Engineering Commons^™

Hashtables For Real-Time And Embedded Systems, Anand Krishnan

All Computer Science and Engineering Research

Real-time are beginning to appear in advanced, high-level programming languages such as Java. When complemented by a real-time operating system, the Real-Time Specification for Java (RTSJ) offers strong execution constraints for applications developed in Java. While the RTSJ make the basic services of Java such as storage and thread management ready for many real-time applications, the collection objects, and the rest of the application run-time library, cannot be used by RTSJ applications until their run-time properties are examined and modified as necessary to make them suitable for use by real-time applications. In this work, we examine the Hashtable collection facility …

Dynamic Assignment Of Scoped Memory Regions In The Translation Of Java To Real-Time Java, Morgan G. Deters

All Computer Science and Engineering Research

Advances in middleware, operating systems, and popular, general-purpose languages have brought the ideal of reasonably-bound execution time closer to developers who need such assurances for real-time and embedded systems applications. Extensions to the Java libraries and virtual machine have been proposed in a real-time Java standard, which provides for specification of release times, execution costs, and deadlines for a restricted class of threads. To use such features, the programmer is required to use unwieldy code constructs to create region-like areas of storage, associate them with execution scopes, and allocate objects from them. Further, the developer must ensure that they do …

Multiflow Tcp, Udp, Ip, And Atm Traffic Generation Module, Eliot I. Sinclair, John W. Lockwood

All Computer Science and Engineering Research

Networking devices must be capable of processing traffic flows from multiple sources. In order to verify that such devices operates properly, a network testbench can be used to inject traffic into the device. The specification of the traffic flows can be difficult. At the low level, there are header fields, data checksums, and packet length fields that all must be formatted correctly. Further, there can be multiple flows of traffic that will arrive simultaneously. It is desirable to specify traffic at a high level of abstraction. A software program can then be written to parse the specification and generate the …

Integrated Coverage And Connectivity Configuration In Wireless Sensor Networks, Xiaorui Wang, Guoliang Xing, Yuanfang Zhang, Chenyang Lu, Robert Pless, Christopher Gill

All Computer Science and Engineering Research

An effective approach for energy conservation in wireless sensor networks is scheduling sleep intervals for extraneous nodes, while the remaining nodes stay active to provide continuous service. For the sensor network to operate successfully, the active nodes must maintain both sensing coverage and network connectivity. Furthermore, the network must be able to configure itself to any feasible degrees of coverage and connectivity in order to support different applications and environments with diverse requirements. This paper presents the design and analysis of novel protocols that can dynamically configure a network to achieve guaranteed degrees of coverage and connectivity. This work differs …

System-On-Chip Packet Processor For An Experimental Network Services Platform, David Taylor, Alex Chandra, Yuhua Chen, Sarang Dharmapurikar, John Lockwood, Wenjing Tang, Jonathan Turner

All Computer Science and Engineering Research

As the focus of networking research shifts from raw performance to the delivery of advanced network services, there is a growing need for open-platform systems for extensible networking research. The Applied Research Laboratory at Washington University in Saint Louis has developed a flexible Network Services Platform (NSP) to meet this need. The NSP provides an extensible platform for prototyping next-generation network services and applications. This paper describes the design of a system-on-chip Packet Processor for the NSP which performs all core packet processing functions including segmentation and reassembly, packet classification, route lookup, and queue management. Targeted to a commercial configurable …

A Thesis On A 3d Input Device For Sketching Characters, Mark A. Schroering

All Computer Science and Engineering Research

The goal of this project is to develop a 3D input device using a stiff piece of paper and a camera. The camera tracks the piece of paper in 3D space. The user orients the paper in 3D space and then draws on the paper using a pen-like device. The camera tracks the movement of the pen on the piece of paper. The location of the pen in 3D space can then be calculated from the orientation of the paper. A drawing application that uses this 3D input device was also developed. The application allows a user to make characters …

A Study In Java Bytecode Engineering With Pcesjava, Martin R. Linenweber

All Computer Science and Engineering Research

This thesis reports on experience with PCESjava, a collection of tools which we have developed for the purpose of aiding programmers. Particular applications optimize and instrument JAVA bytecode programs. Using these tools, we have successfully identified impediments to real-time performance in a popular JAVA collections object. Our approach here is based on automatic instruction to obtain traces that show paths whose execution time is not reasonably bounded. We also report on the application of our tool to reduce program footprint in JAVA programs by rewriting the bytecodes to occupy less space. Our transformations also improves the running time of set …

Parallel Computation Of The Topological Skeleton Of Vector Fields, Thomas Wischgoll, Gerik Scheuermann

Computer Science and Engineering Faculty Publications

Vector fields occur in many of the problems in science and engineering. In combustion processes, for instance, vector fields describe the flow of the gas. This process can be enhanced using vector field visualization techniques. Also, wind tunnel experiments can be analyzed. An example is the design of an air wing. The wing can be optimized to create a smoother flow around it.

To analyze such kind of datasets topological methods that clearly show the whole structure of the vector field in one picture are a very good tool. During the last years, many extensions were proposed for this method. …

User Interface Improvement For Mlpq System, Shasha Wu

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

An Iterative Loop Matching Approach To The Prediction Of Rna Secondary Structures With Pseudoknots, Jianhua Ruan, Weixiong Zhang

All Computer Science and Engineering Research

Motivation: Pseudoknots have generally been excluded from the prediction of RNA secondary structures due to the difficulty in modeling and complexity in computing. Although several dynamic programming algorithms exist for the prediction of pseudoknots using thermodynamic approaches, they are neither reliable nor efficient. On the other hand, comparative methods are more reliable, but are often done in an ad hoc manner and require expert intervention. Maximum weighted matching (Tabaska et. al, Bioinformatics, 14:691-9, 1998), an algorithm for pseudoknot prediction with comparative analysis, suffers from low prediction accuracy in many cases. Here we present an algorithm, iterative loop matching, for predict-ing …

Pc–Based Data Acquisition For A Solid Substrate Cultivation Deep Bed Reactor, Mari S. Chinn, Sue E. Nokes, Richard S. Gates

Biosystems and Agricultural Engineering Faculty Publications

This work describes an instrumentation and data acquisition system designed for a deep bed reactor used to cultivate Trichoderma longibrachiatum on wheat bran. The system allowed on–line measurements of substrate temperature, oxygen concentration within the reactor headspace, relative humidity and temperature of the inlet air, and inlet airflow rates while maintaining aseptic conditions and without disturbing the cultivation process. An error analysis for the instrumentation and data acquisition equipment was completed and provided insight into the reliability of the sensor readings. The collected data provided quantitative information about the reactor system dynamics which can be used to evaluate and apply …

Development Of A Systems Engineering Model Of The Chemical Separations Process: Quarterly Progress Report 11/16/02- 2/15/03, Yitung Chen, Randy Clarksean, Darrell Pepper

Separations Campaign (TRP)

Two activities are proposed in this Phase I task: the development of a systems engineering model and the refinement of the Argonne code AMUSE (Argonne Model for Universal Solvent Extraction). The detailed systems engineering model is the start of an integrated approach to the analysis of the materials separations associated with the TRP Program. A second portion of the project is to streamline and improve an integral part of the overall systems model, which is the software package AMUSE. AMUSE analyzes the UREX process and other related solvent extraction processes and defines many of the process streams that are integral …

Towards A Performance Model For Special Purpose Orb Middleware, Venkita Subramonian, Guoliang Xing, Christopher Gill, Ron Cytron

All Computer Science and Engineering Research

General purpose middleware has been shown effective in meeting diverse functional requirements for a wide range of distributed systems. Advanced middleware projects have also supported single quality-of-service dimensions such as real-time, fault tolerance, or small memory foot-print. However, there is limited experience supporting multiple quality-of-service dimensions in middleware to meet the needs of special purpose applications. Even though general purpose middleware can cover an entire spectrum of functionality by supporting the union of all features required by each application, this approach breaks down for distributed real-time and embedded sys-tems. For example, the breadth of features supported may interfere with small …

Twinscan: A Software Package For Homology-Based Gene Prediction, Paul Flicek

All Computer Science and Engineering Research

A complete mapping from genome to proteome would constitute a foundation for genome-based biology and provide targets for pharmaceutical and therapeutic intervention. This is one reason gene structure prediction has been a major subfield of computational biology for over 20 years. Many of the widely used gene prediction systems were developed in the 1990s and are unable to take advantage of the revolution in comparative genomics brought on by the sequencing of the entire genomes of an increasing numbers of vertebrates. Twinscan is a new system for high-throughput gene-structure prediction that exploits the patterns of conservation observed in alignments between …

Personality Types In Software Engineering, Luiz Fernando Capretz

Electrical and Computer Engineering Publications

No abstract provided.

Storage Allocation In Bounded Time, Sharath Reddy Cholleti

All Computer Science and Engineering Research

The correctness of a real-time system is very much dependent on the time at which a specific task is completed. Hence, satisfying a storage allocation request within bounded time is important. Fragmentation of the heap after repeated allocations and deallocations is a major issue for real-time systems, as most allocators depend on garbage collection for defragmentation of the heap, which might not finish in time to honor deadlines. We present the storage requirement for a defragmentation-free binary-buddy allocator. We also study a localized defragmentation algorithm to satisfy a single allocation request, within bounded time, instead of requiring defragmentation of the …

Development Of A Systems Engineering Model Of The Chemical Separations Process, Lijian Sun, Haritha Royyuru, Yitung Chen, Randy Clarksean, Darrell Pepper, George Vandegrift, James Laidler

Separations Campaign (TRP)

Project Overview:

• Two Components

– Refine AMUSE Code

– Develop Systems Engineering Model

• Research Objectives

– Develop a framework and environment for a systems engineering analysis of the chemical separations system for the AAA program.

– Establish a baseline systems engineering model from which modifications and improvements can be made.

– Refine the existing AMUSE program that gives a detailed examination of the UREX process, a critical component of the overall separation scheme.

The Design And Performance Of Special Purpose Middleware: A Sensor Networks Case Study, Venkita Subramonian, Guoliang Xing, Christopher Gill, Ron Cytron

All Computer Science and Engineering Research

General purpose middleware has been shown to be effective in meeting diverse functional requirements for a wide range of distributed systems. Advanced middleware projects have also supported a single quality-of-service dimension such as real-time, fault tolerance, or small memory footprint. However, there is limited experience supporting multiple quality-of-service dimensions in mid-dleware to meet the needs of special purpose applications. Even though general purpose middleware can cover an entire spectrum of applications by supporting the union of all features required by each application, this approach breaks down for distributed real-time and embedded systems. In particular, features from one dimension such as …

Searching Sequence Databases, Dan E. Krane, Michael L. Raymer

Computer Science and Engineering Faculty Publications

Presentation prepared for BIO/CS 471: Algorithms for Bioinformatics. The lecture comprises material from the text Fundamental Concepts of Bioinformatics.

A Gentle Introduction To (Or Review Of) Fundamentals Of Chemistry And Organic Chemistry, Dan E. Krane, Michael L. Raymer

Computer Science and Engineering Faculty Publications

Presentation prepared for CS 790: Bioinformatics. The lecture comprises material from the text Fundamental Concepts of Bioinformatics.

Sequence Alignments And Database Searches, Dan E. Krane, Michael L. Raymer

Computer Science and Engineering Faculty Publications

Presentation prepared for Intro to Bioinformatics. The lecture comprises material from the text Fundamental Concepts of Bioinformatics.

Analyzing Algorithms & Asymptotic Notation, Dan E. Krane, Michael L. Raymer

Computer Science and Engineering Faculty Publications

Presentation prepared for BIO/CS 471: Algorithms for Bioinformatics. The lecture comprises material from the text Fundamental Concepts of Bioinformatics.

The Structure And Functions Of Proteins, Dan E. Krane, Michael L. Raymer

Computer Science and Engineering Faculty Publications

Presentation prepared for BIO 271/CS 399: Bioinformatics. The lecture comprises material from the text Fundamental Concepts of Bioinformatics.

Physical Mapping Of Dna, Dan E. Krane, Michael L. Raymer

Computer Science and Engineering Faculty Publications

Presentation prepared for BIO/CS 471: Algorithms for Bioinformatics. The lecture comprises material from the text Fundamental Concepts of Bioinformatics.

Protein Alignment Scoring - Pam And Blosum, Dan E. Krane, Michael L. Raymer

Computer Science and Engineering Faculty Publications

Presentation prepared for Intro to Bioinformatics. The lecture comprises material from the text Fundamental Concepts of Bioinformatics.

Fragment Assembly Of Dna, Dan E. Krane, Michael L. Raymer

Computer Science and Engineering Faculty Publications

Presentation prepared for BIO/CS 471: Algorithms for Bioinformatics. The lecture comprises material from the text Fundamental Concepts of Bioinformatics.

Example Protein Folds, Dan E. Krane, Michael L. Raymer

Computer Science and Engineering Faculty Publications

Presentation prepared for BIO/CS 471: Algorithms for Bioinformatics. The lecture comprises material from the text Fundamental Concepts of Bioinformatics.

Protein Structure, Function, And Folding, Dan E. Krane, Michael L. Raymer

Computer Science and Engineering Faculty Publications

Presentation prepared for Intro to Bioinformatics. The lecture comprises material from the text Fundamental Concepts of Bioinformatics.

Common Data Administration, Data Management, And Data Alignment As A Necessary Requirement For Coupling C4isr Systems And M&S Systems, Andreas Tolk

Computational Modeling & Simulation Engineering Faculty Publications

Within the application domain of military simulation systems, training and exercises as well as support to real operations require the coupling of the simulation system delivering the needed functionality with the Command, Control, Computing, Communications, Intelligence, Surveillance, and Reconnaissance (C4ISR) system providing the necessary data. The solution to this challenge is to build appropriate interfaces. Although in long term a more integrated approach will be necessary, in short and mid term, gateways and interfaces are likely to remain the standard. However, in order to succeed with the respective efforts, at least on the data level of interoperability, a common solution …

Jsb Composability And Web Services Interoperability Via Extensible Modeling & Simulation Framework (Xmsf), Model Driven Architecture (Mda), Component Repositories, And Web-Based Visualization, Don Brutzman, Andreas Tolk

Computational Modeling & Simulation Engineering Faculty Publications

"Study Report prepared for the U. S. Air Force, Joint Synthetic Battlespace Analysis of Technical Approaches (ATA) Studies & Prototyping"

Overview: This paper summarizes research work conducted by organizations concerned with interoperable distributed information technology (IT) applications, in particular the Naval Postgraduate School (NPS) and Old Dominion University (ODU). Although the application focus is distributed modeling & simulation (M&S) the results and findings are in general easily applicable to other distributed concepts as well, in particular the support of operations by M&S applications, such as distributed mission operations. The core idea of this work is to show the necessity of …