Physical Sciences and Mathematics Commons^™

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

Department of Computer Science and Engineering: Dissertations, Theses, 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 …

Structured P2p Technologies For Distributed Command And Control, Daniel R. Karrels, Gilbert L. Peterson, Barry E. Mullins

Faculty Publications

The utility of Peer-to-Peer (P2P) systems extends far beyond traditional file sharing. This paper provides an overview of how P2P systems are capable of providing robust command and control for Distributed Multi-Agent Systems (DMASs). Specifically, this article presents the evolution of P2P architectures to date by discussing supporting technologies and applicability of each generation of P2P systems. It provides a detailed survey of fundamental design approaches found in modern large-scale P2P systems highlighting design considerations for building and deploying scalable P2P applications. The survey includes unstructured P2P systems, content retrieval systems, communications structured P2P systems, flat structured P2P systems and …

A Neural Network Approach To Border Gateway Protocol Peer Failure Detection And Prediction, Cory B. White

Master's Theses

The size and speed of computer networks continue to expand at a rapid pace, as do the corresponding errors, failures, and faults inherent within such extensive networks. This thesis introduces a novel approach to interface Border Gateway Protocol (BGP) computer networks with neural networks to learn the precursor connectivity patterns that emerge prior to a node failure. Details of the design and construction of a framework that utilizes neural networks to learn and monitor BGP connection states as a means of detecting and predicting BGP peer node failure are presented. Moreover, this framework is used to monitor a BGP network …

Coherent Phrase Model For Efficient Image Near-Duplicate Retrieval, Yiqun Hu, Xiangang Cheng, Liang-Tien Chia, Xing Xie, Deepu Rajan, Ah-Hwee Tan

Research Collection School Of Computing and Information Systems

This paper presents an efficient and effective solution for retrieving image near-duplicate (IND) from image database. We introduce the coherent phrase model which incorporates the coherency of local regions to reduce the quantization error of the bag-of-words (BoW) model. In this model, local regions are characterized by visual phrase of multiple descriptors instead of visual word of single descriptor. We propose two types of visual phrase to encode the coherency in feature and spatial domain, respectively. The proposed model reduces the number of false matches by using this coherency and generates sparse representations of images. Compared to other method, the …

A Robust Damage Assessment Model For Corrupted Database Systems, Ge Fu, Hong Zhu, Yingjiu Li

Research Collection School Of Computing and Information Systems

An intrusion tolerant database uses damage assessment techniques to detect damage propagation scales in a corrupted database system. Traditional damage assessment approaches in a intrusion tolerant database system can only locate damages which are caused by reading corrupted data. In fact, there are many other damage spreading patterns that have not been considered in traditional damage assessment model. In this paper, we systematically analyze inter-transaction dependency relationships that have been neglected in the previous research and propose four different dependency relationships between transactions which may cause damage propagation. We extend existing damage assessment model based on the four novel dependency …

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

Department of Computer Science and Engineering: Dissertations, Theses, 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 expandable and will not …

Real-World Performance Of Current Proactive Multi-Hop Mesh Protocols, M. Abolhasan, Brett Hagelstein, Jerry Chun-Ping Wang

Faculty of Informatics - Papers (Archive)

The proliferation of mesh or ad hoc network protocols has lead to a push for protocol standardisation. While there are a number of both open-source and proprietary mesh routing protocols being developed, there is only a small amount of literature available that shows relative strengths and weaknesses of different protocols. This paper investigates the performance of a number of available routing protocols using a real-world testbed. Three routing protocols - Optimised Link State Routing (OLSR), Better Approach To Mobile Ad hoc Network (B.A.T.M.A.N.) and BABEL - were chosen for this study. Our investigations focus on the multi-hopping performance and the …

Ceg 210: Pc Networking I, Chris P. Fickert

Computer Science & Engineering Syllabi

Introduction to networking technologies including infrastructure and architectures, standards, protocols and directory services, administration, security and management. Integrated lecture and lab.

Cs 141: Computer Programming - I, Michael Ondrasek

Computer Science & Engineering Syllabi

This course provides a general introduction to the fundamentals of computer programming. Examples from and applications to a broad range of problems are given. No prior knowledge of programming is assumed. The concepts covered will be applied to the Java programming language. Students must register for both lecture and one laboratory section. 4 credit hours. Prerequisite: MTH 127 (College Algebra) or equivalent.

Cs 205-08: Introduction To Computers And Office Productivity Software, Kim Gros

Computer Science & Engineering Syllabi

Focus on learning MS Office software applications including word processing (intermediate), spreadsheets, database and presentation graphics using a case study approach where critical thinking and problem solving skills are required. Computer concepts are integrated throughout the course to provide an understanding of the basics of computing, the latest technological advances and how they are used in industry. Ethics and issues encountered in business are discussed to challenge students on societal impact of technology.

Cs 208: Computer Programming For Business I, David M. Hutchison

Computer Science & Engineering Syllabi

CS 208 is the first In a sequence of two programming classes required for MIS majors. This course will introduce students to the basic concepts of programming. Examples are from business applications and display graphics and emphasis is on problem solving with the computer as a tool.

Cs 209: Computer Programming For Business Ii, Dennis Kellermeier

Computer Science & Engineering Syllabi

CS 209 is the second of a two quarter sequence in programming for business students. It is required for Management Information Science majors. The courses are designed to help students achieve a high degree of facility in intermediate level programming.

Cs 240: Computer Programming I, Sarah Gothard

Computer Science & Engineering Syllabi

Basic concepts of programming and programming languages are introduced.
Emphasis is on structured programming and stepwise refinement.

Cs 214: Visual Basic Programming, Vanessa Starkey

Computer Science & Engineering Syllabi

This course will cover the fundamentals of object-oriented computer
programming including design, structure, debugging, and testing. Visual Basic 2008 will be used for
developing programs.

Cs 242: Computer Programming Iii, Mateen M. Rizki

Computer Science & Engineering Syllabi

No abstract provided.

Cs 302-01: Introduction To Oracle Sql Databases, Karen Meyer

Computer Science & Engineering Syllabi

No abstract provided.

Cs 241: Computer Science Ii, Travis E. Doom

Computer Science & Engineering Syllabi

A continuation of CS240. The emphasis is on data abstraction and software engineering. Prerequisite: CS240.

Cs 340: Programming Language Workshop In Python, Krishnaprasad Thirunarayan

Computer Science & Engineering Syllabi

This course is designed as a self-study in Python. You are expected to learn the language and solve a set of programming problems assigned to you from Dietel et al using Python available from http://www.python.org. There are no exams. We officially meet only once in the quarter. However, I will be available in the posted office hours for clarifications and discussions about the programming problems.

Cs 405/605-02: Introduction To Database Management Systems, Keke Chen

Computer Science & Engineering Syllabi

This course will cover the following topics: (1) Logical and physical aspects of database management systems (2) Data models including entity-relationship (ER) and relational models (3) Physical implementation (data organization and indexing) methods. (4) Query languages including SQL, relational algebra, and relational calculus. Students will gain experience in creating and manipulating a database, and gain knowledge on professional and ethical responsibility and on the importance of privacy/security of data.

Cs 410/610: Theoretical Foundations Of Computing, Thomas Sudkamp

Computer Science & Engineering Syllabi

This course is an introduction to one of the fundamental topics in the theory of computer science: computability theory. Computability theory is concerned with determining whether there is an algorithmic solution to a problem. The study of computability uses the Turing machine as the basic computational model. A Turing machine is a random access, read-write, finite state automaton. Although the Turing machine provides a simple computational framework, the Church-Turing thesis asserts that any problem that can be solved in any algorithmic manner can be solved by a Turing machine.

Cs 409/609: Principles Of Artificial Intelligence, Shaojun Wang

Computer Science & Engineering Syllabi

No abstract provided.

Cs 475/675: Web Information Systems, Amit P. Sheth

Computer Science & Engineering Syllabi

This course covers advanced topics in managing W eh-based resources, with a focus on building applications involving heterogeneous data. It will expose students to the following concept, topics, architectures, techniques, and technologies:

• data, metadata, information, knowledge, and ontologies
• unstructured, semi-structured, structured, multimodal, multimedia, and sensor data syntax,
structural/representational, and semantic aspects of data
• architectures: federated databases, mediator, information brokering
• integration and analysis of Web-based information
• automatic information/metadata extraction (entity identification/recognition, disambiguation)
• Web search engines, social networks, Web 2.0
• Semantic Web and Web 3.0
• relevant Web standards and technologies
• real-world examples that …

Cs 466/666: Introduction To Formal Languages, Guozhu Dong

Computer Science & Engineering Syllabi

CS 466/666 is an introduction to formal language and automata theory. In this course we will examine methods for defining syntax of languages and recognizing patterns: the syntax of languages can be defined using grammars and patterns accepted by finite state machines. Along with presenting the fundamentals of these two topics, the course will develop and investigate the relationships between language definition and pattern recognition. The text will be the third edition of Languages and Machines: An Introduction to the Theory of Computer Science, by Thomas Sudkamp.

Cs 480/680: Comparative Languages, Krishnaprasad Thirunarayan

Computer Science & Engineering Syllabi

This course will introduce fundamental concepts and paradigms underlying the design of modem programming languages. For concreteness, we study the details of an object-oriented language (e.g. Java), and a functional language (e.g., Scheme) . The overall goal is to enable comparison and evaluation of existing languages. The programming assignments will be coded in Java 5 and in scheme.

Cs 499/699: Special Topics In Information Security, Meilin Liu

Computer Science & Engineering Syllabi

This course gives a comprehensive study of security vulnerabilities in information systems and the basic techniques for developing secure applications and practicing safe computing. Topics include: Conventional encryption; Data Encryption Standard; Advanced Encryption Standard; Hashing functions and data integrity; Basic Number Theory; Public-key encryption (RSA); Digital signature; Security standards and applications; Access Control; Management and analysis of security. After taking this course, students will have the knowledge of several well-known security standards and their applications; and the students should be able to increase system security and develop secure applications.

Cs 705: Introduction To Data Mining, Guozhu Dong

Computer Science & Engineering Syllabi

Data mining is concerned with the extraction of novel and useful knowledge from large amounts of data. This course introduces and studies the fundamental concepts, issues, tasks and techniques of data mining. Topics include data preparation and feature selection, association rules, classification, clustering, evaluation and validation, scalability, spatial and sequence mining, privacy, and data mining applications. 3 hours lecture, 2 hours lab.

Cs 784: Programming Languages, Krishnaprasad Thirunarayan

Computer Science & Engineering Syllabi

This course introduces concepts related to the specification and design of high-level programming languages. It discusses different programming paradigms, algebraic specification and implementation of data types, and develops interpreters for specifying operationally the various programming language features/constructs. It also introduces attribute grammar formalism and axiomatic semantics briefly. The programming assignments will be coded in Scheme.

Cs/Mth 316/516: Numerical Methods For Digital Computers, Ronald F. Taylor

Computer Science & Engineering Syllabi

Introduction to numerical methods used in the sciences and engineering. Included will be methods for interpolation, data smoothing, integration, differentiation, and solution of systems of linear and nonlinear equations. Discussion of sources of error in numerical methods. Applications to science, engineering and applied mathematics are an
integral part of the course. Special topics presented as schedule permits. Four hours lecture.

Cs/Bio 471/671: Algorithms For Bioinformatics, Michael L. Raymer

Computer Science & Engineering Syllabi

Theory-oriented approach to the application of contemporary algorithms to bioinformatics. Graph theory, complexity theory, dynamic programming and optimization techniques are introduced in the context of application toward solving specific computational problems in molecular genetics. 4 credit hours.

Cs 499/699: Cloud Computing, Keke Chen

Computer Science & Engineering Syllabi

In this course, we will explore a few aspects of cloud computing: distributed data crunching with MapReduce, cloud and datacenter filesystems, virtualization, security&privacy, Amazon Web Services, and interactive web-based applications. Students are expected to finish a few mini projects, read some papers, and take the final exam. Participation in the class discussion is strongly encouraged. Guest speakers might be invited for some particular topics. (3 Hours Lecture+ 1 Hour lab).