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Computer Science and Engineering: Theses, Dissertations, and Student Research

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Full-Text Articles in Computer Engineering

Identifying Horizontal Gene Transfer Using Anomalies In Protein Structures And Sequences, Venkat Ram B. Santosh Feb 2011

Identifying Horizontal Gene Transfer Using Anomalies In Protein Structures And Sequences, Venkat Ram B. Santosh

Computer Science and Engineering: Theses, Dissertations, and Student Research

Genetics has traditionally focused on vertical gene transfer, which is the passing of the genetic material of an organism to its offspring. However, recent studies in genetics increased the awareness that horizontal gene transfer, which is the passing of the genetic material of an organism to another organism that is not its offspring, is also a significant phenomenon. Horizontal gene transfer is thought to play a major role in the natural evolution of bacteria, such as, when several different types of bacteria all suddenly develop the same drug resistance genes. Artificial horizontal gene transfer occurs in genetic engineering.

This thesis ...


Testing Embedded System Applications, Tingting Yu Dec 2010

Testing Embedded System Applications, Tingting Yu

Computer Science and Engineering: Theses, Dissertations, and Student Research

Embedded systems are becoming increasingly ubiquitous, controlling a wide variety of popular and safety-critical devices. Testing is the most commonly used method for validating software systems, and effective testing techniques could be helpful for improving the dependability of these systems. However, there are challenges involved in developing such techniques. Embedded systems consist of layers of software – application layers utilize services provided by underlying system service and hardware support layers. A typical embedded application consists of multiple user tasks. Interactions between application layers and lower layers, and interactions between the various user tasks that are initiated by the application layer, can ...


Experimental Evaluation Of Transmission Link Characteristics In Body Area Networks, Apoorva Kiran Pandya Nov 2010

Experimental Evaluation Of Transmission Link Characteristics In Body Area Networks, Apoorva Kiran Pandya

Computer Science and Engineering: Theses, Dissertations, and Student Research

Recent advances in digital electronics, embedded systems, and wireless communications have led the way to a new class of distributed Wireless Sensor Networks (WSNs). A Body Area Network (BAN) is a WSN consisting of miniaturized, low-power, autonomous, wireless biosensors, which are seamlessly placed or implanted in the human body to provide an adaptable and smart health care system. The possible applications of BAN are in health care services and medicine, assisting persons with disabilities, and entertainment and sports. The nodes in a BAN generally use IEEE 802.15.4 radios which have low- power consumption and are relatively immune to ...


Simsight: A Virtual Machine Based Dynamic Call Graph Generator, Xueling Chen Aug 2010

Simsight: A Virtual Machine Based Dynamic Call Graph Generator, Xueling Chen

Computer Science and Engineering: Theses, Dissertations, and Student Research

One problem with using component-based software development approach is that once software modules are reused over generations of products, they form legacy structures that can be challenging to understand, making validating these systems difficult. Therefore, tools and methodologies that enable engineers to see interactions of these software modules will enhance their ability to make these software systems more dependable. To address this need, we propose SimSight, a framework to capture dynamic call graphs in Simics, a widely adopted commercial full-system simulator. Simics is a software system that simulates complete computer systems. Thus, it performs nearly identical tasks to a real ...


Jvm-Based Techniques For Improving Java Observability, Peng Du Aug 2010

Jvm-Based Techniques For Improving Java Observability, Peng Du

Computer Science and Engineering: Theses, Dissertations, and Student Research

Observability measures the support of computer systems to accurately capture, analyze, and present (collectively observe) the internal information about the systems. Observability frameworks play important roles for program understanding, troubleshooting, performance diagnosis, and optimizations. However, traditional solutions are either expensive or coarse-grained, consequently compromising their utility in accommodating today’s increasingly complex software systems. New solutions are emerging for VM-based languages due to the full control language VMs have over program executions. Existing such solutions, nonetheless, still lack flexibility, have high overhead, or provide limited context information for developing powerful dynamic analyses. In this thesis, we present a VM-based infrastructure ...


A Framework For Automatically Repairing Gui Test Suites, Si Huang Aug 2010

A Framework For Automatically Repairing Gui Test Suites, Si Huang

Computer Science and Engineering: Theses, Dissertations, and Student Research

Testing is an effective means for assuring the quality of software. In programs with Graphical User Interfaces (GUIs), event sequences serve as test cases for executing system tests. To aid in the test generation process, researchers have developed methods that automatically derive graph models from GUIs, which can then be traversed to create sequences for testing. Recent advances using these graph models incorporate combinatorial interaction testing sampling techniques to generate longer GUI test cases, which exercise more event interactions and have been shown to improve fault detection. However, because the models extracted are only approximations of the actual event interactions ...


Managing Large Data Sets Using Support Vector Machines, Ranjini Srinivas Aug 2010

Managing Large Data Sets Using Support Vector Machines, Ranjini Srinivas

Computer Science and Engineering: Theses, Dissertations, and Student Research

Hundreds of Terabytes of CMS (Compact Muon Solenoid) data are being accumulated for storage day by day at the University of Nebraska-Lincoln, which is one of the eight US CMS Tier-2 sites. Managing this data includes retaining useful CMS data sets and clearing storage space for newly arriving data by deleting less useful data sets. This is an important task that is currently being done manually and it requires a large amount of time. The overall objective of this study was to develop a methodology to help identify the data sets to be deleted when there is a requirement for ...


Designing Software Product Lines For Testability, Isis Cabral Jul 2010

Designing Software Product Lines For Testability, Isis Cabral

Computer Science and Engineering: Theses, Dissertations, and Student Research

Software product line (SPL) engineering offers several advantages in the development of families of software products such as reduced costs, high quality and a short time to market. A software product line is a set of software intensive systems, each of which shares a common core set of functionalities, but also differs from the other products through customization tailored to fit the needs of individual groups of customers. The differences between products within the family are well-understood and organized into a feature model that represents the variability of the SPL. Products can then be built by generating and composing features ...


Analysis And Transformation Of Pipe-Like Web Mashups For End User Programmers, Kathryn T. Stolee Jun 2010

Analysis And Transformation Of Pipe-Like Web Mashups For End User Programmers, Kathryn T. Stolee

Computer Science and Engineering: Theses, Dissertations, and Student Research

Mashups are becoming increasingly popular as end users are able to easily access, manipulate, and compose data from several web sources. To support end users, communities are forming around mashup development environments that facilitate sharing code and knowledge. We have observed, however, that end user mashups tend to suffer from several deficiencies, such as inoperable components or references to invalid data sources, and that those deficiencies are often propagated through the rampant reuse in these end user communities.

In this work, we identify and specify ten code smells indicative of deficiencies we observed in a sample of 8,051 pipe-like ...


Channel Characterization For Wireless Underground Sensor Networks, Agnelo R. Silva Apr 2010

Channel Characterization For Wireless Underground Sensor Networks, Agnelo R. Silva

Computer Science and Engineering: Theses, Dissertations, and Student Research

Wireless Underground Sensor Networks (WUSNs) are natural extensions of the established Wireless Sensor Network (WSN) phenomenon and consist of sensors buried underground which communicate through soil. WUSNs have the potential to impact a wide variety of applications including precision agriculture, environmental monitoring, border patrol, and infrastructure monitoring. The main difference between WUSNs and traditional wireless networks is the communication medium. However, a comprehensive wireless underground channel model for WUSNs has not been developed so far. In this thesis, the Soil Subsurface Wireless Communication (SSWC) channel model is developed based on an extensive empirical study in a large agriculture field. The ...


Service-Differentiated And Reliable Communication In Event-Based Wireless Sensor Networks, Yuyan Xue Mar 2010

Service-Differentiated And Reliable Communication In Event-Based Wireless Sensor Networks, Yuyan Xue

Computer Science and Engineering: Theses, Dissertations, and Student Research

Wireless Sensor Networks (WSNs) consist of low-power embedded devices with integrated sensing, computing and wireless communication capabilities. These devices, called sensor nodes or motes, are often battery-powered and deployed in a distributed manner to provide observations on the physical world. Reliably and promptly collecting the sensing data to convey the features of a surveillance area, especially the events of interest, to the sink is one of the most critical requirements of WSN design. However, dynamic wireless channel conditions and the constrained energy resources make it a challenging task to provide the end-to-end performance guarantees in multi-hop WSNs.

The objective of ...


Biological Sequence Simulation For Testing Complex Evolutionary Hypotheses: Indel-Seq-Gen Version 2.0, Cory L. Strope Dec 2009

Biological Sequence Simulation For Testing Complex Evolutionary Hypotheses: Indel-Seq-Gen Version 2.0, Cory L. Strope

Computer Science and Engineering: Theses, Dissertations, and Student Research

Reconstructing the evolutionary history of biological sequences will provide a better understanding of mechanisms of sequence divergence and functional evolution. Long-term sequence evolution includes not only substitutions of residues but also more dynamic changes such as insertion, deletion, and long-range rearrangements. Such dynamic changes make reconstructing sequence evolution history difficult and affect the accuracy of molecular evolutionary methods, such as multiple sequence alignments (MSAs) and phylogenetic methods. In order to test the accuracy of these methods, benchmark datasets are required. However, currently available benchmark datasets have limitations in their sizes and evolutionary histories of the included sequences are unknown. These ...


Classification, Clustering And Data-Mining Of Biological Data, Thomas Triplet Nov 2009

Classification, Clustering And Data-Mining Of Biological Data, Thomas Triplet

Computer Science and Engineering: Theses, Dissertations, and Student Research

The proliferation of biological databases and the easy access enabled by the Internet is having a beneficial impact on biological sciences and transforming the way research is conducted. There are currently over 1100 molecular biology databases dispersed throughout the Internet. However, very few of them integrate data from multiple sources. To assist in the functional and evolutionary analysis of the abundant number of novel proteins, we introduce the PROFESS (PROtein Function, Evolution, Structure and Sequence) database that integrates data from various biological sources. PROFESS is freely available athttp://cse.unl.edu/~profess/. Our database is designed to be versatile and ...


Deployed Software Analysis, Madeline M. Diep May 2009

Deployed Software Analysis, Madeline M. Diep

Computer Science and Engineering: Theses, Dissertations, and Student Research

Profiling can offer a valuable characterization of software behavior. The richer the characterization is, the more effective the client analyses are in supporting quality assurance activities. For today's complex software, however, obtaining a rich characterization with the input provided by in-house test suites is becoming more difficult and expensive. Extending the profiling activity to deployed environments can mitigate this shortcoming by exposing more program behavior reflecting real software usage. To make profiling of deployed software plausible, however, we need to take into consideration that there are fundamental differences between the development and the deployed environments. Deployed environments allow for ...


Adaptive Interpolation Algorithms For Temporal-Oriented Datasets, Jun Gao Jun 2006

Adaptive Interpolation Algorithms For Temporal-Oriented Datasets, Jun Gao

Computer Science and Engineering: Theses, Dissertations, and Student Research

Spatiotemporal datasets can be classified into two categories: temporal-oriented and spatial-oriented datasets depending on whether missing spatiotemporal values are closer to the values of its temporal or spatial neighbors. We present an adaptive spatiotemporal interpolation model that can estimate the missing values in both categories of spatiotemporal datasets. The key parameters of the adaptive spatiotemporal interpolation model can be adjusted based on experience.


Experimental Evaluation Of Constraint Automata Solutions To The Genome Map Assembly Problem, Viswanathan Ramanathan Dec 2003

Experimental Evaluation Of Constraint Automata Solutions To The Genome Map Assembly Problem, Viswanathan Ramanathan

Computer Science and Engineering: Theses, Dissertations, and Student Research

DNA sequences are really huge having a length of around 3-4 million base pairs. Hence, each DNA sequence has to be cut down into small fragments using restriction enzymes. Once analyzed, these fragments have to be arranged or assembled into a single set of sequences called a genome map, to obtain the original DNA sequence. This problem is called the Genome Map Assembly Problem. A Constraint-Automata Solution was proposed for this purpose [11]. This thesis improves and implements the Constraint-Automata Solution to find all the possible solutions. The Modified Constraint-Automata Solution was implemented in Perl and executed on parts of ...


Constraint Datalog In Trust Management, Scot Anderson Dec 2003

Constraint Datalog In Trust Management, Scot Anderson

Computer Science and Engineering: Theses, Dissertations, and Student Research

Constraint Datalog holds an increasing role in Trust Management. We discuss several Trust Management systems and give a description of the environment and requirements for Trust Management. Constraint Datalog using addition constraints and approximation theory provides an expressive semantic with which to describe security policies for credentials, delegations and authorizations. Approximation theory allows halting in Constraint Datalog over addition constraints. We use the decision problem of Diophantine equations to show that Constraint Datalog over addition constraints is complete. Combining these two concepts provides an approximately complete, safe language. The problem of constant additions to closed languages provides reasons for using ...


User Interface Improvement For Mlpq System, Shasha Wu Apr 2003

User Interface Improvement For Mlpq System, Shasha Wu

Computer Science and Engineering: Theses, Dissertations, and Student Research

This thesis describes the experience of migrating the MLPQ constraint database system, a complex standalone Multiple Document Interface (MDI) application, to a server-based remote accessible application. Centralized, standalone MDI application is a common style for personal software products in Windows. For a database management system, server-based, thin-client computing is a more popular infrastructure. Migrating an existing standalone constraint database application to be a web accessible constraint database server is the main goal of this thesis. This migration process provides a method for the constraint database system to collaborate with other specific applications. We rebuild the desktop MLPQ constraint database system ...


Implementation Of A Database System With Boolean Algebra Constraints, András Salamon May 1998

Implementation Of A Database System With Boolean Algebra Constraints, András Salamon

Computer Science and Engineering: Theses, Dissertations, and Student Research

This thesis describes an implementation of a constraint database system with constraints over a Boolean Algebra of sets. The system allows within the input database as well as the queries equality, subset-equality and monotone inequality constraints between Boolean Algebra terms built up using the operators of union, intersection and complement. Hence the new system extends the earlier DISCO system, which only allowed equality and subset-equality constraints between Boolean algebra variables and constants. The new system allows Datalog with Boolean Algebra constraints as the query lan- guage. The implementation includes an extension of Naive and Semi-Naive evaluation methods for Datalog programs ...


Mlpq: A Linear Constraint Database System With Aggregate Operators, Yiming Li Apr 1997

Mlpq: A Linear Constraint Database System With Aggregate Operators, Yiming Li

Computer Science and Engineering: Theses, Dissertations, and Student Research

In this project report, I will discuss a Multiple Linear Programming Query (MLPQ) system and the theoretical background of this system.The MPLQ system is developed to solve some realistic problems involving both linear programming (UP) techniques and linear constraint databases (LCDBs) theory. The MLPQ system is aimed at providing a mechanism of bridging these two important areas. system basically consists of three parts which are a linear constraint database, an LP solver, and an interface between the LCDB and the LP solver. The LCDB of the MLPQ system contains multiple linear programming problems. The LP solver used in the ...


A Sign-To-Speech Translation System, Koka Veera Raghava Rao Jan 1993

A Sign-To-Speech Translation System, Koka Veera Raghava Rao

Computer Science and Engineering: Theses, Dissertations, and Student Research

This thesis describes sign-to-speech translation using neural networks. Sign language translation is an interesting but difficult problem for which neural network techniques seem promising because of their ability to adjust to the user's hand movements, which is not possible to do by most other techniques. However, even using neural networks and artificial sign languages, the translation is hard, and the best-known system, that of Fels & Hinton (1993), is capable of translating only 66 root words and 203 words including their conjugations. This research improves their results to 790 root signs and 2718 words including their conjugations while preserving a ...