Physical Sciences and Mathematics Commons^™

The Noesy Jigsaw: Automated Protein Secondary Structure And Main-Chain Assignment From Sparse, Unassigned Nmr Data, Chris Bailey-Kellogg, Alik Widge, John J. Kelley Iii, Marcelo J. Berardi, John H. Bushweller, Bruce Randall Donald

Dartmouth Scholarship

High-throughput, data-directed computational protocols for Structural Genomics (or Proteomics) are required in order to evaluate the protein products of genes for structure and function at rates comparable to current gene-sequencing technology. This paper presents the Jigsaw algorithm, a novel high-throughput, automated approach to protein structure characterization with nuclear magnetic resonance (NMR). Jigsaw consists of two main components: (1) graph-based secondary structure pattern identification in unassigned heteronuclear NMR data, and (2) assignment of spectral peaks by probabilistic alignment of identified secondary structure elements against the primary sequence. Jigsaw's deferment of assignment until after secondary structure identification differs greatly from traditional approaches, …

Restricted Delegation: Seamlessly Spanning Administrative Boundaries, Jon Howell, David Kotz

Dartmouth Scholarship

Historically and currently, access control and authentication is managed through ACLs. Examples include:

• the list of users in /etc/password, the NIS passwd map, or an NT domain

• permissions on Unix files or ACLs on NT objects

• a list of known hosts in .ssh/known hosts

• a list of IP addresses in .rhosts (for rsh) or .htaccess (http)

The limitations of ACLs always cause problems when spanning administrative domains (and often even inside administrative domains). The best example is the inability to express transitive sharing. Alice shares read access to object X with Bob (but not access to …

A Semantic-Based Middleware For Multimedia Collaborative Applications, Agustin Jose Gonzalez

Computer Science Theses & Dissertations

The Internet growth and the performance increase of desktop computers have enabled large-scale distributed multimedia applications. They are expected to grow in demand and services and their traffic volume will dominate. Real-time delivery, scalability, heterogeneity are some requirements of these applications that have motivated a revision of the traditional Internet services, the operating systems structures, and the software systems for supporting application development. This work proposes a Java-based lightweight middleware for the development of large-scale multimedia applications. The middleware offers four services for multimedia applications. First, it provides two scalable lightweight protocols for floor control. One follows a centralized model …

An Object-Oriented Algorithmic Laboratory For Ordering Sparse Matrices, Gary Karl Kumfert

Computer Science Theses & Dissertations

We focus on two known NP-hard problems that have applications in sparse matrix computations: the envelope/wavefront reduction problem and the fill reduction problem. Envelope/wavefront reducing orderings have a wide range of applications including profile and frontal solvers, incomplete factorization preconditioning, graph reordering for cache performance, gene sequencing, and spatial databases. Fill reducing orderings are generally limited to—but an inextricable part of—sparse matrix factorization.

Our major contribution to this field is the design of new and improved heuristics for these NP-hard problems and their efficient implementation in a robust, cross-platform, object-oriented software package. In this body of research, we (1) examine …

A Digital Pressure Sensor Data Acquisition System In A Wind Tunnel Model, John J. Novakoski

Electrical & Computer Engineering Theses & Dissertations

Pressure measurements on wind tunnel models provide an important aid to overall aerodynamic analysis and design of aircraft and vehicles. Most pressure measurements in wind tunnels are made using analog pressure sensors with interfacing electronics that connect to an external data acquisition unit. Some of desirable features of an improved pressure measurement system are that it be: 1) model embeddable, 2) inherently digital in nature, 3) intelligent, and 4) controllable by a remote computer.

An intelligent, model-embedded, eight-channel digital pressure sensor system has been developed and tested in a wind tunnel. The implemented system consists of Micro-Electro-Mechanical System (MEMS) digital …

Process Flow Optimization Studies Through Discrete Event Simulation, Milind Chokshi

Electrical & Computer Engineering Theses & Dissertations

Computer-aided simulation has begun to emerge as a powerful tool for numerical analysis of the behavior and anticipated performance of industrial systems and their optimization. Applications include materials handling, storage and controls systems, prediction of manufacturing efficiencies, and production optimization. Simulations are used to test baseline models and subsequently analyze new production concepts, operating strategies, and planned procedures prior to costly implementation.

The study of process flows in a manufacturing environment is difficult due to its inherent stochastic nature. Breakdown of the sub-systems and failures of machines is a random process and needs to be solved based on concepts of …

A Generic Object-Oriented Server Model, Brian Douglas Jones

Electrical & Computer Engineering Theses & Dissertations

The purpose of this paper is to introduce a generic, object-oriented model for the simulation of networks of queues. Generic simulation modeling provides robust ways of laying out processes in stochastic, event driven simulations. The approach taken is to define a methodology that will be implementation independent, termed the Generic Server Simulation Model (GSSM); thus, leaving the implementers to choose the best (most suited for their use) means of implementation. GSSM uses many object-oriented concepts to provide its basic structure and has in its design the ability to take advantage of these object-oriented concepts, including reuse of (existing) code. GSSM …

A Formal Semantics For Spki, Jon Howell, David Kotz

Computer Science Technical Reports

We extend the logic and semantics of authorization due to Abadi, Lampson, et al. to support restricted delegation. Our formal model provides a simple interpretation for the variety of constructs in the Simple Public Key Infrastructure (SPKI), and lends intuition about possible extensions. We discuss both extensions that our semantics supports and extensions that it cautions against.

Landmarks For Absolute Localization, Jon Howell, Keith Kotay

Computer Science Technical Reports

For certain experiments in mobile robotics, it is convenient to eliminate positional estimation error in the interest of analyzing other parts of the experiment. We designed and implemented a simple, accurate scheme for encoding and recovering absolute position information. The encoding is a two-dimensional image printed on the plane of the floor, and the absolute position information is recovered using a downward-looking video camera mounted on a mobile robot.

Fine Tuning Interfacea Relaxation Methods For Elliptic Differential, John R. Rice, P. Tsompanopoulou, E. Vavalis

Department of Computer Science Technical Reports

No abstract provided.

Information Management In A Ubiquitous Global Postioning Environment, Walid G. Aref, Susanne E. Hambrusch, Sunil Prabhakar

Department of Computer Science Technical Reports

No abstract provided.

The Bond Agent System And Applications, Ladislau Boloni, Kyungkoo Jun, Krzysztof Palacz, Radu Sion, Dan C. Marinescu

Department of Computer Science Technical Reports

No abstract provided.

On The Future Of Problem Solving Environments, Elias N. Houstis, John R. Rice

Department of Computer Science Technical Reports

No abstract provided.

Wright State University College Of Engineering And Computer Science Bits And Pcs Newsletter, Volume 16, Number 3, March 2000, College Of Engineering And Computer Science, Wright State University

BITs and PCs Newsletter

A ten page newsletter created by the Wright State University College of Engineering and Computer Science that addresses the current affairs of the college.

A Framework For Acquiring Domain Semantics And Knowledge For Database Integration, Roger Hsiang-Li Chiang, Ee Peng Lim, Veda C. Storey

Research Collection School Of Computing and Information Systems

Database integration research has traditionally focused on understanding integration issues from the schema and instance perspectives. As a result, database integration approaches tend to rely on a direct comparison of schema and instance elements. However, when the integration of heterogeneous databases is performed without considering the domain semantics and knowledge of local databases such as context information and requirement specifications, an incorrect integrated database may be produced. In this research, a framework for carrying out database integration tasks using the above knowledge is proposed. The framework provides a thorough foundation to: 1. analyze database integration issues from a broad scope, …

Improving The Analyst And Decision-Maker’S Perspective Through Uncertainty Visualization, Evan T. Watkins

Theses and Dissertations

This thesis constructs the Taxonomy of Uncertainty and an approach for enhancing the information in decision support systems. The hierarchical categorization of numerous causes for uncertainty defines the taxonomy, which fostered the development of a technique for visualizing uncertainty. This technique is fundamental to expressing the multi-dimensional uncertainty that can be associated with any object. By including and intuitively expressing uncertainty, the approach facilitates and enhances intuition and decision-making without undue information overload. The resulting approach for enhancing the information involves recording uncertainty, identifying the relevant items, computing and visualizing uncertainty, and providing interaction with the selection of uncertainty. A …

Data Warehouse Techniques To Support Global On-Demand Weather Forecast Metrics, Meriellen C. Joga

Theses and Dissertations

Air Force pilots and other operators make crucial mission planning decisions based on weather forecasts; therefore, the ability to forecast the weather accurately is a critical issue to Air Force Weather (AFW) and its customers. The goal of this research is to provide Air Force Weather with a methodology to automate statistical data analysis for the purpose of providing on-demand metrics. A data warehousing methodology is developed and applied to the weather metrics problem in order to present an option that will facilitate on-demand metrics. On-line analytical processing (OLAP) and data mining solutions are also discussed.

A Human-Centered Approach For Designing Decision Support Systems, Sean G. Kern

Theses and Dissertations

The choice to include the human in the decision process affects four key areas of system design: problem representation, system analysis and design, solution technique selection, and interface requirements specification. I introduce a design methodology that captures the necessary choices associated with each of these areas. In particular I show how this methodology is applied to the design of an actual decision Support system for satellite operations scheduling. Supporting the user's ability to monitor the actions of the system and to guide the decision process of the system are two key considerations in the successful design of a decision support …

Extracting Mission Semantics From Unmanned Aerial Vehicle Telemetry And Flight Plans, Walter T. Berridge

Theses and Dissertations

With the acceptance of Unmanned Aerial Vehicles (UAVs) as a primary platform within the Department of Defense (DOD) for gathering intelligence data, the amount of video information being recorded, analyzed, and archived continues to grow. Mechanisms for quickly locating and retrieving video segments of interest amongst the many hours of recorded video are required to accommodate the rapid turnaround expected in today's wartime planning environments. This research demonstrates that text-based data accompanying UAV video yields sufficient information to identify and create data items that can be indexed to provide for rapid identification and retrieval of video segments of interest. Four …

Stochastic Modeling-Based Dgps Estimation Algorithm, James T. Broaddus

Theses and Dissertations

A Kinematic Differential Global Positioning System (KDGPS) algorithm is developed. A number of mobile receivers is considered, one of which will be designated the reference station' which will have known position and velocity information at the beginning of the time interval examined. Satellite clock biases are used to model Selective Availability. The measurement situation on hand is properly modeled and a centralized estimation algorithm processing several epochs of data. The effect of uncertainty in the reference receiver's position and the level of receiver noise is examined. Monte Carlo simulations are performed to examine the ability of the algorithm to correctly …

Global Positioning System (Gps) Error Source Prediction, Marcus G. Ferguson

Theses and Dissertations

With the initiation of the navigation accuracy prediction algorithm used to estimate the amount of GPS solution (location and time) error for receivers, the capability to accurately predict solution errors due to the major GPS error sources is growing. Although some sources of error within the GPS solution have been previously analyzed, modeled, and/or accounted for within various modeling efforts, a formal evaluation of the seven major error sources that distort GPS activity has not been officially conducted up until this point. This research offers a logical assessment of all the major GPS error sources and their definitive impact on …

A Comparative Analysis Of Cockpit Display Development Tools, Matthew J. Gebhardt

Theses and Dissertations

Currently, no standard methodology exists that enables cockpit display engineers to evaluate software tools used in the development of graphical cockpit displays. Furthermore, little research has been accomplished in comparing current software development tools with traditional hand-coded methods, This research effort discusses a framework for analyzing cockpit display software development tools and follows through with a detailed analysis comparing today's hand-coding standard, OpenGL, with two of today's cockpit display software development suites, Virtual Application Prototyping System (VAPS) and Display Editor. The comparison exploits the analysis framework establishing the advantages and disadvantages of the three software development suites. The analysis framework …

A Java Universal Vehicle Router In Support Of Routing Unmanned Aerial Vehicles, Robert W. Harder

Theses and Dissertations

Unmanned Aerial Vehicles (UAVs) help the military gather information in times of peace and war. During a mission, typically 100 sites or more, a UAV will frequently be re-tasked to visit a pop-up threat, leaving the operator to determine the best way to finish the day's list of sites after the re-tasking. I develop a prototype application to serve the needs of a specific customer, the 11th Reconnaissance Squadron, by helping them preplan missions and dynamically re-task UAVs. This prototype application is built on a reusable airframe router called the core AFIT Router, which can later be added to more …

A Distributed Agent Architecture For A Computer Virus Immune System, Paul K. Harmer

Theses and Dissertations

Information superiority is identified as an Air Force core competency and is recognized as a key enabler for the success of future missions. Information protection and information assurance are vital components required for achieving superiority in the Infosphere, but these goals are threatened by the exponential birth rate of new computer viruses. The increased global interconnectivity that is empowering advanced information systems is also increasing the spread of malicious code and current anti-virus solutions are quickly becoming overwhelmed by the burden of capturing and classifying new viral stains. To overcome this problem, a distributed computer virus immune system (CVIS) based …

An Intelligent User Interface To Support Air Force Weather Product Generation And Automated Metrics, Darryl N. Leon

Theses and Dissertations

Air Force pilots require dependable weather reports so they may avoid unsafe flying conditions. In order to better gauge the accuracy of its weather products, Air Force Weather has established the requirement for an Air Force-wide automated weather metrics program. Under the guidelines for this program, forecasts will automatically be compared to observed weather to determine their accuracy. Statistics will be collected in the hopes of determining forecast error trends that can be corrected through education and training. In order for the statistical data produced by such a program to draw reliable conclusions about forecast accuracy, however, the correct format …

Explicitly Modeling Hierarchically Heterogeneous Software Architectures In An Object-Oriented Formal Transformation System, Darin L. Williams

Theses and Dissertations

Formal software transformation systems are software development environments typified by the semi-automated application of a series of correctness-preserving transformations to formal data models. The range of software architectures such systems are capable of producing is often restricted by the limited ability to accept high-level design inputs as constraints on the transformation process. When architectural inputs are acceptable, often the modeling language excludes the explicit representation of architectural constructs and provides, at best, an extremely limited architectural analysis capability. This research defines a high-level taxonomy of software architectures and proposes a way to explicitly model a broad class of architectures by …

A Method Of Focusing The Attention Of The Decision-Maker On Uncertain Information, John F. Moesner Iv

Theses and Dissertations

Military decision-makers need to be able to synthesize large amounts of information quickly and make accurate and timely decisions. However, all too often, when a decision-maker is bombarded with important information that has an uncertainty associated with it, that information is often neglected. One method of dealing with this type of information overload is through proper data orientation. By reducing the clutter of irrelevant information, the proportions of useful and relevant data can be increased. At the same time, the attention of the decision-maker is directed to the critical tasks or centers of gravity. The WATCHDOG Decision Support Tool is …

Knowledge Base Support For Design And Synthesis Of Multi-Agent Systems, Marc J. Raphael

Theses and Dissertations

AgentTool is an AFIT-produced, AFOSR-sponsored multi-agent system (MAS) development tool intended for production of MASs that meet military requirements. This research focuses on enabling MAS design and synthesis tools like agentTool to store, retrieve, and filter persistent, reusable, and reliable agent domain knowledge. This "enabling" is vital if such tools are expected to produce consistent, maintainable, and verifiable agent applications on short timetables. Enabling requires: 1) modeling the agent knowledge domain, 2) designing and employing a persistent knowledge base, and 3) bridging that domain model to the knowledge base with an extensible domain interchange grammar. The achieved interchange grammar, called …

An Object-Oriented Repository-Based Software Synthesis System, Gary L. Cornn Jr.

Theses and Dissertations

This research provides a repository on which various Air Force Institute of Technology (AFIT) transformational software synthesis tools can store, share, and manage data using a common repository information model. This information model was created by integrating a variety of separately developed AFIT software synthesis object models into a "wide-spectrum" model. Additionally, a methodology for describing complex relationships between artifacts in the repository is described. These relationships can be used to relate software synthesis artifacts created in a variety of formats, including text, binary, and the AFIT Wide-Spectrum Object Modeling Environment (AWSOME) information model. The relationships can be exploited for …

A 3d Display System For Lightning Detection And Ranging (Ldar) Data, Michael W. Darwin

Theses and Dissertations

Lightning detection is an essential part of safety and resource protection at Cape Canaveral. In order to meet the unique needs of launching space vehicles in the thunderstorm prone Florida environment, Cape Canaveral has the only operational three- dimensional (3D) lightning detection network in the world, the Lightning Detection and Ranging (LDAR) system. Although lightning activity is detected in three dimensions, the current LDAR display, developed 20 years ago, is two-dimensional. This thesis uses modern three-dimensional graphics, object-oriented software design, and innovative visualization techniques to develop a 3D visualization application for LDAR data.