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Full-Text Articles in Computer Engineering

Classification For Mass Spectra And Comprehensive Two-Dimensional Chromatograms, Xue Tian Aug 2011

Classification For Mass Spectra And Comprehensive Two-Dimensional Chromatograms, Xue Tian

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

Mass spectra contain characteristic information regarding the molecular structure and properties of compounds. The mass spectra of compounds from the same chemically related group are similar. Classification is one of the fundamental methodologies for analyzing mass spectral data. The primary goals of classification are to automatically group compounds based on their mass spectra, to find correlation between the properties of compounds and their mass spectra, and to provide a positive identification of unknown compounds.

This dissertation presents a new algorithm for the classification of mass spectra, the most similar neighbor with a probability-based spectrum similarity measure (MSN-PSSM). Experimental results demonstrate ...


Molecular Dynamics Simulation Based On Hadoop Mapreduce, Chen He Jul 2011

Molecular Dynamics Simulation Based On Hadoop Mapreduce, Chen He

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

Molecular Dynamics (MD) simulation is a computationally intensive application used in multiple fields. It can exploit a distributed environment due to inherent computational parallelism. However, most of the existing implementations focus on performance enhancement. They may not provide fault-tolerance for every time-step.

MapReduce is a framework first proposed by Google for processing huge amounts of data in a distributed environment. The simplicity of the programming model and fault- tolerance for node failure during run-time make it very popular not only for commercial applications but also in scientific computing.

In this thesis, we develop a novel communication-free and each time-step fault- ...


Real-Time Divisible Load Scheduling For Cluster Computing, Anwar Mamat Jul 2011

Real-Time Divisible Load Scheduling For Cluster Computing, Anwar Mamat

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

Cluster computing has become an important paradigm for solving large-scale problems. However, as the size of a cluster increases, so does the complexity of resource management and maintenance. Therefore, automated performance control and re- source management are expected to play critical roles in sustaining the evolution of cluster computing. The current cluster scheduling practice is similar in sophistication to early supercomputer batch scheduling algorithms, and no consideration is given to desired quality-of-service (QoS) attributes. To fully avail the power of computational clusters, new scheduling algorithms that provides high performance, QoS assurance, fault-tolerance, energy savings and streamlined management of the cluster ...


A Reservation-Based Smart Parking System, Hongwei Wang Jul 2011

A Reservation-Based Smart Parking System, Hongwei Wang

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

In metropolitan areas, parking management influences drivers search time and cost for parking spaces, parking revenue, and traffic congestion. The wide deployment of wireless parking meters with sensing and communications capabilities allows the parking authority to monitor the state of each parking space in real time and optimize the parking management.

In this thesis, we study state-of-the-art parking policies in smart parking systems, and show that the smart parking system needs to be "smarter". Our design goals of the smart parking systems include: (1) simplify the operations of parking systems, (2) improve drivers' satisfaction, (3) increase parking revenue, and (4 ...


Campus Grids: A Framework To Facilitate Resource Sharing, Derek J. Weitzel May 2011

Campus Grids: A Framework To Facilitate Resource Sharing, Derek J. Weitzel

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

It is common at research institutions to maintain multiple clusters. These might fulfill different needs and policies, or represent different owners or generations of hard- ware. Many of these clusters are under utilized while researchers at other departments may require these resources. This may be solved by linking clusters with grid mid- dleware. This thesis describes a distributed high throughput computing framework to link clusters without changing security or execution environments. The framework initially keeps jobs local to the submitter, overflowing if necessary to the campus, and regional grid. The framework is implemented spanning two campuses at the Holland Computing ...


Ontology For Psychophysiological Dysregulation Of Anger/Aggression, Swathi Vasanthapuram May 2011

Ontology For Psychophysiological Dysregulation Of Anger/Aggression, Swathi Vasanthapuram

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

The advancement of Information Technology in the last four decades led to the use of computers in medicine. A new area called Medical Informatics has emerged. This area comprises the application of IT to healthcare with the aim of creating tools that help healthcare personnel diagnose and treat patients more accurately and efficiently. IT not only provides tools for storing, integrating, and updating patient information base but also for processing information efficiently. One of such tools is a Clinical Decision Support System. Ontologies are an integral part of clinical decision support systems because they help formalize and integrate domain knowledge ...


Protein Structure – Based Method For Identification Of Horizontal Gene Transfer In Bacteria, Swetha Billa May 2011

Protein Structure – Based Method For Identification Of Horizontal Gene Transfer In Bacteria, Swetha Billa

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

Horizontal Gene Transfer is defined as the movement of genetic material from one strain of species to another. Bacteria, being an asexual organism were always believed to transfer genes vertically. But recent studies provide evidence that shows bacteria can also transfer genes horizontally.

HGT plays a major role in evolution and medicine. It is the major contributor in bacterial evolution, enabling species to acquire genes to adapt to the new environments. Bacteria are also believed to develop drug resistance to antibiotics through the phenomenon of HGT. Therefore further study of HGT and its implications is necessary to understand the effects ...


Multi-Channel Peer-To-Peer Streaming Systems As Resource Allocation Problems, Miao Wang Apr 2011

Multi-Channel Peer-To-Peer Streaming Systems As Resource Allocation Problems, Miao Wang

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

In the past few years, the Internet has witnessed the success of Peer-to-Peer (P2P) streaming technology, which has attracted millions of users. More recently, commercial P2P streaming systems have begun to support multiple channels and a user in such systems is allowed to watch more than one channel at a time. We refer to such systems as multi-channel P2P streaming systems. In this dissertation, we focus on designing multi-channel P2P streaming systems with the goal of providing optimal streaming quality for all channels, termed as system-wide optimal streaming quality. Specifically, we design the systems from the perspective of how to ...


Offline Optimization Of Advance Reservation Of Bandwidth Over Dynamic Circuit Networks, Pragatheeswaran Angu Apr 2011

Offline Optimization Of Advance Reservation Of Bandwidth Over Dynamic Circuit Networks, Pragatheeswaran Angu

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

E-science projects require very high-speed and reliable networks to transfer data across various destinations in the world. Dynamic Circuit Network (DCN) is a networking service to make advance reservation of bandwidth between a source and a destination in a network. In this thesis we solve the problem of advance reservation of bandwidth in next-generation wavelength-division multiplexing (WDM) networks using a simulation based approach.
We implement a greedy algorithm and a genetic algorithm in parallel, in separate threads. The request for advance reservation is processed by both but the user gets the response only from the greedy algorithm. The genetic algorithm ...


Polygonal Spatial Clustering, Deepti Joshi Apr 2011

Polygonal Spatial Clustering, Deepti Joshi

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

Clustering, the process of grouping together similar objects, is a fundamental task in data mining to help perform knowledge discovery in large datasets. With the growing number of sensor networks, geospatial satellites, global positioning devices, and human networks tremendous amounts of spatio-temporal data that measure the state of the planet Earth are being collected every day. This large amount of spatio-temporal data has increased the need for efficient spatial data mining techniques. Furthermore, most of the anthropogenic objects in space are represented using polygons, for example – counties, census tracts, and watersheds. Therefore, it is important to develop data mining techniques ...


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.


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 ...


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 ...