Digital Commons Network^™

New Computational Approaches For Multiple Rna Alignment And Rna Search, Daniel Deblasio

Electronic Theses and Dissertations

In this thesis we explore the the theory and history behind RNA alignment. Normal sequence alignments as studied by computer scientists can be completed in O(n2) time in the naive case. The process involves taking two input sequences and finding the list of edits that can transform one sequence into the other. This process is applied to biology in many forms, such as the creation of multiple alignments and the search of genomic sequences. When you take into account the RNA sequence structure the problem becomes even harder. Multiple RNA structure alignment is particularly challenging because covarying mutations make sequence …

Apco Project 25 Wireless Data Services Over Land Mobile Radio Channel For Smaller Law Enforcement Agencies, Ivan Elhart

Master's Theses and Capstones

Digital data messages are very important in modern communication systems and advanced mobile data technologies have opened the door to a wide range of applications and services in the public safety environment. Still, the availability of mobile data services among public safety agencies is hampered by two issues of the implementation of data communication: the reliability of commercial data services and the high cost of the equipment needed to support mixed voice and data transmissions over private land mobile radio channels.

This thesis describes the design and development of an inexpensive Software Defined APCO Project 25 Data Base Station that …

A Computer Science Approach To Identify And Classify Hyperactivated Spermatozoa, Norbert Kaula

Electronic Theses and Dissertations

Effective Assisted Reproductive Technology (ART) relies in part upon accurate but easily conducted measurements of sperm motion parameters. Several established methods are widely used to assess possible reasons for male infertility, in human and veterinary Andrology clinics. Computer-assisted sperm analysis (CASA) devices quantitatively assess sperm motion parameters, which have been defined by the World Health Organization, and include the percentage of motile cells in a sample and the motion characteristics of individual cells, such as curvilinear velocity (VCL), average path velocity (VAP) and straight line velocity (VSL). However, CASA analyses fail to define hyperactive sperm motility or determine the prevalence …

Adaptive Middleware For Resource-Constrained Mobile Ad Hoc And Wireless Sensor Networks, Chien-Liang Fok

All Theses and Dissertations (ETDs)

Mobile ad hoc networks: MANETs) and wireless sensor networks: WSNs) are two recently-developed technologies that uniquely function without fixed infrastructure support, and sense at scales, resolutions, and durations previously not possible. While both offer great potential in many applications, developing software for these types of networks is extremely difficult, preventing their wide-spread use. Three primary challenges are: 1) the high level of dynamics within the network in terms of changing wireless links and node hardware configurations,: 2) the wide variety of hardware present in these networks, and: 3) the extremely limited computational and energy resources available. Until now, the burden …

Statistical Aggregation: Theory And Applications, Ruibin Xi

All Theses and Dissertations (ETDs)

Due to their size and complexity, massive data sets bring many computational challenges for statistical analysis, such as overcoming the memory limitation and improving computational efficiency of traditional statistical methods. In the dissertation, I propose the statistical aggregation strategy to conquer such challenges posed by massive data sets. Statistical aggregation partitions the entire data set into smaller subsets, compresses each subset into certain low-dimensional summary statistics and aggregates the summary statistics to approximate the desired computation based on the entire data. Results from statistical aggregation are required to be asymptotically equivalent. Statistical aggregation processes the entire data set part by …

Networking Mechanisms For Delay-Sensitive Applications, Maxim Podlesny

All Theses and Dissertations (ETDs)

The diversity of applications served by the explosively growing Internet is increasing. In particular, applications that are sensitive to end-to-end packet delays become more common and include telephony, video conferencing, and networked games. While the single best-effort service of the current Internet favors throughput-greedy traffic by equipping congested links with large buffers, long queuing at the congested links hurts the delay-sensitive applications. Furthermore, while numerous alternative architectures have been proposed to offer diverse network services, the innovative alternatives failed to gain widespread end-to-end deployment. This dissertation explores different networking mechanisms for supporting low queueing delay required by delay-sensitive applications. In …

Design And Evaluation Of Distributed Algorithms For Placement Of Network Services, Todd Sproull

All Theses and Dissertations (ETDs)

Network services play an important role in the Internet today. They serve as data caches for websites, servers for multiplayer games and relay nodes for Voice over IP: VoIP) conversations. While much research has focused on the design of such services, little attention has been focused on their actual placement. This placement can impact the quality of the service, especially if low latency is a requirement. These services can be located on nodes in the network itself, making these nodes supernodes. Typically supernodes are selected in either a proprietary or ad hoc fashion, where a study of this placement is …

Scheduling Policy Design Using Stochastic Dynamic Programming, Robert Glaubius

All Theses and Dissertations (ETDs)

Scheduling policies for open soft real-time systems must be able to balance the competing concerns of meeting their objectives under exceptional conditions while achieving good performance in the average case. Balancing these concerns requires modeling strategies that represent the range of possible task behaviors, and solution techniques that are capable of effectively managing uncertainty in order to discover scheduling policies that are effective across the range of system modes. We develop methods for solving a particular class of task scheduling problems in an open soft real-time setting involving repeating, non-preemptable tasks that contend for a single shared resource. We enforce …

Structural Rna Homology Search And Alignment Using Covariance Models, Eric Nawrocki

All Theses and Dissertations (ETDs)

Functional RNA elements do not encode proteins, but rather function directly as RNAs. Many different types of RNAs play important roles in a wide range of cellular processes, including protein synthesis, gene regulation, protein transport, splicing, and more. Because important sequence and structural features tend to be evolutionarily conserved, one way to learn about functional RNAs is through comparative sequence analysis - by collecting and aligning examples of homologous RNAs and comparing them. Covariance models: CMs) are powerful computational tools for homology search and alignment that score both the conserved sequence and secondary structure of an RNA family. However, due …

Isolation And Dependency Resolution Of Presentation, Processing And Persistence, Mehrab Monjur

Master's Theses (2009 -)

For business application development it is important to isolate programming efforts of the concerns: Presentation, Processing and Persistence. Development of each of these concerns has an independent thinking process and requires somewhat different programming languages and development tools. In order to isolate the concerns, we provide passages between the concerns and control the flow of execution by following essentially three rules: 1. Presentation and Processing are coroutines, 2. Processing is finished before Presentation can begin to show output, and 3. Persistence is a subsystem of Processing. We explain how these rules come to existence, and what the implications are in …

Comparative Genomics Exploration Tools, Shilpa M. Kulkarni

Master's Theses and Capstones

Comparative Genomics focuses on elucidating the genetic differences between different species or different strains of the same species by the comparative analysis of DNA sequences to identify functional elements and regulatory regions. This thesis describes the design and development of two software tools to support comparative genomics research. These tools were specifically developed to support the analysis and assembly of sequence data produced from innovative new DNA sequencing technology from 454 Life Sciences using the PicoTiterPlate(TM) device. This technology will dramatically affect comparative genomics research. Currently available software tools were developed to handle traditional shotgun sequences averaging 500-1000 base pairs …