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Title: Multiple Anchor Staged Local Sequence Alignment Algorithm - MASAA.
Contributors: Bharath Govinda Reddy (author), Waqar Haque (Thesis advisor), Alex Aravind (Thesis advisor), University of Northern British Columbia (Degree granting institution)
Abstract: Technology advancements have helped biologists gather massive amount of biological data including genomic sequences of various species today. Sequence alignment techniques play a central role in investigating the adaptive significance of organism traits and revealing evolutionary relations among organisms by comparing these biological data. This thesis presents an algorithm to perform pairwise local sequence alignment. Recent pairwise local sequence alignment algorithms are either slow and sensitive or fast and less sensitive. Our algorithm is faster and at the same time sensitive. The algorithm employs suffix tree data structure to accurately identify long common subsequences in the two given sequences quickly. Regions of high similarity are again identified between segments of long subsequences already found. Several measures are taken into consideration to design the algorithm, such that the output is biologically meaningful. Data sets are carefully chosen and the output is compared with a well known algorithm, BLASTZ. Experiments conducted demonstrate that our algorithm performs better than BLASTZ in computation time, while either preserving or exceeding the accuracy of alignments at times.
Discipline: Computer Science
Date added: 2017-03-30T17:03:59.361Z

Title: A flexible simulation framework for processor scheduling algorithms in multicore systems.
Contributors: Viswanathan Manickam (author), Alex Aravind (Thesis advisor), University of Northern British Columbia (Degree granting institution)
Abstract: In traditional uniprocessor systems, processor scheduling is the responsibility of the operating system. In high performance computing (HPC) domains that largely involve parallel processors, the responsibility of scheduling is usually left to the applications. So far, parallel computing has been confined to a small group of specialized HPC users. In this context, the hardware, operating system, and the applications have been mostly designed independently with minimal interactions. As the multicore processors are becoming the norm, parallel programming is expected to emerge as the mainstream software development approach. This new trend poses several challenges including performance, power management, system utilization, and predictable response. Such a demand is hard to meet without the cooperation from hardware, operating system, and applications. Particularly, an efficient scheduling of cores to the application threads is fundamentally important in assuring the above mentioned characteristics. We believe, operating system requires to take a larger responsibility in ensuring efficient multicore scheduling of application threads. To study the performance of a new scheduling algorithm for the future multicore systems with hundreds and thousands of cores, we need a flexible scheduling simulation testbed. Designing such a multicore scheduling simulation testbed and illustrating its functionality by studying some well known scheduling algorithms Linux and Solaris are the main contributions of this thesis. In addition to studying Linux and Solaris scheduling algorithms, we demonstrate the power, flexibility, and use of the proposed scheduling testbed by simulating two popular gang scheduling algorithms - adaptive first-come-first-served (AFCFS) and largest gang first served (LGFS). As a result of this performance study, we designed a new gang scheduling algorithm and we compared its performance with AFCFS. The proposed scheduling simulation testbed is developed using Java and expected to be released for public use.
Discipline: Computer Science
Date added: 2017-03-30T17:13:54.402Z

Title: Gridsim: a flexible simulator for grid integration study
Contributors: Suresh Rathnaraj Chelladurai (author), Alex Aravind (Thesis advisor), University of Northern British Columbia College of Science and Management (Degree granting institution), Matthew Reid (Committee member), lliya Bluskov (Committee member)
Abstract: Global warming and the increasing cost of fossil fuels have driven researchers to focus on renewable and cleaner sources of energy like wind, water, and solar. These energy sources show promise for sustainability and reduced greenhouse gas emissions, the only disadvantage of them is that they are intermittent and currently expensive. Measuring the impact of integrating new energy sources into an existing grid system is not feasible. Therefore, Modeling and Simulation becomes an indispensable approach. Several tools exist for modeling and simulation of the power grid. They primarily focus on analyzing smart grids and are complex to use for integration studies. Designing and implementing software that allows the users to model and simulate power grid system for integration study is the primary motivation of this thesis. We propose, GridSim, an easy, intuitive software to perform grid integration analysis and its use is illustrated through case studies.
Discipline: Computer Science
Date added: 2017-05-15T21:06:49.267Z

Title: A flexible simulaton framework for the study of deadlock resolution algorithms in multicore systems
Contributors: Dhruv Desai (author), Alex Aravind (Thesis advisor), University of Northern British Columbia (Degree granting institution)
Abstract: Deadlock is a common phenomenon in software applications, yet it is ignored by most operating systems. Although the occurrence of a deadlocks in systems is not frequent, in some cases, the effects are drastic when deadlock occurs. The ongoing trend in processor technology indicates that future systems will have hundreds and thousands of cores. Due to this imminent trend in hardware development, the problem of deadlock has gained renewed attention in research. Deadlock handling techniques that are developed for earlier processors and distributed systems might not work well with multicore systems, due to their architectural differences. Hence, to maximize the utility of multicore systems, new programs have to be carefully designed and tested before they can be adopted for practical use. Many approaches have been developed to handle deadlock in multicore systems, but very little attention has been paid to comparing the performance of those approaches with respect to different performance parameters. To fulfil the above mentioned shortfalls, we need a flexible simulation testbed to study deadlock handling algorithms and to observe their performance differences in multicore systems. The development of such a framework is the main goal of this thesis. In the framework, we implemented a general a scenario, scenario for the Dining Philosopher's problem and scenario for the Banker's algorithm. In addition to these scenarios, we demonstrate the flexibility, soundness, and use of the proposed framework by simulating two different deadlock handling strategies "" deadlock avoidance (the Banker's algorithm) and deadlock detection (Dreadlocks). The deadlock detection is followed by deadlock recovery to resolve the detected deadlock. We also present result analysis for the different set of experiments performed on the implemented strategies. The proposed simulation testbed to study deadlocks in multicore systems is developed using Java. --Leaf i.
Discipline: Computer Science
Date added: 2017-03-29T17:29:56.073Z

Title: Fair and efficient CPU scheduling algorithms.
Contributors: Jeyaprakash Chelladurai (author), Alex Aravind (Thesis advisor), University of Northern British Columbia (Degree granting institution)
Abstract: No abstract available.
Discipline: Computer Science
Date added: 2017-03-30T17:02:54.645Z

Title: A study of the Destination Guided Mobility models.
Contributors: Md. Azizur Rahman (author), Alex Aravind (Thesis advisor), University of Northern British Columbia (Degree granting institution)
Abstract: Mobility models play a critical role in the simulation studies of Mobile Ad hoc Networks (MANETs). They greatly influence the performance of MANET routing protocols. For MANET simulations, random mobility models have been used in nearly all research studies in the past. In recent times, several studies have criticised the use of random mobility models in the performance studies of MANETs for the lack of realism in modelling mobility. Therefore, questions have been raised regarding the credibility of MANET simulation studies. Realism and simplicity are two attractive properties of mobility models achieving both together in modelling mobility has been a challenging task. Recently, a framework of mobility models called Destination Guided Mobility (DGM) models for MANETs with a basic software tool was proposed. This framework can be used to develop several simple DGM models with improved realism. This thesis is primarily interested in studying DGM models for their suitability in modelling mobility in various MANET scenarios. Our study requires a suitable simulation testbed for DGM models. Designing such a tool, referred to as DGMGen, with suitable functionality to study DGM models is the secondary objective of this thesis. More specifically, after the design and implementation of DGMGen, we study: i) the generality of the DGM models by modelling different real world scenarios ii) the connectivity analysis of three basic DGM models in comparison with the widely used Random Waypoint (RWP) mobility model iii) how to model a real life scenario using DGM models, based on the trace collected from that scenario and iv) the impact of DGM models on the Ad hoc On-demand Distance Vector (AODV) routing protocol using NS2. Our study shows that i) the DGM framework is powerful in capturing various MANET scenarios simply and more accurately, ii) DGM models confirm higher level connectivity prevailed in most real world scenarios, iii) DGM models can generate approximately the similar trace based on the insights of a real trace
Discipline: Computer Science
Date added: 2017-03-30T17:12:44.903Z

Title: Development of a trace generation and analysis software for random mobility models.
Contributors: Xiang Cui (author), Alex Aravind (Thesis advisor), University of Northern British Columbia (Degree granting institution)
Abstract: No abstract available.
Discipline: Computer Science
Date added: 2017-03-30T17:01:31.307Z

Title: Generation and analysis of realistic mobility models for mobile ad hoc networks.
Contributors: Hassan Tahir (author), Alex Aravind (Thesis advisor), University of Northern British Columbia (Degree granting institution)
Abstract: Simulation modeling is an integral part of conducting research in communication networks and distributed systems. In systems involving mobile nodes, accurate modeling of mobility has primary importance. Mobility has a fundamental influence on the behavior and performance of the system. However, only few mobility models have been used in nearly all simulations in the past. These models are simple and highly random. As a result, the simulation studies based on these random mobility models have been heavily criticized for their credibility. We feel that availability of a software tool with the following capability, at least in part, would alleviate this crisis. The software must facilitate researchers to: (i) model a wide range of mobility with varying degrees of realism (ii) analyze the modeled mobility visually and statistically and (iii) transport the mobility trace in a format that can be used in most widely used simulators. The development of a software tool with the above mentioned capabilities is the main contribution of this thesis. In this thesis, after presenting a comprehensive survey on realistic mobility models, we present a realistic mobility generator software called RLMobiGen that can be used to specify, generate, analyze, and then export the mobility trace. The mobility trace can then be used in the simulation studies of mobile ad hoc networks. RLMobiGen is a comprehensive, highly interactive, and user friendly software. --P.iii.
Discipline: Computer Science
Date added: 2017-03-30T17:08:05.043Z

Title: Design and implementation of a simulation tool to study wait times in cataract surgery
Contributors: Adiba Mahjabin Nitu (author), Alex Aravind (Thesis advisor), University of Northern British Columbia (Degree granting institution)
Abstract: Eye cataracts are a common problem for senior people. Long wait times for cataract surgery degrade the patients' quality of life. Reduction in long wait times in eye cataract surgery has got importance as one of the five major priority areas in the health care systems in Canada. The main contribution of this thesis is to design and develop a discrete event simulation tool in JAVA to study the wait times (wait time 1 and wait time 2) for patients in cataract surgical procedure. Two cataract surgical procedures are simulated in the simulation tool Northern Health Cataract Surgical Model (NHCS Model) and Cataract Surgery Generic Model (CSG Model). Two alternative patient referral methods (refer patients to the surgeon with the least number of patients and uniform distribution of patients) are proposed and compared to the existing method to examine which method results in reduced wait times. The impacts of changing the resources (surgeon and OR) on wait times were analysed. The Manitoba Cataract Waiting List Program (MCWLP) priority system is simulated and compared to the existing FCFS policy to see whether the scheduling of patients for surgery based on priority improves wait times. Experimental results show that the two proposed methods significantly reduce wait times. It is found that Northern Health would meet the target wait time 2 (16 weeks) if one more OR (total of two ORs) is allocated for cataract surgery. The use of priority scheduling did not show any improvement in wait time 2. Increasing budget or number of resources is not always easy for any health care authority. This thesis suggests that, if Northern Health authority changes the existing patient referral method, it would definitely reduce wait times for patients.
Discipline: Computer Science
Date added: 2017-03-29T17:27:54.158Z

Title: Design and implementation of virtual network testbeds for routing protocols
Contributors: Julius A. Bankole (author), David Casperson (Thesis advisor), Alex Aravind (Thesis advisor), University of Northern British Columbia (Degree granting institution)
Abstract: In this project, we present the design and implementation of virtual network testbeds for studying routing changes. A virtual network testbed is a computer network that is completely created in software, while routing changes directly impact on the reliability and the reachability information of the network. We used testbeds to emulate a small and a large-scale network on a single Linux machine. These emulated networks allow the study of network behavior and operations which are examined using two routing protocols: Routing Information Protocol (RIP) and Open Shortest Path First (OSPF). We implemented a fifteen-node network to study RIP, and a model of the GÈANT network to examine OSPF in virtual network testbeds. Each testbed represents an autonomous system (AS) or an intra-domain environment. Therefore, these environments provided us with the opportunities to evaluate routing changes in an AS. We used the testbeds to compare the routing of the original network with the new routing of the missing links and routers to see what changes occur. The GÈANT network is the large-scale network used for investigations in this project. We then used our emulation results of the large-scale network to compare with the simulation work for the same network topology-the GÈANT network, and confirmed that our emulation studies also identified important links and routers in the same network. --P.ii.
Discipline: Computer Science
Date added: 2017-04-10T22:09:29.242Z

Title: On-site tracking in wireless sensor networks.
Contributors: Baljeet Singh Malhotra (author), Alex Aravind (Thesis advisor), University of Northern British Columbia (Degree granting institution)
Abstract: Tracking is one of the oldest practices that has evolved along with the advancement of technology. The task of tracking a moving target may have different objectives. Based on how these objectives are achieved, we classify the tracking problems into two broad categories: 'On-site tracking' and ' Off-site tracking'. The basic difference between these two approaches is the need for the physical presence of a mobile sink to track the target. This thesis deals with the On-site tracking problem in wireless sensor networks. First, we characterize the problem for a single target case and generalize it for the multiple targets case. Then, we propose a class of efficient algorithms to solve the problem. We also developed simulation software, OSTSim, for the performance study of the proposed algorithms. Theoretical bounds for the tracking time and the number of messages generated have been derived for our algorithms. An extensive simulation study shows that our algorithms are efficient.
Discipline: Computer Science
Date added: 2017-03-30T16:59:12.343Z

Title: Dance training and feedback system using wearable wireless sensors.
Contributors: Baldeep (author), Alex Aravind (Thesis advisor), University of Northern British Columbia (Degree granting institution)
Abstract: Teaching and learning the art of human body motion practices such as dance are interesting activities and they are usually performed at traditional training centres. Nowadays, learning the art of dance is becoming challenging proposition with a huge time and energy commitment. In recent times, there has been a vast advancement in computing and sensing technologies, and they are easily accessible. Based on these observations, we proposed a wireless sensor-based dance training and feedback system, which is convenient, flexible, and portable. This system is unique in terms of providing prompt feedback with various teaching and learning flexibilities to both trainees and trainers. In this thesis, an architectural framework of generic body movement training system, proposed in [1], is tuned and expanded to develop a dance training and feedback system. The proposed feedback system and its prototype implementation is the main contributions of this thesis. The proposed teaching and learning tool presents a method for generating meaningful feedback by capturing and analyzing the motion data in real time. The usage of the proposed system is demonstrated using Tap dance. Performance metrics are devised to evaluate the performance and a weighted scoring scheme is applied to compute the performance. The functionalities of the feedback system are illustrated using suitable scenarios. A combination of quantitative and qualitative feedbacks can be generated and presented to the trainees in three different forms: textual, graphical, and audio. The system also accommodates varying teaching styles and preferences of different trainers. We believe that such a two-end customization is a unique feature of the proposed system. With further tunning, we expect it will be a useful tool for teaching and learning of dance at the beginner's level.
Discipline: Computer Science
Date added: 2017-03-30T17:13:09.551Z