. In taking a peer-to-peer approach, I present a low-cost and scalable system without the inherent constraints imposed by the client-server model. I present a new class of applications specifically designed for this peer-to-peer style of display system, and provide an easy-to-use framework for developers to use in creating this type of system. / Graduate / 0984

Networking multiple "smart" displays together is an affordable way of creating large high-resolution display systems. In this work I propose a new structure and data distribution paradigm for displays of this nature. I model my work on the peer-to-peer style of content distribution, as opposed to the traditional client-server model for this kind of system. In taking a peer-to-peer approach, I present a low-cost and scalable system without the inherent constraints imposed by the client-server model. I present a new class of applications specifically designed for this peer-to-peer style of display system, and provide an easy-to-use framework for developers to use in creating this type of system. / Graduate / 0984