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An Integrated Placement And Routing Approach , Min Pan Jan 2006

An Integrated Placement And Routing Approach , Min Pan

Retrospective Theses and Dissertations

As the feature size continues scaling down, interconnects become the major contributor of signal delay. Since interconnects are mainly determined by placement and routing, these two stages play key roles to achieve high performance. Historically, they are divided into two separate stages to make the problem tractable. Therefore, the routing information is not available during the placement process. Net models such as HPWL, are employed to approximate the routing to simplify the placement problem. However, the good placement in terms of these objectives may not be routable at all in the routing stage because different objectives are optimized in placement ...


Interactive Visualization Of Metabolic Networks Using Virtual Reality , Yuting Yang Jan 2006

Interactive Visualization Of Metabolic Networks Using Virtual Reality , Yuting Yang

Retrospective Theses and Dissertations

A combination of graph layouts in 3D space, interactive computer graphics, and virtual reality (VR) can increase the size of understandable networks for metabolic network visualization. Two models, the directed graph and the compound graph, were used to represent a metabolic network. The directed graph, or nonhierarchical visualization, considers the adjacency relationships. For the nonhierarchical visualization, the weighted GEM-3D layout was adopted to emphasize the reactions among metabolite nodes. The compound graph, or hierarchical visualization, explicitly takes the hierarchical relationships like the pathway-molecule hierarchy or the compartment-molecule hierarchy into consideration to improve the performance and perception. An algorithm was designed ...


Isecube: A Portable Iseage , Ryan Roger Rathje Jan 2006

Isecube: A Portable Iseage , Ryan Roger Rathje

Retrospective Theses and Dissertations

As the Internets' potential continues to grow in functionality and services, malicious activity becomes more prevalent. Professionals and researchers are working hard to create and implement secure systems, but this can require extensive tools and training to arising situations.;ISECUBE has been developed to be used in conjunction with Iowa State University's Internet Scale Event and Attack Generation Environment (ISEAGE) to act as a self sustaining portable environment as well as an extension of its functionality and services. ISECUBE is a transportable device that provides different realistic environments. These environments were designed with the classroom, research collaboration, and corporate ...


Survivable Design In Wdm Mesh Networks , Wensheng He Jan 2006

Survivable Design In Wdm Mesh Networks , Wensheng He

Retrospective Theses and Dissertations

This dissertation addresses several important survivable design issues in WDM mesh networks;Shared backup path protection has been shown to be efficient in terms of capacity utilization, due to the sharing of backup capacity. However, sharing of backup capacity also complicates the restoration process, and leads to slow recovery. The p-cycle scheme is the most efficient ring-type protection method in terms of capacity utilization. Recently, the concept of pre-cross-connected protection was proposed to increase the recovery speed of shared path protection. We overview these protection methods. The recovery time of these schemes are compared analytically. We formulate integer programming optimization ...


Improving Text Clustering For Functional Analysis Of Genes, Jing Ding Jan 2006

Improving Text Clustering For Functional Analysis Of Genes, Jing Ding

Retrospective Theses and Dissertations

Continued rapid advancements in genomic, proteomic and metabolomic technologies demand computer-aided methods and tools to efficiently and timely process large amount of data, extract meaningful information, and interpret data into knowledge. While numerous algorithms and systems have been developed for information extraction (i.e. profiling analysis), biological interpretation still largely relies on biologists' domain knowledge, as well as collecting and analyzing functional information from various public databases. The goal of this project was to build a text clustering-based software system, called GeneNarrator, for functional analysis of genes (microarray experiments);GeneNarrator automatically collected MEDLINE citations for a list of genes as ...


Uniform Resource Visualization , Kukjin Lee Jan 2006

Uniform Resource Visualization , Kukjin Lee

Retrospective Theses and Dissertations

Computing environments continue to increase in scale, heterogeneity, and hierarchy, with resource usage varying dynamically during program execution. Computational and data grids and distributed collaboration environments are examples. To understand performance and gain insights into developing applications that efficiently use system resources, performance visualization has proven useful. Performance visualization tools, however, often are specific to a particular resource at a certain level of the system, possibly with fixed views. Thus, they limit a user's ability to observe a performance problem associated with multiple resources across system levels and platforms. To address this limitation, information integration is necessary. In this ...


Security Enhancement In Passive Optical Networks Through Wavelength Hopping And Sequences Cycling Technique , Walid Suleiman Shawbaki Jan 2006

Security Enhancement In Passive Optical Networks Through Wavelength Hopping And Sequences Cycling Technique , Walid Suleiman Shawbaki

Retrospective Theses and Dissertations

Growth in the telecommunication industry continues to expand with requirements evolving around increased bandwidth and security. Advances in networking technologies have introduced low cost optical components that has made passive optical networks (PON) the choice for providing huge bandwidth to end users. PON are covered by established standards such as IEEE 802.3ah and ITU-T G.983.1/984.1, with star topology of broadcast and select (B&S) on shared fiber links that poses security vulnerability in terms of confidentiality and privacy;Research and reports in the literature focus around increasing cardinality via coding schemes that lack in addressing security, which was left for implementation in application layers via cryptography. This dissertation presents an ...


Large-Scale Methods In Computational Genomics , Anantharaman Kalyanaraman Jan 2006

Large-Scale Methods In Computational Genomics , Anantharaman Kalyanaraman

Retrospective Theses and Dissertations

The explosive growth in biological sequence data coupled with the design and deployment of increasingly high throughput sequencing technologies has created a need for methods capable of processing large-scale sequence data in a time and cost effective manner. In this dissertation, we address this need through the development of faster algorithms, space-efficient methods, and high-performance parallel computing techniques for some key problems in computational genomics;The first problem addressed is the clustering of DNA sequences based on a measure of sequence similarity. Our clustering method: (i) guarantees linear space complexity, in contrast to the quadratic memory requirements of previously developed ...


The Virtual Storm: An Exploratory Virtual Environment Of A Supercell Tornadic Thunderstorm For Meteorological Education , Galen William Faidley Jan 2006

The Virtual Storm: An Exploratory Virtual Environment Of A Supercell Tornadic Thunderstorm For Meteorological Education , Galen William Faidley

Retrospective Theses and Dissertations

The driving motivation behind the Virtual Storm is to provide students with a hands-on means to learning about severe weather. Hands-on experiences are considered an important teaching method. The Virtual Storm addresses the lack of hands-on experience in severe weather education through the use of computer graphics and virtual reality technology.;Formal user studies were used to determine the effectiveness of the Virtual Storm as a teaching tool. The study results did not show a measurable benefit of using the Virtual Storm. However, the user tests may not have captured the true value of the Virtual Storm since they focused ...


Partial Information Use In Uncertainty Quantification , Jianzhong Zhang Jan 2006

Partial Information Use In Uncertainty Quantification , Jianzhong Zhang

Retrospective Theses and Dissertations

Uncertainty exists frequently in our knowledge of the real world. Two forms of uncertainty are considered. One is variability coming from stochasticity. The other is epistemic uncertainty, also called 2nd order uncertainty and other names as well. Often it comes from ignorance or imprecision. In principle, this kind of uncertainty can be reduced by additional empirical data;Stochasticity is well studied in the field of probability theory. A variety of methods have been developed to address epistemic uncertainty. Some of these approaches are confidence limits, discrete convolutions, probabilistic arithmetic, Monte Carlo simulation, copulas, stochastic dominance, clouds, and distribution envelope determination ...


Distributed Real-Time Operating System (Drtos) Modeling In Specc , Ziyu Zhang Jan 2006

Distributed Real-Time Operating System (Drtos) Modeling In Specc , Ziyu Zhang

Retrospective Theses and Dissertations

System level design of an embedded computing system involves a multi-step process to refine the system from an abstract specification to an actual implementation by defining and modeling the system at various levels of abstraction. System level design supports evaluating and optimizing the system early in design exploration.;Embedded computing systems may consist of multiple processing elements, memories, I/O devices, sensors, and actors. The selection of processing elements includes instruction-set processors and custom hardware units, such as application specific integrated circuit (ASIC) and field programmable gate array (FPGA). Real-time operating systems (RTOS) have been used in embedded systems as ...


Secure Execution Environments Through Reconfigurable Lightweight Cryptographic Components , Mahadevan Gomathisankaran Jan 2006

Secure Execution Environments Through Reconfigurable Lightweight Cryptographic Components , Mahadevan Gomathisankaran

Retrospective Theses and Dissertations

Software protection is one of the most important problems in the area of computing as it affects a multitude of players like software vendors, digital content providers, users, and government agencies. There are multiple dimensions to this broad problem of software protection. The most important ones are: (1) protecting software from reverse engineering. (2) protecting software from tamper (or modification). (3) preventing software piracy. (4) verification of integrity of the software;In this thesis we focus on these areas of software protection. The basic requirement to achieve these goals is to provide a secure execution environment, which ensures that the ...