Software Engineering Commons^™

Phr: Patient Health Record, Quinn Nelson

Theses/Capstones/Creative Projects

The rapid development of information technology systems has expanded into multiple disciplines and results in systems that are limited by initial design and implementation: the Healthcare Information Technology (HIT) space is no different. The introduction of the Electronic Health Record (EHR) system has changed the way healthcare operates. Initial designs of these systems were focused on serving the needs of insurance companies and healthcare billing departments. Research shows that the design of EHR systems negatively impact provider-patient interactions and the care they receive. This capstone project capitalizes on the collaboration efforts between UNO and UNMC – by joining a research …

Space Operations In The Suborbital Space Flight Simulator And Mission Control Center: Lessons Learned With Xcor Lynx, Pedro Llanos, Christopher Nguyen, David Williams, Kim O. Chambers, Erik Seedhouse, Robert Davidson

Journal of Aviation/Aerospace Education & Research

This study was conducted to better understand the performance of the XCOR Lynx vehicle. Because the Lynx development was halted, the best knowledge of vehicle dynamics can only be found through simulator flights. X-Plane 10 was chosen for its robust applications and accurate portrayal of dynamics on a vehicle in flight. The Suborbital Space Flight Simulator (SSFS) and Mission Control Center (MCC) were brought to the Applied Aviation Sciences department in fall 2015 at Embry-Riddle Aeronautical University, Daytona Beach campus. This academic and research tool is a department asset capable of providing multiple fields of data about suborbital simulated flights. …

Software Development For Genome Sequence Analysis, David Farr

Symposium Of University Research and Creative Expression (SOURCE)

The cost of genome sequencing has decreased rapidly, expanding availability for many biological applications (Muir 2016). For example, researchers can now obtain genome sequences from multiple populations under different types of selection. Comparison of these sequences allows for identification of chromosome regions and specific genes associated with adaptive evolution (Kelly 2013). As an increasing number of researchers engage in this type of inquiry, many have created in-house computer scripts to analyze the raw sequence data (e.g., Kelly 2013), creating a gap in both continuity and standardization.

Using a test dataset and preliminary results from an ongoing artificial selection experiment in …

K-Mer Analysis Pipeline For Classification Of Dna Sequences From Metagenomic Samples, Russell Kaehler

Graduate Student Theses, Dissertations, & Professional Papers

Biological sequence datasets are increasing at a prodigious rate. The volume of data in these datasets surpasses what is observed in many other fields of science. New developments wherein metagenomic DNA from complex bacterial communities is recovered and sequenced are producing a new kind of data known as metagenomic data, which is comprised of DNA fragments from many genomes. Developing a utility to analyze such metagenomic data and predict the sample class from which it originated has many possible implications for ecological and medical applications. Within this document is a description of a series of analytical techniques used to process …

Ifly: Code Development For An App To Support Automating Entomological Data Collection, Michael P. Cosentino, Trevor Stamper

The Summer Undergraduate Research Fellowship (SURF) Symposium

We are developing a prototype entomological data-collection application called "iFly," which runs on a field-capable iPad device. In this phase, we tackled refining screens and introducing a database manager to streamline operations as info is entered, stored, retrieved and delivered. We used SQLite3 database in Apple's Xcode Integrated Development Environment (IDE). Xcode gives mixed programming results. Apple's iOS environment ensures functional and fairly error-free apps can be built. But the sophisticated Xcode IDE requires specialist developers and valuable project time is spent as new programmers learn key techniques. The iFly prototype was advanced with improved database integration; however, more work …

Ciliate Codon Translator Program Manual, Quentin D. Altemose

Mathematics Summer Fellows

Understanding the evolutionary history of organisms allows us to better comprehend selective pressures and their effects on larger populations. In our study, we focused on analyzing the DNA of ciliate groups, which are single celled protozoans characterized by the presence of cilia on their outer membrane. We utilized the DNA of the organisms to analyze the changes in population genotype over time. We tested existing evolutionary models (designed to represent natural genetic variation over time in populations) against our data to identify the model with the best fit and likelihood. From the DNA and the evolutionary model with the highest …

Chipathlon: A Competitive Assessment For Gene Regulation Tools, Avi Knecht, Adam Caprez, Istvan Ladunga

UCARE: Research Products

When gene regulation of the cell cycle malfunctions, it frequently causes cancer.

Adult, differentiated cells can be reprogrammed to induced pluripotent stem cell; which can then be reprogrammed to heart muscle, skin, etc, to repair damaged tissue (to limited extent in clinical practice).

ChIPathlon: Evaluate the performance of all transcription factor mapping (peak calling) methods. To this end, we will develop a scalable and easy to use super computing pipeline to stage data, compare many different peak calling and differential binding site tools, and store all results into a single database.

Evaluating And Improving The Efficiency Of Software And Algorithms For Sequence Data Analysis, Hugh L. Eaves

Theses and Dissertations

With the ever-growing size of sequence data sets, data processing and analysis are an increasingly large portion of the time and money spent on nucleic acid sequencing projects. Correspondingly, the performance of the software and algorithms used to perform that analysis has a direct effect on the time and expense involved. Although the analytical methods are widely varied, certain types of software and algorithms are applicable to a number of areas. Targeting improvements to these common elements has the potential for wide reaching rewards. This dissertation research consisted of several projects to characterize and improve upon the efficiency of several …

Design, Programming, And User-Experience, Kaila G. Manca

Honors Scholar Theses

This thesis is a culmination of my individualized major in Human-Computer Interaction. As such, it showcases my knowledge of design, computer engineering, user-experience research, and puts into practice my background in psychology, com- munications, and neuroscience.

I provided full-service design and development for a web application to be used by the Digital Media and Design Department and their students.This process involved several iterations of user-experience research, testing, concepting, branding and strategy, ideation, and design. It lead to two products.

The first product is full-scale development and optimization of the web appli- cation.The web application adheres to best practices. It was …

Mapping Legume Roots Can Determine Best Performing Crops, Frédérique C. Guinel

Clear Language Summaries

Legume plants have a mutually beneficial relationship with bacteria. These beneficial bacteria live in nodules found on plant roots. Until recently there was no way to systematically measure the roots the nodules are found on and to place accurately the nodules on these roots. The research team created software and a method to measure multiple root parameters which were not available previously. This allows different plant varieties to be compared with precise measurements of the root structure in order to figure out which plants will grow better.

Taming The Software Chaos: True To Its Promise, Iftdss Eases The Burden Of Fuels Treatment Planning—And Does A Lot More Besides, Gail Wells

Joint Fire Science Program Digests

A key problem reported by the fuels treatment planning community is the difficulty and inefficiency of evaluating and then applying many planning tools and applications. Fuels specialists have struggled to find, load, and learn all the different fuels and fire planning models, not to mention the interface of running, adjusting, and inputting data specific to each model without the ability to easily share inputs/outputs between models.

The Interagency Fuels Treatment Decision Support System (IFTDSS) was conceived as a way for users to learn one interface, access a variety of data and models all in one place, and pass data (inputs …

Improving Structural Features Prediction In Protein Structure Modeling, Ashraf Yaseen

Computer Science Theses & Dissertations

Proteins play a vital role in the biological activities of all living species. In nature, a protein folds into a specific and energetically favorable three-dimensional structure which is critical to its biological function. Hence, there has been a great effort by researchers in both experimentally determining and computationally predicting the structures of proteins.

The current experimental methods of protein structure determination are complicated, time-consuming, and expensive. On the other hand, the sequencing of proteins is fast, simple, and relatively less expensive. Thus, the gap between the number of known sequences and the determined structures is growing, and is expected to …

Mobile Applications For Indian Agriculture Sector: A Case Study, Pratik Shah, Niketa Gandhi, Leisa Armstrong

Research outputs 2014 to 2021

Government, private agencies and the general public are often interested in the decisions made by the Indian farmers as they have large influences beyond the farm boundary. Over many years, the process of adoption of new technologies and policies in the Indian agricultural sector has received considerable academic attention highlighting the role of many social, financial and other influences on their decision making. The Indian government and other development agencies promote income generating projects as a way of encouraging growth through increased agricultural production and the protection of the natural resource base. The impact of new technology to economic growth …

Application Of Cellular Neural Networks And Naive Bayes Classifier In Agriculture, Oluleye H. Babatunde, Leisa Armstrong, Jinsong Leng, Dean Diepeveen

Research outputs 2014 to 2021

This article describes the use of Cellular Neural Networks (a class of Ordinary Differential Equation (ODE)), Fourier Descriptors (FD) and NaiveBayes Classifier (NBC) for automatic identification of images of plant leaves. The novelty of this article is seen in the use of CNN for image segmentation and a combination FDs with NBC. The main advantage of the segmentation method is the computation speed compared with other edge operators such as canny, sobel, Laplacian of Gaussian (LoG). The results herein show the potential of the methods in this paper for examining different agricultural images and distinguishing between different crops and weeds …

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 and 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 …

Experiences With Tracking The Effects Of Changing Requirements On Morphbank: A Web-Based Bioinformatics Application, Subhajit Datta, Robert Van Engelen, David Gaitros, Neelima Jammigumpula

Research Collection School Of Computing and Information Systems

In this paper, we present a case study of applying the metrics Mutation Index, Component Set, Dependency Index on Morphbank- a web based bioinformatics application - to track the effects of changing requirements on a software system and suggest design modifications to mitigate such impact. Morphbank is "an open web repository of biological images documenting specimen-based research in comparative anatomy, morphological phylogenetics, taxonomy and related fields focused on increasing our knowledge about biodiversity". This paper discusses the context of the case study, analyzes the results, highlights observations and learning, and mentions directions of future work.

Acquiring Three-Dimensional Data From Small Mammalian Teeth : Laser Scanning Eocene Marsupials, Nicholas E. Smith

Theses, Dissertations and Capstones

Three-dimensional laser scanning is an effective method of digitization in paleontology, but has traditionally been restricted to larger specimens. The goal of this study was to develop a laser scanning technique applicable to small mammalian (< 5 mm) dentition. Modeling protocols were developed, and a morphometric error study showed the system highly accurate (percent error = 1D- 0.4%, 2D- 0.05%, 3D- 1.74%). Automation and standardization were accomplished by implementation of a multiscan platform and autosurfacing macro reducing modeling time by 60%. To highlight one morphometric application, 3D models (n=61) of three sympatric Eocene marsupials were digitized, and traditionally qualitative diagnostic characters were quantified and assessed. All but two of the 19 characters examined proved diagnostic (p < 0.05), and exploratory canonical discriminant analysis confirmed three distinct species. Incorporating type specimens revealed a familial overlap, therefore, this novel modeling technique can be employed in a full revision of early Eocene marsupials.

Development Of Web Tools For Nlx Simulation Software, Daniel Chai Siriphongs

Loma Linda University Electronic Theses, Dissertations & Projects

Valuable mathematical equations have developed within biology and other sciences (physics, chemistry, etc.) that model various processes, but the complexity of the equations are not easily understood by students, scientists, and those with limited knowledge of the subject area. Simulation software used to visually explain a model is normally proprietary to the specific model equations and cannot be easily adapted to new models by non-programmers. Simulation software needs to be modular and based upon web technologies so that the software can be run on multiple platforms. The NLX simulation software is a group of Java-based objects that can be combined …

Computer Aided Learning Environment For Biology, Pek Hin Foong

Student Works (2000-2009)

Traditional learning on biology requires of memory rather than understanding. As better educational technology emerges, we are able to utilise the computer as an important tool in learning. Many educational and pedagogical issues, particularly in the field or Artificial intelligence are looked at to help consider a good design for a computer learning tool. Existing computer aided learning materials are also studied to pinpoint their better features and incorporate them into the learning tool. A learning tool is proposed for effective learning in relating facts, rules, text and graphics. This system will have a Study Section containing notes that incorporates …

Herba Online, Dol Bakri Zen Akmal

Student Works (2000-2009)

Sistem Herba Online merupakan satu sistem informasi dengan pangkalan data berasaskan web yang dibangunkan untuk membantu memperkembangkan pengetahuan rakyat Malaysia amnya tentang herba di Malaysia serta kepentingannya dalam kehidupan. Objektif utama sistem dibangunkan ialah selaku pemangkin meningkatkan pengetahuan pengguna dalam topik herba dengan memudahkan cara mencapai maklumat yang mereka inginkan. Sasaran pengguna bagu sistem ini ialah individu atau organisasi yang terlibat dalam pembelajaran, kajian, penghasilan, pemprosesan atau pemasaran tumbuhan-tumbuhan herba atau produk-produk yang dihasilkannya. Bab pertama laporan ini menceritakan secara ringkas pengenalan, objektif dan skop projek. Bab kedua merupakan hasil daripada kajian literasi yang telah dilakukan berkaitan dengan topik. Secara …

Crop Updates 2000 Cereals - Part 3, Roslyn J. Jettner, Blakely Paynter, Glenn Macdonald, Pierre Fievez, Ian Foster, David Tennant, Wal Anderson, James Ridsdill-Smith, Celia Pavri, Ross Chapman, Senthold Asseng, Steve Carr, Brad Nutt, Lindrea Latham, Roger Jones, Anyou Liu, Clinton K. Revell, David Ferris, Roy Latta, Lisa-Jane Blacklow, Chris Matthews, Ted Woodburn, Paul Yeoh, Ian Rose, Anita Lyons, Simon Cook, Matthew L. Adams, Robert J. Corner

Crop Updates

This session covers eighteen papers from different authors:

BARLEY AND OAT AGRONOMY

1. Unicorn barley must meet malting specifications to be a viable option, Roslyn Jettnerand Blakely Paynter, Agriculture Western Australia

2. Optimum oat seed rates, Glenn McDonald, Agriculture Western Australia

3. Production and Quality of export Oaten Hay (1998 and 1989), Pierre Fievez, Pierre Fievez and Associates

FROST

4. Climatology of Frost in Southern Western Australia, Ian Foster, Agriculture Western Australia

5. Flowering calculator, David Tennant, Agriculture Western Australia

6. Some options for managing the risk of frost damage, Wal Anderson, Agriculture Western Australia

PASTURE

7. …

Sistem Pakar Bermultimedia Untuk Pengenalpastian Serangga, Osman Aizul Hussin

Student Works (2000-2009)

Sistem Pakar Bermultimedia untuk domain pengenalpastian serangga ,Insect Identification Expert System,(IIES ) merupakan sistem pakar untuk membantu proses pengenalpastian pangkat serangga dalam Hierarki Linnean. Sistem ini menggunakan pendekatan berorientasikan objek di mana konsep kelas dan objek akan digunakan untuk merekodkan pengetahuan ke bentuk yang akan difahami oleh sistem pakar. Strategi inferens yang digunakan ialah teknik rantaian ke hadapan di mana sistem pakar akan menghasilkan konklusi berdasarkan data-data yang diberi. Sistem pakar mempunyai ciri-ciri multimedia untuk membantu memberi panduan bagi pengguna untuk mengenal pasti ciri-ciri kunci serangga dan memberi penjelasan tentang domain di samping memberi pendekatan yang berlainan dari sistem pakar …

Flower : Predicting Flowering Times Of Cereal Crops, G A B Elliott, Stephen Loss

Journal of the Department of Agriculture, Western Australia, Series 4

FLOWER is a computer program which predicts the flowering date of a given wheat or barley variety at a specified location and sowing date. Department of Agriculture agronomists, breeders and advisers are using the program to provide useful information on how the development of cereals responds to different environments across Western Australia's cereal growing areas.