Software Engineering Commons^™

An Automatic Framework For Embryonic Localization Using Edges In A Scale Space, Zachary Bessinger

Masters Theses & Specialist Projects

Localization of Drosophila embryos in images is a fundamental step in an automatic computational system for the exploration of gene-gene interaction on Drosophila. Contour extraction of embryonic images is challenging due to many variations in embryonic images. In the thesis work, we develop a localization framework based on the analysis of connected components of edge pixels in a scale space. We propose criteria to select optimal scales for embryonic localization. Furthermore, we propose a scale mapping strategy to compress the range of a scale space in order to improve the efficiency of the localization framework. The effectiveness of the proposed ...

A Polyglot Approach To Bioinformatics Data Integration: Phylogenetic Analysis Of Hiv-1, Steven Reisman, Catherine Putonti, George K. Thiruvathukal, Konstantin Läufer

Computer Science: Faculty Publications & Other Works

RNA-interference has potential therapeutic use against HIV-1 by targeting highly-functional mRNA sequences that contribute to the virulence of the virus. Empirical work has shown that within cell lines, all of the HIV-1 genes are affected by RNAi-induced gene silencing. While promising, inherent in this treatment is the fact that RNAi sequences must be highly specific. HIV, however, mutates rapidly, leading to the evolution of viral escape mutants. In fact, such strains are under strong selection to include mutations within the targeted region, evading the RNAi therapy and thus increasing the virus’ fitness in the host. Taking a phylogenetic approach, we ...

Spring­11: Pdc In Cs1/2 And A Mobile/Cloud Intermediate Mobile/Cloud Intermediate Software Design Course, Joseph P. Kaylor, Konstantin Läufer, Chandra N. Sekharan, George K. Thiruvathukal

Computer Science: Faculty Publications & Other Works

Recent changes in the environment of Loyola University Chicago’s Department of Computer Science include a better differentiation of our four undergraduate majors, growing interest in computing among science majors, and an increased demand for graduates with mobile and cloud skills. In our continued effort to incorporate parallel and distributed computing topics into the undergraduate curriculum, we are focusing on these three existing courses:

CS1: In response to a request from the physics department, we started to offer a CS1 section aimed at majors in physics and other hard sciences this spring semester. This section includes some material on numerical ...

Building Capable, Energy-Efficient, Flexible Visualization And Sensing Clusters From Commodity Tablets, Thomas Delgado Dias, Xian Yan, Konstantin Läufer, George K. Thiruvathukal

Computer Science: Faculty Publications & Other Works

We explore the application of clusters of commodity tablet devices to problems spanning a “trilogy” of concerns: visualization, sensing, and computation. We conjecture that such clusters provide a low-cost, energy-efficient, flexible, and ultimately effective platform to tackle a wide range of problems within this trilogy. This is a work in progress, and we now elaborate our position and give a preliminary status report.

A wide range of Android tablet devices are available in terms of price and capabilities. “You get what you pay for” w.r.t. display resolution, sensors, and chipset---corresponding to the trilogy. $200 gets one a 1280x800-pixel ...

Network Technologies Used To Aggregate Environmental Data, Paul Stasiuk, Konstantin Läufer, George K. Thiruvathukal

Computer Science: Faculty Publications & Other Works

The goal of the Loyola Weather Service (lws) project is to design and build a system of functioning environmental monitoring widgets that can intelligently and autonomously control the environment around them based on set thresholds and triggers. The widgets will also have the ability to aggregate their data and easily display this data in various ways: through a user interface in the room that the widget is placed, via a web application, and programmatically via a RESTful web service.

Ikriya: Simulating Software Quality Enhancement With Selected Replacement Policies, Sindhu Dharani Murthy

Masters Theses & Specialist Projects

The quality of information systems in any organization helps to determine the
efficiency of the organization. Many organizations maintain a custom software portfolio, whose quality is important to the organization. Management would like to optimize the portfolio’s quality. Decisions about software replacement or enhancement are made based on organizational needs and priorities. The development resources allocated help in determining the quality of new software, and should be put to optimal use. Enhancing existing software might sound cheap and easy but it is not always efficient. This thesis proposes a simulation model - iKriya - for this problem. It explores the consequences ...

Application Of Swarm And Reinforcement Learning Techniques To Requirements Tracing, Hakim Sultanov

Theses and Dissertations--Computer Science

Today, software has become deeply woven into the fabric of our lives. The quality of the software we depend on needs to be ensured at every phase of the Software Development Life Cycle (SDLC). An analyst uses the requirements engineering process to gather and analyze system requirements in the early stages of the SDLC. An undetected problem at the beginning of the project can carry all the way through to the deployed product.

The Requirements Traceability Matrix (RTM) serves as a tool to demonstrate how requirements are addressed by the design and implementation elements throughout the entire software development lifecycle ...

Simulating Inflation, Ryan M. Heathcote

Senior Honors Papers

Inflation is a common problem in modern economics, and it seems to persist, requiring government financial policy intervention on a regular basis in order to properly manage. The mechanics of inflation are difficult to understand, since the best metric modern society has for inflation involves taking samples of prices across the country. A simulation can give deeper insight into more than the mere fact that prices rise over time: a simulation can help to answer the “why” question. The problem with this statement is that developing a simulation is not as simple as writing some code. A simulation is developed ...

Integrated Development And Parallelization Of Automated Dicentric Chromosome Identification Software To Expedite Biodosimetry Analysis, Yanxin Li

University of Western Ontario - Electronic Thesis and Dissertation Repository

Manual cytogenetic biodosimetry lacks the ability to handle mass casualty events. We present an automated dicentric chromosome identification (ADCI) software utilizing parallel computing technology. A parallelization strategy combining data and task parallelism, as well as optimization of I/O operations, has been designed, implemented, and incorporated in ADCI. Experiments on an eight-core desktop show that our algorithm can expedite the process of ADCI by at least four folds. Experiments on Symmetric Computing, SHARCNET, Blue Gene/Q multi-processor computers demonstrate the capability of parallelized ADCI to process thousands of samples for cytogenetic biodosimetry in a few hours. This increase in speed ...

An Architecture For Believable Socially Aware Agents, Arvand Dorgoly

University of Western Ontario - Electronic Thesis and Dissertation Repository

The main focus of this thesis is to solve the believability problem in video game agents by integrating necessary psychological and sociological foundations by means of role based architecture. Our design agent also has the capability to reason and predict the decisions of other actors by using its own mental model. The agent has a separate mental model for every actor.

Validation Of Weak Form Thermal Analysis Algorithms Supporting Thermal Signature Generation, Elton Lewis Freeman

Masters Theses

Extremization of a weak form for the continuum energy conservation principle differential equation naturally implements fluid convection and radiation as flux Robin boundary conditions associated with unsteady heat transfer. Combining a spatial semi-discretization via finite element trial space basis functions with time-accurate integration generates a totally node-based algebraic statement for computing. Closure for gray body radiation is a newly derived node-based radiosity formulation generating piecewise discontinuous solutions, while that for natural-forced-mixed convection heat transfer is extracted from the literature. Algorithm performance, mathematically predicted by asymptotic convergence theory, is subsequently validated with data obtained in 24 hour diurnal field experiments for ...

Dynamic Task Execution On Shared And Distributed Memory Architectures, Asim Yarkhan

Doctoral Dissertations

Multicore architectures with high core counts have come to dominate the world of high performance computing, from shared memory machines to the largest distributed memory clusters. The multicore route to increased performance has a simpler design and better power efficiency than the traditional approach of increasing processor frequencies. But, standard programming techniques are not well adapted to this change in computer architecture design.

In this work, we study the use of dynamic runtime environments executing data driven applications as a solution to programming multicore architectures. The goals of our runtime environments are productivity, scalability and performance. We demonstrate productivity by ...

Senior Project Report - Doctest, Stephen Weessies

Computer Engineering

DocTest is a program that, simply put, allows a programmer or user to document STANAG 4586 (a standard for unmanned aerial vehicle interoperability) messages and test the vehicle system at Lockheed Martin [5]. The program is extensible to allow for further development aiding our software team to do what they do best and not get bogged down in tedious but necessary documentation. DocTest is also used to aid in testing, keeping track of the issues and bugs found and creating a document that captures each issue so an issue is not missed or forgotten. This program was made for use ...

Fuzzy Expert-Cocomo Risk Assessment And Effort Contingency Model In Software Project Management, Ekananta Manalif

University of Western Ontario - Electronic Thesis and Dissertation Repository

Software development can be considered to be the most uncertain project when compared to other types of projects due to the uncertainty in the customer requirements, the complexity of the process, and the intangible nature of the product. In order to increase the likelihood of success in managing a software project, the project manager(s) must invest more time and effort in the project planning phase. The two main activities in project planning phase are effort estimation and risk management which has to be executed together because the accuracy of the effort estimation is highly dependent on the size and ...

Network Structure Of Social Coding In Github, Ferdian Thung, David Lo, Lingxiao Jiang

Research Collection School of Information Systems (Open Access)

Social coding enables a different experience of software development as the activities and interests of one developer are easily advertized to other developers. Developers can thus track the activities relevant to various projects in one umbrella site. Such a major change in collaborative software development makes an investigation of networkings on social coding sites valuable. Furthermore, project hosting platforms promoting this development paradigm have been thriving, among which GitHub has arguably gained the most momentum. In this paper, we contribute to the body of knowledge on social coding by investigating the network structure of social coding in GitHub. We collect ...

Adoption Of Software Testing In Open Source Projects---A Preliminary Study On 50,000 Projects, Pavneet Singh Kochhar, Tegawendé F. Bissyandé, David Lo, Lingxiao Jiang

Research Collection School of Information Systems (Open Access)

In software engineering, testing is a crucial activity that is designed to ensure the quality of program code. For this activity, development teams spend substantial resources constructing test cases to thoroughly assess the correctness of software functionality. What is however the proportion of open source projects that include test cases? What kind of projects are more likely to include test cases? In this study, we explore 50,000 projects and investigate the correlation between the presence of test cases and various project development characteristics, including the lines of code and the size of development teams.

Empirical Evaluation Of Bug Linking, Tegawendé F. Bissyandé, Thung Ferdian, Shaowei Wang, David Lo, Lingxiao Jiang, Laurent Réveillère

Research Collection School of Information Systems (Open Access)

To collect software bugs found by users, development teams often setup bug trackers using systems such as Bugzilla. Developers would then fix some of the bugs and commit corresponding code changes into version control systems such as svn or git. Unfortunately, the links between bug reports and code changes are missing for many software projects as the bug tracking and version control systems are often maintained separately. Yet, linking bug reports to fix commits is important as it could shed light into the nature of bug fixing processes and expose patterns in software management. Bug linking solutions, such as ReLink ...

Understanding Widespread Changes: A Taxonomic Study, Shaowei Wang, David Lo, Lingxiao Jiang

Research Collection School of Information Systems (Open Access)

Many active research studies in software engineering, such as detection of recurring bug fixes, detection of copyand- paste bugs, and automated program transformation tools, are motivated by the assumption that many code changes (e.g., changing an identifier name) in software systems are widespread to many locations and are similar to one another. However, there is no study so far that actually analyzes widespread changes in software systems. Understanding the nature of widespread changes could empirically support the assumption, which provides insight to improve the research studies and related tools. Our study in this paper addresses such a need. We ...

Diffusion Of Software Features: An Exploratory Study, Ferdian Thung, David Lo, Lingxiao Jiang

Research Collection School of Information Systems (Open Access)

New features are frequently proposed in many software libraries. These features include new methods, classes, packages, etc. These features are utilized in many open source and commercial software systems. Some of these features are adopted very quickly, while others take a long time to be adopted. Each feature takes much resource to develop, test, and document. Library developers and managers need to decide what feature to prioritize and what to develop next. As a first step to aid these stakeholders, we perform an exploratory study on the diffusion or rate of adoption of features in Java Development Kit (JDK) library ...

Multi-Point Stride Coverage: A New Genre Of Test Coverage Criteria, Mohammad Mahdi Hassan

University of Western Ontario - Electronic Thesis and Dissertation Repository

We introduce a family of coverage criteria, called Multi-Point Stride Coverage (MPSC). MPSC generalizes branch coverage to coverage of tuples of branches taken from the execution sequence of a program. We investigate its potential as a replacement for dataflow coverage, such as def-use coverage. We find that programs can be instrumented for MPSC easily, that the instrumentation usually incurs less overhead than that for def-use coverage, and that MPSC is comparable in usefulness to def-use in predicting test suite effectiveness. We also find that the space required to collect MPSC can be predicted from the number of branches in the ...