Computer Sciences Commons^™

An Approach To The Virtual Flora Of Mongolia – From A Data Repository To An Expert System, Http://Greif.Uni-Greifswald.De/Floragreif/, Jörg Hartleib, Martin Schnittler, Sabrina Rilke, Anne Zemmrich, Bernd Bobertz, Ulrike Najmi, Reinhard Zölitz, Susanne Starke

Erforschung biologischer Ressourcen der Mongolei / Exploration into the Biological Resources of Mongolia, ISSN 0440-1298

FloraGREIF is an internet accessible information system providing taxonomic, phytogeographic and ecological information on Mongolia’s flora in terms of descriptions, high-resolution plant images and an interactive WebGIS application. Organised along an updated checklist of the approx. 3000 Mongolian vascular plants that serves as a taxonomic backbone, information is split into the taxon level, referring to plant species, and the record level, referring to record or a collected plant specimen. At the latter level, images of living plants, scans of herbarium sheets, habitat photos and further notes can be found. Both data levels are linked by the name of the respective …

The Ontology For Parasite Lifecycle (Opl): Towards A Consistent Vocabulary Of Lifecycle Stages In Parasitic Organisms, Priti Parikh, Jie Zheng, Flora J. Logan-Klumpler, Christian J. Stoeckert, Pantelis Topalis, Anna Protasio, Amit P. Sheth, Mark Carrington, Matthew Berriman, Satya S. Sahoo

Kno.e.sis Publications

Background

Genome sequencing of many eukaryotic pathogens and the volume of data available on public resources have created a clear requirement for a consistent vocabulary to describe the range of developmental forms of parasites. Consistent labeling of experimental data and external data, in databases and the literature, is essential for integration, cross database comparison, and knowledge discovery. The primary objective of this work was to develop a dynamic and controlled vocabulary that can be used for various parasites. The paper describes the Ontology for Parasite Lifecycle (OPL) and discusses its application in parasite research.

Results

The OPL is based on …

Towards Cloud Mobile Hybrid Application Generation Using Semantically Enriched Domain Specific Languages, Ajith Harshana Ranabahu, Amit P. Sheth, Ashwin Manjunatha, Krishnaprasad Thirunarayan

Kno.e.sis Publications

The advancements in computing have resulted in a boom of cheap, ubiquitous, connected mobile devices as well as seemingly unlimited, utility style, pay as you go computing resources, commonly referred to as Cloud computing. Taking advantage of this computing landscape, however, has been hampered by the many heterogeneities that exist in the mobile space as well as the Cloud space.

This research attempts to introduce a disciplined methodology to develop Cloud-mobile hybrid applications by using a Domain Specific Language (DSL) centric approach to generate applications. A Cloud-mobile hybrid is an application that is split between a Cloud based back-end and …

Resident Identification Using Kinect Depth Image Data And Fuzzy Clustering Techniques, Tanvi Banerjee, James M. Keller, Marjorie Skubic

Kno.e.sis Publications

As a part of our passive fall risk assessment research in home environments, we present a method to identify older residents using features extracted from their gait information from a single depth camera. Depth images have been collected continuously for about eight months from several apartments at a senior housing facility. Shape descriptors such as bounding box information and image moments were extracted from silhouettes of the depth images. The features were then clustered using Possibilistic C Means for resident identification. This technology will allow researchers and health professionals to gather more information on the individual residents by filtering out …

An Exhibit Wordle, Allison Marsh

Handouts

No abstract provided.

A Crossword Puzzle For Kids, Allison Marsh

Handouts

No abstract provided.

Word Find, Allison Marsh

Handouts

No abstract provided.

Images From The Exhibit, Page 1, Allison Marsh

Handouts

No abstract provided.

Lesson Plans, Activities, And Further Reading, Allison Marsh

Handouts

No abstract provided.

Title Panel, Allison Marsh

Section 1: Introduction

No abstract provided.

Fact Or Fiction?, Allison Marsh

Section 5: Imaging at the Nano Scale

No abstract provided.

Spotlight On Usc: Department Of Art, Allison Marsh

Section 5: Imaging at the Nano Scale

No abstract provided.

Usc's Nanocenter, Allison Marsh

Section 5: Imaging at the Nano Scale

No abstract provided.

Art Versus Image, Allison Marsh

Section 5: Imaging at the Nano Scale

No abstract provided.

Nano Imaging, Allison Marsh

Section 5: Imaging at the Nano Scale

No abstract provided.

What Is Nanotechnology?, Allison Marsh

Section 5: Imaging at the Nano Scale

No abstract provided.

Nanotechnology In Everyday Life, Allison Marsh

Section 5: Imaging at the Nano Scale

No abstract provided.

Choosing An Instrument, Allison Marsh

Section 5: Imaging at the Nano Scale

No abstract provided.

Conclusion Panel, Allison Marsh

Section 6: Conclusion

No abstract provided.

The Development Of Parallel Adaptive Sampling Algorithms For Analyzing Biological Networks, Kathryn Dempsey Cooper, Kanimathi Duraisamy, Sanjukta Bhowmick, Hesham Ali

Interdisciplinary Informatics Faculty Proceedings & Presentations

The availability of biological data in massive scales continues to represent unlimited opportunities as well as great challenges in bioinformatics research. Developing innovative data mining techniques and efficient parallel computational methods to implement them will be crucial in extracting useful knowledge from this raw unprocessed data, such as in discovering significant cellular subsystems from gene correlation networks. In this paper, we present a scalable combinatorial sampling technique, based on identifying maximum chordal subgraphs, that reduces noise from biological correlation networks, thereby making it possible to find biologically relevant clusters from the filtered network. We show how selecting the appropriate filter …

A Novel Multithreaded Algorithm For Extracting Maximal Chordal Subgraphs, Mahantesh Halappanavar, John Feo, Kathryn Dempsey Cooper, Hesham Ali, Sanjukta Bhowmick

Interdisciplinary Informatics Faculty Proceedings & Presentations

Chordal graphs are triangulated graphs where any cycle larger than three is bisected by a chord. Many combinatorial optimization problems such as computing the size of the maximum clique and the chromatic number are NP-hard on general graphs but have polynomial time solutions on chordal graphs. In this paper, we present a novel multithreaded algorithm to extract a maximal chordal sub graph from a general graph. We develop an iterative approach where each thread can asynchronously update a subset of edges that are dynamically assigned to it per iteration and implement our algorithm on two different multithreaded architectures - Cray …

Images From The Exhibit, Page 2, Allison Marsh

Handouts

No abstract provided.

Secondary Structure Prediction Of Long Rna Sequences Based On Inversion Excursions And A Modularized Mapreduce Framework, Daniel Tesfai Yehdego

Open Access Theses & Dissertations

Ribonucleic acid (RNA) molecules and their secondary structures play important roles in many biological processes including gene expression and regulation. The genomes of many viruses are also RNA molecules. Since secondary structures are crucial for RNA functionality, computational predictions of the RNA secondary structures have been widely studied. However, the tremendous demands on computer memory and computing time for complex secondary structures limit the capability of existing thermodynamically based algorithms for structure predictions to handling only short RNA sequences with a few hundred bases. One approach to overcome this limitation is by first cutting long RNA sequences into shorter, non-overlapping …

Differential Modeling For Cancer Microarray Data, Omar Odibat

Wayne State University Dissertations

Capturing the changes between two biological phenotypes is a crucial task in understanding the mechanisms of various diseases. Most of the existing computational approaches depend on testing the changes in the expression levels of each single gene individually. In this work, we proposed novel computational approaches to identify the differential genes between two phenotypes. These approaches aim to quantitatively characterize the differences between two phenotypes and can provide better insights and understanding of various diseases. The purpose of this thesis is three-fold. Firstly, we review the state-of-the-art approaches for differential analysis of gene expression data.

Secondly, we propose a novel …

Volume 04, Matt Szemborski, Phillip Van Ness, Sarah Croughwell, Sarah Mayfield, Alyssa Strackbein, Marley Kimmel, Stephanie Skipp, Jamie Yurasits, Katherine Taggart, Alex Leonhart, Kristen Rawls, Andrew Armes, Amanda Haymens, Allison Paqlowski, Erica May, Stephanie Lane, Luke Acree, Cassandra L. Wilson, Stephanie Pishock, Erica Hopson, K. Juston Osborne, Katheryn Grayson, Kyle Fowlkes, Jessica Cox, Kaity Byrum, John-Harwood Scott, Ashley Johnson, Samantha Hockman, Emily Staskiel, Nancy Macdonald, R. Kruger Bressin, Benjamin P. Bilodeau, Andrea Irby, Kristin Macquarrie, Sarah Bietsch, Elizabeth Bednar

Incite: The Journal of Undergraduate Scholarship

Please note that part of pages 92-95 are redacted, in the digital copy, due to a misprint of the original printed article.

Introduction from Dean Dr. Charles Ross

The Internal Other: Transculturation and Postcolonial Magical Realism in Rushdie’s Midnight’s Children by Matt Szemborski

Photography by Phillip Van Ness

Photography “Waterfall” by Sarah Croughwell

Romancing the Bite: Statistical Analysis of Young Adult Vampire Novels by Sarah Mayfield

Photography by Alyssa Strackbein

Photography by Marley Kimmel

Wine and Society in the Viceroyalty of Peru by Stephanie Skipp

Analysis of Claud Monet’s Impression, Sunrise by Jamie Yurasits

Exploring Meaning: The Lindisfarne Gospels by …

The Application Of A Visual Data Mining Framework To Determine Soil, Climate And Land-Use Relationships, Yunous Vagh

Research outputs 2012

In this research study, the methodology of action research dynamics and a case study was employed in constructing a visual data mining framework for the processing and analysis of geographic land-use data in an agricultural context. The geographic data was made up of a digital elevation model (DEM), soil and land use profiles that were juxtaposed with previously captured climatic data from fixed weather stations in Australia. In this pilot study, monthly rainfall profiles for a selected study area were used to identify areas of soil variability. The rainfall was sampled for the beginning (April) of the rainy season for …

Learning Sparse Representations For Fruit Fly Gene Expression Pattern Image Annotation And Retreival, Lei Yuan, Alexander Woodard, Shuiwang Ji, Yuan Jiang, Zhi-Hua Zhou, Sudhir Kumar, Jieping Ye

Computer Science Faculty Publications

Background: Fruit fly embryogenesis is one of the best understood animal development systems, and the spatiotemporal gene expression dynamics in this process are captured by digital images. Analysis of these high-throughput images will provide novel insights into the functions, interactions, and networks of animal genes governing development. To facilitate comparative analysis, web-based interfaces have been developed to conduct image retrieval based on body part keywords and images. Currently, the keyword annotation of spatiotemporal gene expression patterns is conducted manually. However, this manual practice does not scale with the continuously expanding collection of images. In addition, existing image retrieval systems based …

Multivariate Models And Algorithms For Systems Biology, Lipi Rani Acharya

LSU New Orleans Theses and Dissertations

Rapid advances in high-throughput data acquisition technologies, such as microarraysand next-generation sequencing, have enabled the scientists to interrogate the expression levels of tens of thousands of genes simultaneously. However, challenges remain in developingeffective computational methods for analyzing data generated from such platforms. In thisdissertation, we address some of these challenges. We divide our work into two parts. Inthe first part, we present a suite of multivariate approaches for a reliable discovery of geneclusters, often interpreted as pathway components, from molecular profiling data with replicated measurements. We translate our goal into learning an optimal correlation structure from replicated complete and incomplete …

A Study Of Correlations Between The Definition And Application Of The Gene Ontology, Yuji Mo

Department of Computer Electronics and Engineering: Dissertations, Theses, and Student Research

When using the Gene Ontology (GO), nucleotide and amino acid sequences are annotated by terms in a structured and controlled vocabulary organized into relational graphs. The usage of the vocabulary (GO terms) in the annotation of these sequences may diverge from the relations defined in the ontology. We measure the consistency of the use of GO terms by comparing GO's defined structure to the terms' application. To do this, we first use synthetic data with different characteristics to understand how these characteristics influence the correlation values determined by various similarity measures. Using these results as a baseline, we found that …

Overview Of Contrast Data Mining As A Field And Preview Of An Upcoming Book, Guozhu Dong, James Bailey

Kno.e.sis Publications

This report provides an overview of the field of contrast data mining and its applications, and offers a preview of an upcoming book on the topic. The importance of contrasting is discussed and a brief survey is given covering the following topics: general definitions and terminology for contrast patterns, representative contrast pattern mining algorithms, applications of contrast mining for fundamental data mining tasks such as classification and clustering, applications of contrast mining in bioinformatics, medicine, blog analysis, image analysis and subgroup mining, results on contrast based dataset similarity measure, and on analyzing item interaction in contrast patterns, and open research …