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Student Theses Supervised by Eileen Kraemer
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| Name : |
Philippa Rhodes |
| Date : |
PhD, UGA, Summer 2007 |
| Title : |
Software Visualization: Using Perceptual, Attentional, and Cognitive Concepts to Quantify Quality
and Improve Effectiveness
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| Abstract: |
Software visualization (SV) involves the use of the crafts of typography, graphic design,
animation, and cinematography with modern Human-Computer Interaction technology to
facilitate both the human understanding and effective use of computer software. Software
visualizations are often used to portray both concrete and abstract concepts and range from
depictions of source code to performance characteristics to the execution of an algorithm as a
discrete or continuous sequence of graphical images, or algorithm visualization. Numerous
algorithm visualizations have been developed for use in educational settings. However, studies
that were designed to demonstrate the pedagogic effectiveness of algorithm visualizations have
been markedly unsuccessful, in spite of high expectations. In response to these results, lists of
recommended features have been suggested to algorithm visualization system designers, but
most of these features have not been proven to be beneficial.
The broad goal of this research is to provide an empirically-validated method for
designing and evaluating the effectiveness of dynamic visualizations. Our approach has been to
identify features of these visualizations and systems that may improve learning, to create
software that can isolate features of interest and aid in evaluating the usefulness of these features,
and to then use the software to conduct and analyze user studies.
This research:
i) assembles an initial listing of features of SVs and SV systems and introduces a
framework for testing the effectiveness of each,
ii) provides verified design guidelines for dynamic visualizations,
iii) applies concepts already researched and established in perceptual psychology and
cognitive psychology to the design of effective SVs,
iv) offers an explanation of the inevitable variability present in studies involving
human subjects through the investigation of the effects of individual differences
on comprehending SVs, and
v) objectively classifies SV systems and makes them widely and easily available in a
way never done before, with VisIOn, an Interactive Visualization Ontology.
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| Name : |
Manish Agarwal |
| Date : |
MS, UGA, Spring 2007 |
| Title : |
Viewing Behavior Model Graphs (VBMGs) for Characterizing User Viewing
Behavior in Program Visualizations
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| Abstract: |
We present a methodology for characterizing the gaze behavior of viewers of animated displays. We
introduce a transition graph called Viewing Behavior Model Graph (VBMG) to characterize the behavior
of users with similar viewing patterns into separate groups. We apply this methodology to the viewing
of program visualizations. In this method the user's eye-fixation sequences are obtained using an
Eye-Tracker and per-user viewing behavior models are created. We then cluster these per-user models to
build VBMGs for each cluster. The VBMGs are useful because they help us classify users into separate
groups, each user within a group having viewing behavior similar to others in the group. One useful
application of VBMGs would be to dynamically capture viewing behavior and predict the cluster to which
a user belongs, thus permitting on-the-fly adaptation of displays and other teaching materials.
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| Name : |
Shradha Kaldate |
| Date : |
MS, UGA, Spring 2007 |
| Title : |
Analysis of Viewing Behavior of Program Visualization and Interaction with Individual Differences
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| Abstract: |
Program Visualization (PV) is believed to be useful in Computer Science education. However, while
some PVs have been found to help users learn, other PVs have not been beneficial. In this thesis we
studied the user's gaze pattern to find effects of popup questions on an individual's visual attention.
We further analyzed the correlation of gaze behavior with the individual's preferred learning style,
performance based on a pre-test and post-test and a variety of perceptual, attentional and cognitive
abilities as determined by a battery of paper-and-pencil and computer-based assessments. While popups
appear to be effective for directing attention, no significant effect on comprehension of the depicted
algorithm was detected. Individual with different learning styles have distinctive viewing patterns and
this finding should be utilized in designing PVs that consider individual differences.
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| Name : |
Hongyu Yang |
| Date : |
MS, UGA, Spring 2007 |
| Title : |
Phylogenetic Tree Display: A Web-based Visualization Tool of Phylogenetic Data |
| Abstract: |
To be added.
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|
| Name : |
Ashley George Hamilton-Taylor |
| Date : |
PhD, UGA, Summer 2006 |
| Title : |
The Study and Design of Algorithm Animations
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| Abstract: |
Algorithm Animations (AAs) portray the high-level dynamic operation of an algorithm.
The computer science education community held great expectations that AA would assist
students in understanding algorithms. However, many studies of the instructional effectiveness
of AAs have produced inconclusive results. We investigated a number of issues pertinent to AA
effectiveness: the study of AA user needs, user-centered design and the role of perception in AA.
Existing algorithm animation systems typically have been designed without formal study
of related teaching practices. We conducted an observational study of instructors teaching data
structure and algorithm topics, focusing on activities involving the use of diagrams and
algorithms. The results of this study were used to inform the user-centered design of SKA, the
Support Kit for Animation. SKA combines interactive data structure diagram manipulation with
flexible pseudocode execution, simple algorithm animation authoring support, a visual data
structure library, and an animation engine designed for perceptual pacing and timing.
The role of perception in AAs had not been formally considered in the past. We
collaborated on a number of empirical studies to investigate this role, and the design of software
to be used to conduct these studies. We found that some animation techniques can assist user
perception and mapping in AA in some contexts, which will inform future AA design and
studies.
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| Name : |
Bina Reed |
| Date : |
MS, UGA, Spring 2006 |
| Title : |
Investigating characteristics of effective program visualizations: a testing environment and the effect of comparison cueing and exchange techniques on viewer comprehension in algorithm animations
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| Abstract: |
We describe SSEA, a System for Studying the Effectiveness of Animations, and an
empirical study that evaluates two visualization design attributes. SSEA was created as a testing
environment for studying the effects of various attributes in visualization design on viewer
comprehension. Researchers create a series of animations in SSEA with a design characteristic in
mind. SSEA allows these animations to be viewed while recording the viewer's interactions and
responses to questions about the underlying algorithm. At the conclusion of running all experiments,
the researchers can examine the log files generated, and perform analysis of the responses and timings
with respect to the attribute being examined. The first in a series of studies to be conducted
examined the attributes: comparison queueing and exchange techniqe using traditional and popup questions,
measuring comprehension and perception, respectively. No significant effects were observed in
comprehension questions. Significant effects were found in the perceptual questions.
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| Name : |
Nivedita Kaluskar |
| Date : |
MS, UGA, Fall 2005 |
| Title : |
XML-based specification and automatic code generation for easy customization
of view in the GUS WDK framework
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| Abstract: |
An automatic custom view generation method for the Genomics Unified Schema (GUS) frame-work has been
designed and implemented in this thesis work. The Genomics Unified Schema is a database schema and
application framework used to store, integrate, analyze and present functional genomics data.
Cryptosporidium, The Genome Resource (CryptoDB) is a project developed at the University of Georgia
under the GUS framework. CryptoDB offers a number of queries that a user can ask of the database
and uses the GUS Web Development Kit (WDK) to generate a default view for the database. Although the
earlier WDK offered an easy way of generatinga view for any given data model, the view generated was
too closely tied to Model and Controller. The method for generating a custom view enables a more
clear separation between the Model, View and Controller in the MVC type application and allows
on-the-fly generation of custom views. It uses an XML-based custom view specifications file containing
the specifications a user is allowed to make in order to generate a custom view. This gives the user
much more flexibility in designing a custom view and allows the View to be less closely tied to the
Model and the Controller.
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| Name : |
Yanqi Su |
| Date : |
MS, UGA, Fall 2005 |
| Title : |
Comparative genomics visualization
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| Abstract: |
As an increasing number of genomes are sequenced, comparative genomics analysis at different
evolutionary distances plays a crucial role in decoding genomic information and discovering the
similarities and differences between the genomes. It consists of three process steps: data preparation,
sequence alignment, and visualization. In this thesis the major alignment methods and visualization
tools are discussed. Based on an analysis of current work, we have designed and implemented a comparison
visualization approach that satisfies the specific requirements of the CryptoDB project
(http://cryptodb.org). Our approach is written in Perl and based on the GBrowse framework. In addition,
this study also presents an analysis of the comparison of C. hominis and C. parvum to find candidate
insertions, deletions, and synteny blocks. Future work is also discussed.
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| Name : |
Sujith Thomas |
| Date : |
MS, UGA, Fall 2004 |
| Title : |
An experiment designer tool for evaluation of program visualization quality
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| Abstract: |
Program Visualization refers to the graphical representation of a program in execution. They are
used to facilitate better understanding of the underlying algorithm or other program behavior. However,
doubts exist about the usefulness of program visualizations and the extent to which the visualizations
are employed in practice. Some studies of program and algorithm visualizations have shown that
visualizations have helped the instructional effort, while others argue that they have little or no
effect on the learning of subjects. Explaining the discrepancy is part of the research to be carried
out. One theory is that the quality of the program visualization used has varied among experiments. An
experiment generation application called TestCreator has been developed to design experiments that
assist in identification of the attributes associated with program visualization quality and
quantification of the effects of these attributes on the ability of visualizations to facilitate
learning.
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| Name : |
Matthew Ross |
| Date : |
MS, UGA, Summer 2004 |
| Title : |
A testing environment for the evaluation of program visualization quality
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| Abstract: |
Program visualizations have the potential to convey information about the behavior of the
programs they depict. However, program visualizations in use vary widely in their ability to
convey the desired information. In this work we conduct a study of the quality of the
visualizations, the ability of those visualizations to present information in a way that
is both effective and efficient in creating understanding. In order to measure program
visualization quality, many traits of the visualization need to be considered: size, shape,
color, and location of graphical elements, cueing and motion styles, etc. A testing environment
called TestTaker has been developed that allows the experimenter to display visualizations to
the user and receive feedback. The feedback is then used to evaluate the quality of the program
visualizations based on the metrics specified. These quality metrics will be used to create a
standard way of measuring the quality of program visualizations.
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| Name : |
Jian Wang |
| Date : |
MS, UGA, Summer 2004 |
| Title : |
Feature search in biological sequence data |
| Abstract: |
Genome projects continue to produce large quantities of sequence data. Annotation of this sequence data
to indicate the location of genes, start and stop codons, inverted and direct repeats, and other patterns
of interest is a challenging problem. In this thesis we present three contributions to solving this
problem. First, we have performed an analysis of several gene-finding programs for the fungus N. crassa ,
and applied both standard metrics and new metrics we have defined. Next, we have developed a general tool
that can automatically evaluate any gene-finding program and report performance metrics. Finally, we have
developed an Interactive Pattern Search Tool (IPST) to facilitate finding complex patterns in nucleotide
sequence data. The hashtable based approach employed in IPST is compared with the suffix tree approach
for pattern search. IPST is applied to the problems of locating Long Terminal Repeat (LTR)
retrotransposons and Miniature Inverted repeat Transposable Elements (MITEs) in rice sequences.
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| Name : |
Shiming Dong |
| Date : |
MS, UGA, Summer 2004 |
| Title : |
Calculation, visualization, and manipulation of MASTs (Maximum Agreement Subtrees)
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| Abstract: |
Phylogenetic trees are used to represent the evolutionary history of a set of species. Comparison of
multiple phylogenetic trees can help researchers find the common classification of a tree group, compare
tree construction inferences or obtain distances between trees. We present TreeAnalyzer, a freely
available package for phylogenetic tree comparison. A MAST (Maximum Agreement Subtree) algorithm is
implemented to compare the trees. Additional features of this software include tree comparison,
visualization, manipulation, labeling, and printing.
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|
| Name : |
Vinay Sachdev (supervised jointly with Prof. Maria Hybinette ) |
| Date : |
MS, UGA, Spring 2004 |
| Title : |
Overcoming over-optimism in Time Warp via aggregation of fast processes
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| Abstract: |
The parallel Time Warp protocol is widely used to improve the performance of large-scale discrete event
simulations such as simulations of the air traffic control system and the World Wide Web. However, a
concern regarding optimistic simulation processing is that some logical processes (LPs) may progress
far beyond others into the simulated future, causing an imbalance that may degrade performance. The
degradation is due to long and excessive rollbacks, inefficient use of memory resources, and
communication overheads. Allowing this "over-optimistic" processing may bring the simulation to a halt.
This is unacceptable for long running simulations that may take days to complete. We present a new
mechanism that controls over-optimistic processing through aggregation and isolation of fast processes
and redistribution of the slow, less optimistic processes. Our performance results demonstrate that our
techniques can improve the useful work by a factor of 1.75 and also improve execution time, while keeping
the overhead small.
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|
| Name : |
Qin Zhang |
| Date : |
MS, UGA, Spring 2004 |
| Title : |
Mini-Lab: A Tool to Visualize
Normal Modes of Vibration Using Java-3D |
| Abstract: |
Vibrational analysis of polyatomic molecules requires tools with the capability to construct the
system and display the normal modes. Mini-Lab, developed in this thesis work, is a 3D visualization
tool and vibration analyzer that serves both educational and research needs. The goal is to help the
user visualize the atoms and bonds, compute the normal modes for the system, and generate the animated
vibrational pattern. Users can experiment with different masses and bonds to construct a vibration
system and understand the normal modes when studying harmonic oscillation or small vibrations in
classical mechanics. This tool has been used in research that analyzes the vibration of nanocrystals.
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| Name : |
Weicheng Zhang |
| Date : |
MS, UGA, Summer 2003 |
| Title : |
A user friendly environment for gene-finding program evaluation (GFPE)
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| Abstract: |
A graphical, user friendly environment for GFPE (Gene-Finding Program Evaluation), written in Java,
is developed to evaluate the prediction accuracy of gene-finding programs GenScan, HMMGene, GeneMark,
Pombe and FFG. This tool aims to simplify and/or automate the process of executing the gene-finding
programs on sequences of interest and of collecting and analyzing the results. The GUI is designed to
be similar to a spreadsheet table. The user can add, cut, copy or paste gene sequence files and
annotation files to the table, add, delete, or modify the GFPE program and parameters, select an area
on the table to represent the execution of various gene-finding programs on remote servers, automatically
collect the prediction results, and draw bar charts to compare evaluation accuracy at the coding level,
exon level and protein level. It provides a convenient, user-friendly environment and an efficient file
management and execution system, thus saving the user substantial time.
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| Name : |
Chetna Warade |
| Date : |
MS, UGA, Fall 2003 |
| Title : |
Web Services Composition for Microarray Data Analysis |
| Abstract: |
To be added. |
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| Name : |
Arumugaraja Selvaraj |
| Date : |
MS, UGA, Fall 2002 |
| Title : |
Interactive computational steering : conservative vs optimistic steering approaches
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| Abstract: |
Interactive Computational Steering is the online, interactive allocation and adjustment of system
resources and application parameters. Causal consistency is an important feature of interactive
steering of distributed computations, as it is often required to maintain the correctness of the
computation. However, due to the asynchronous nature of distributed computations, it is difficult
to coordinate steering changes across processes to guarantee that the changes are applied consistently
at all processes. Two general approaches exist for achieving interactive computational steering:
conservative steering and optimistic steering. In this thesis, we present algorithms for the
conservative steering approach. We also compare the performance of the conservative steering
approach with that of the optimistic steering approach with regard to perturbation and lag.
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| Name : |
Jinhua Guo |
| Date : |
PhD, UGA, Summer 2002 |
| Title : |
Consistent, Interactive Steering of Distributed Computations: Algorithms and Implementation
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| Abstract: |
Interactive computational steering provides users with the opportunity to tackle new problems in a way that helps
them to learn about the computation in a highly engaging, interactive, visual environment. Causal consistency is
an important feature of interactive steering of distributed computations, as it is often required to maintain the
correctness of the computation. However, due to the asynchronous nature of distributed computations, it is difficult
to coordinate steering changes across processes to guarantee that the changes are applied consistently at all processes.
This thesis introduces a transaction-based computation model for distributed computation. This abstract model not
only gives users a simple and high-level view of distributed computation, but also simplifies reasoning about
the consistency problem by reducing the amount of information to be handled.
Furthermore, this work investigates two approaches for achieving consistent steering: conservative steering and
optimistic steering. The performance of conservative and optimistic steering approaches is evaluated in terms of
perturbation and lag. Our experiments show that when the percentages of consistency on the first attempt are large
enough and the size of checkpoint is not too large, the optimistic approach will achieve better performance;
otherwise, the conservative approach will be better.
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| Name : |
Mihail Tudoreanu (supervised jointly with Prof. Gruia-Catalin Roman) |
| Date : |
DSc, WUSTL, Spring 2002 |
| Title : |
Economy of Interaction in Program Visualization: Designing
Effective Visualization Tools for Reducing User's Cognitive Effort
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| Abstract: |
Program visualization has the potential to be an important tool for people who
seek to observe and understand the behavior of a running computation. This
thesis focuses on alleviating barriers to the realization of this potential
that pertain to the design of a visualization system and to insufficient
knowledge about how people take advantage of program visualizations. Our
major contribution is the design of a visualization approach capable of
improving user's performance through the use of economy of information and
tasks. We present evidence from our empirical studies that this type of
economy promotes animations capable of significantly improving people's
understanding of the computation. We apply this knowledge to develop
a system for creating application-specific visualizations solely through
interactions with program visualizations and textual views of the computation,
thus promoting economy of interaction. The system is built around the principle
that animation viewers are also the creators of animations and systematically
refine the visualizations to suit their momentary goal.
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| Name : |
David Miller |
| Date : |
MS, UGA, Spring 2002 |
| Title : |
An optimistic approach to computational steering |
| Abstract: |
Computational Steering is the online, interactive allocation of resources and adjustment of
application parameters. Few computational steering systems support the coordinated steering of
multiple processes. Of those that do provide such support, our system is unique in its optimistic
approach; other systems take a conservative approach. Because this requires global synchronization
considerable perturbation can arise. We focus on optimistic steering, which does not require global
synchronization before a steering event may take place. To achieve this requires not only the ability
to determine the consistency of steering transactions but also the ability to correct any inconsistencies
that may occur. To address these issues, we have developed algorithms for consistency detection and a
steering system that has the ability to correct inconsistencies through computational rollback and
re-execution. Presented in this thesis are both the details of our steering system and a performance
analysis of that system.
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| Name : |
Tao Wu |
| Date : |
MS, UGA, Fall 2001 |
| Title : |
An extensible framework for developing visualization software for gene expression data
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| Abstract: |
A design architecture of a software system that analyzes and visualizes gene expression profiles is
proposed. Implementation of core elements in the system is provided and a functional system prototype
is developed. This system is capable of visualizing data through a scrollable user interface (UI) that
only uses a small amount of memory. Current system includes implementation for viewing data as a rooted
tree or colored heat maps and includes support for clustering, filtering and printing.
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| Name : |
Ritu Dhawan |
| Date : |
MS, UGA, Fall 2001 |
| Title : |
Evaluation of web personalization software and visualization with the help of usability study |
| Abstract: |
Evaluation is an important element in the creation of complex software. In this thesis, we describe two
such evaluations. In the first study, we perform usability testing on web-based personalization software
developed by John O'Looney of the Carl Vinson Institute of Government at the University of Georgia.
Personalization of a web page involves dynamically altering the contents of the web pages according to
the preferences of customers or clients, so that each client gets information specific to his needs. This
study assists in and suggests ways to improve the usability and learnability of this software. The second
study was a user study to determine if visualization is beneficial in helping users to learn about and
understand distributed algorithms.
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| Name : |
Rong Wu |
| Date : |
MS, UGA, Fall 2001 |
| Title : |
Visualization as an aid for understanding distributed algorithms
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| Abstract: |
Visualization, the graphical representation of data by computer, is believed to be an aid to cognitive
processes. Algorithm animation, a type of visualization that displays a dynamic visual representation of
the state and behavior of algorithms, is aimed to help students learn and understand complex algorithms
better and more easily. Previous evaluations of algorithm animations have been performed. However, the
results of these studies were mixed and often inconclusive. The visualization community has called for
further studies to answer the question of whether algorithm animation is beneficial. This thesis presents
such a study. Three-dimensional graphics were used to implement algorithm animations for distributed
algorithms. Two studies were conducted to evaluate whether these visualizations helped students to learn
about the distributed algorithms.
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|
| Name : |
Brandon Lee Kohn |
| Date : |
MS, UGA, Summer 2001 |
| Title : |
Practical considerations in monitoring and steering of distributed computations
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| Abstract: |
Tools that assist users in understanding the complex workings of distributed systems are an important
aid to programmers and scientists. Interactive monitoring and steering tools can provide users with
insight into their computations. This thesis describes the PathFinder interactive monitoring and steering
system and the problems involved in making the system a viable solution for monitoring and steering
distributed applications. These problems include MPI support, an Agent Wizard, and a performance
analysis of two agent subsystems and their associated milieu, one implemented in Perl and the other
in Java.
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|
| Name : |
Renyi Liu |
| Date : |
MS, UGA, Summer 2001 |
| Title : |
Strategies for Improving Multiple Alignment of Retrotransposon Sequences |
| Abstract: |
Multiple sequence alignment plays a crucial role in extracting structural, functional, and evolutionary
information from the exponentially growing sequence data from the ongoing genome sequencing. Based on the
case study of retrotransposon sequence alignment, this thesis compares three alignment programs, DIALIGN,
CLUSTALW, and PRRN, and proposes some strategies to improve alignment quality, such as realigning certain
sequences or sequence ranges with different programs or parameters and hand editing. Entropy is used as
an alignment quality indicator. This study also presents the design and development of an alignment tool,
named AlignAgain, which is built to help biologists to improve alignment quality. AlignAgain is written
in Java and allows users to display, edit, realign whole or partial sequences with CLUSTALW or PRRN, and
append sequences with profile alignment.
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|
| Name : |
Piyush Burte |
| Date : |
MS, UGA, Summer 2001 |
| Title : |
A Visualization-based Tool in Support of High Throughput Nuclear Magnetic Resonance Studies |
| Abstract: |
To be added.
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|
| Name : |
Yin Xiong |
| Date : |
MS, UGA, Summer 2001 |
| Title : |
An Exploratory Environment for Concurrency Control Algorithms |
| Abstract: |
To be added.
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|
| Name : |
James Skinner |
| Date : |
MAMS, UGA, Spring 2001 |
| Title : |
Deployment Interface Module for the United States Army |
| Abstract: |
To be added.
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|
| Name : |
Yong Zhang |
| Date : |
MS, UGA, Spring 2001 |
| Title : |
A Visualization System for Protein Interaction Mapping Using Java 3D Technology |
| Abstract: |
To be added.
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| Name : |
Sneha Rao Kadandale |
| Date : |
MS, UGA, Spring 2001 |
| Title : |
Visualizations in Support of Network Monitoring and Control |
| Abstract: |
To be added.
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|
| Name : |
Navin Gupta |
| Date : |
MS, UGA, Summer 2000 |
| Title : |
Performance Considerations in the Monitoring and Visualization of Distributed Computations |
| Abstract: |
To be added.
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|
| Name : |
Delbert Hart (supervised jointly with Prof. Gruia-Catalin Roman) |
| Date : |
DSc, WUSTL, Summer 2000 |
| Title : |
Supporting Exploratory Visualization of Distributed Computations |
| Abstract: |
To be added.
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| Name : |
Himabindu Vuppula |
| Date : |
MS, UGA, Spring 2000 |
| Title : |
Practical Algorithms for Snapshot Collection in Distributed Processes |
| Abstract: |
The collection of global snapshots is an essential task in the monitoring and interactive steering of
distributed systems. In the PathFinder exploratory visualization system we have implemented multiple
snapshot collection algorithms, each providing a di erent balance among performance characteristics,
especially consistency, lag, perturbation and scalability. In this thesis, we describe the PathFinder
system, present the algorithms, describe experiments used to evaluate the algorithms, and present
and explain the results of these experiments.
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