Computer Sciences Commons^™

Risk Prediction With Genomic Data, Bharati Jadhav

Theses

Genome wide association study (GWAS) is widely used with various machine learning algorithms to predict disease risk. This thesis investigates this widely used approach of GWAS using Single Nucleotide Polymorphism (SNP) genotype data and a novel approach of disease risk prediction with whole exome sequencing data, namely Whole Exome Wide Association Study (WEWAS). It further applies a discriminating machine learning algorithm, namely a Support Vector Machine (SVM) with different Kernel functions. For this study, only SNPs generated using genotyping technology, which focuses more on common variants, are used initially for disease prediction. Later, the whole exome data generated using Next …

Comparison Of Different Differential Expression Analysis Tools For Rna-Seq Data, Junfei Zhu

Theses

In molecular biology research, RNA-seq is a relatively new method for transcriptome profiling. It utilizes the next generation sequencing technology to provide huge amount information about the variety and abundance of RNA present in an organism of interest at a specific state and a given time. One of the most important tasks of RNA-seq analysis is finding genes that are expressed differently in different subject groups. A lot of differential expression analysis tools for RNA-seq have been developed, but there is no golden standard in this field. In this research, four commonly used tools (DESeq, edgeR, limma, and cuffdiff) are …

A Decision Making Tool For Sustainable Design In Construction, Enda Collins

Theses

This report defines sustainability and sustainable development before any research is carried out. This is necessary so that the research carried out further in the report makes sense and there is a reason for including such items in this report. The need for this project and what the project aims to achieve is also highlighted in the introduction of this report.

Sustainability is made up of three equal parts; social, economic and environmental. This report goes through each item and gives examples of each type of development. Having discussed sustainability in a broad sense the report then focuses on Legislation …

Group Selection And Key Management Strategies For Ciphertext-Policy Attribute-Based Encryption, Russell F. Martin

Theses

Ciphertext-Policy Attribute-Based Encryption (CPABE) was introduced by Bethencourt, Sahai, and Waters, as an improvement of Identity Based Encryption, allowing fine grained control of access to encrypted files by restricting access to only users whose attributes match that of the monotonic access tree of the encrypted file. Through these modifications, encrypted files can be placed securely on an unsecure server, without fear of malicious users being able to access the files, while allowing each user to have a unique key, reducing the vulnerabilites associated with sharing a key between multiple users.

However, due to the fact that CPABE was designed for …

Rule-Based Conditional Trust With Openpgp., Andrew Jackson

Theses

This thesis describes a new trust model for OpenPGP encryption. This trust model uses conditional rule-based trust to establish key validity and trust. This thesis describes "Trust Rules" that may be used to sort and categorize keys automatically without user interaction. "Trust Rules" are also capable of integrating key revocation status into its calculations so it too is automated. This thesis presents that conditional trust established through "Trust Rules" can enforce stricter security while reducing the burden of use and automating the process of key validity, trust, and revocation.

A Forensic Comparison: Windows 7 And Windows 8, Peter J. Wilson

Theses

Whenever a new operating system or new version of an operating system is released, forensic investigators must re-examine the new operating system or new version. They do so to determine if there are significant differences that will impact and change the way they perform their investigations. With the release of Microsoft's latest operating system, Windows 8, and its update, Windows 8.1, understanding the similarities and differences between Windows 8 and previous operating systems such as Windows 7 is critical. This paper forensically examines Windows 7 and Windows 8 to determine those similarities and differences.

Segmentation And Model Generation For Large-Scale Cyber Attacks, Steven E. Strapp

Theses

Raw Cyber attack traffic can present more questions than answers to security analysts. Especially with large-scale observables it is difficult to identify which packets are relevant and what attack behaviors are present. Many existing works in Host or Flow Clustering attempt to group similar behaviors to expedite analysis; these works often phrase the problem directly as offline unsupervised machine learning. This work proposes online processing to simultaneously model coordinating actors and segment traffic that is relevant to a target of interest, all while it is being received. The goal is not just to aggregate similar attack behaviors, but to provide …

Understanding Effects Of Presentation On Concept Learning In Technology Supported Learning, Nivedita Singh

Theses

The world of technology has had a significant impact on learning and instructional domain. Today, a large number of devices and software are specifically designed to afford faster and effective learning and instruction. They have not only erased the physical boundaries to resources in education but have also helped create new interactions and engagements for learners and instructors. With this changed scenario, the content or instructional material also needs our attention to become usable and compatible with the changed learning styles and preferences of the learners today. Not only does the content need to seamlessly integrate with the delivery methodology …

Genome Wide Search For Pseudo Knotted Non-Coding Rnas, Meghana S. Vasavada

Theses

Non-coding RNAs (ncRNAs) are the functional RNA molecules that are involved in many biological processes including gene regulation, chromosome replication and RNA modification. Searching genomes using computational methods has become an important asset for prediction and annotation of ncRNAs. To annotate an individual genome for a specific family of ncRNAs, a computational tool is interpreted to scan through the genome and align its sequence segments to some structure model for the ncRNA family. With the recent advances in detecting an ncRNA in the genome, heuristic techniques are designed to perform an accurate search and sequence-structure alignment. This study uses a …

A Gpu Program To Compute Snp-Snp Interactions In Genome-Wide Association Studies, Srividya Ramakrishnan

Theses

With the recent advances in the next generation sequencing technologies, short read sequences of human genome are made more accessible. Paired end sequencing of short reads is currently the most sensitive method for detecting somatic mutations that arise during tumor development. In this study, a novel approach to optimize the detection of structural variants using a new short read alignment program is presented.

Pairwise interaction effects of the Single Nucleotide Polymorphisms (SNPs) have proven to uncover the underlying complex disease traits. Computing the disease risk based on the interaction effects of SNPs on a case - control study is a …

Rna-Sequence Analysis Of Human Melanoma Cells, Jharna Miya

Theses

RNA-sequencing refers to the use of high throughput sequencing technologies that are used to sequence cDNA in order to get the complete information of a sample’s RNA content. The objective of this study is to analyze this data in different aspects and to characterize gene expression. Besides this characterization, the data was also used to investigate the effect of sequencing depth on gene expression measurements.

This research focuses on quantitative measurement of expression levels of genes and their transcripts. In this study, complementary DNA fragments of cultured human melanoma cells are sequenced and a total of 139,501,106 million 200-bp reads …

Performance Comparison Of Five Rna-Seq Alignment Tools, Yuanpeng Lu

Theses

Aligning millions of short reads to a reference genome is a critical task in high throughput sequencing. In recent years, a large number of mapping algorithms have been developed, all of which have in common that they align a vast number of reads to genomic or transcriptomic sequences. RNA-Seq data is discrete in nature, therefore with reasonable gene models and comparative metrics RNA-Seq data can be simulated to sufficient accuracy to enable meaningful benchmarking of alignment algorithms. To provide guidance in the choice of alignment algorithms, five different alignment tools for RNA-Seq data are evaluated. In order to compare the …

Polyaseeker: A Computational Framework For Identifying Polyadenylation Cleavage Site From Rna-Seq, Xiao Ling

Theses

Alternative polyadenylation (APA) of mRNA plays a crucial role for post-transcriptional gene regulation. Recently, advances in next generation sequencing technology have made it possible to efficiently characterize the transcriptome and identify the 3’end of polyadenylated RNAs. However, no comprehensive bioi nformatic pipelines have fulfilled this goal. The PolyASeeker, a computational framework for identifying polyadenylation cleavage sites from RNA-Seq data is proposed in this thesis. By using the simulated RNA-seq dataset, a novel method is developed to evaluate the performance of the proposed framework versus the traditional A-stretch approach, and compute accurate Precisions and Recalls that previous estimation could not get. …

Improving Usability: Evaluating The Effect Of Changing Environmental Factors On Cognitive Load, Robin J. Deegan

Theses

Mobile devices are now truly ubiquitous. Their pervasiveness in all facets of our lives brings many advantages. Principle to these advantages is the notion that mobile devices can be used “Anytime, Anywhere”. The size, portability, battery life and computational power of mobile devices mean that they can be used for a diverse range of uses in an equally diverse range of environments.

Usability is primarily concerned with “ease of use” and “learnability”. Mobile devices are challenging this notion of Usability as they are used in new ways. Firstly mobile devices arc used in complex distracting environments and these distractions interfere …

Reducing The Risk Of Software Cost Estimation, Shixian Yang

Theses

Inaccurate cost estimation is a well-known problem in software development. The common cost estimation models are point estimates that are unable to quantify uncertainties. Furthermore, it is difficult to calibrate the uncertainties in cost estimation due to the lack of information. The purpose of this thesis is to prove that probability techniques could be synthesized into COCOMO (Constructive Cost Model) to quantify uncertainties. Another aim is to find out how to get more insight on reducing the risk of cost estimation. In this thesis, some historical data is presented to show the variance in factors of COCOMO. Monte Carlo simulation …

Phenotype Prediction And Feature Selection In Genome-Wide Association Studies, Andrew Roberts

Theses

Genome wide association studies (GWAS) search for correlations between single nucleotide polymorphisms (SNPs) in a subject genome and an observed phenotype. GWAS can be used to generate models for predicting phenotype based on genotype, as well as aiding in identification of specific genes affecting the biological mechanism underlying the phenotype.

In this investigation, phenotype prediction models are constructed from GWAS training data and are evaluated for performance on test data. Three methods are used to rank SNPs by their correlation with the phenotype: the univariate Wald test, a multivariate, support vector machine (SVM) based technique, and a hybrid method where …

Heterogeneity-Aware And Energy-Aware Scheduling And Routing In Wireless Sensor Networks, Mahesh Kumar Vasanthu Somashekar

Theses

A Wireless Sensor Network (WSN) is a group of specialized transducers, called sensor nodes, with a communication infrastructure intended to monitor and record conditions at diverse locations. Since WSN applications are usually deployed in an open environment, the network is exposed to rough weather conditions, such as rain and snow. Another problem that WSN applications need to deal with is the energy constraints of sensor nodes. Both problems adversely affect the lifetime of WSN applications. A lot of research has been conducted to prolong the lifetime of WSN applications considering energy constraints of sensor nodes, but not much research has …

A Comparative Analysis Of Machine Learning Algorithms For Genome Wide Association Studies, Neha Singh

Theses

Variations present in human genome play a vital role in the emergence of genetic disorders and abnormal traits. Single Nucleotide Polymorphism (SNP) is considered as the most common source of genetic variations. Genome Wide Association Studies (GWAS) probe these variations present in human population and find their association with complex genetic disorders. Now these days, recent advances in technology and drastic reduction in costs of Genome Wide Association Studies provide the opportunity to have a plethora of genomic data that delivers huge information of these variations to analyze. In fact, there is significant difference in pace of data generation and …

Data Mining Of Tetraloop-Tetraloop Receptors In Rna Xml Files, Sinan Ramazanoglu

Theses

RNA (Ribonucleic acid) Motifs are tertiary structures that play an important role in the folding mechanism of the RNA molecule. The overall function of a RNA Motif depends on its specific bp (base pairs) sequence that constitutes the secondary structure. Data mining is a novel method in both discovering potential tertiary structures within DNA (Deoxyribonucleic acid), RNA, and protein molecules and storing the information in databases. The RNA Motif of interest is the tetraloop-tetraloop receptor, which is composed of a highly conserved 11 nt (nucleotide) sequence and a tetraloop with the generic form of GNRA (where N = any base …

An Examination Of Coordination Among Friends And Strangers From A Coordination Theory Perspective, Christopher D. Wamble

Theses

Within mobile social coordination, there is a field of study known as outeraction, the communicative processes used by people to manage future interactions. It is an important area of research because it identifies how informal interactions support complex collaboration between individuals and groups. Outeraction is primarily conducted through the interpersonal communication channels of texting, instant messaging (IM), face-to-face, and mobile phone or Skype conversations. Currently this area of research in mobile outeraction support systems is weak. It lacks a firm foundation in system building, has very few if any conceptual frameworks, and little empirical knowledge of user requirements and attitudes …

Visualising Urban Flooding Scenarios Using Video Game Technology, William Elliott Lynn

Theses

This thesis investigates the application of computer graphics to the visualisation of urban flooding scenarios. The demand for urban flooding visualisations is presented in the context of an EU wide climate change response strategy. An analysis of the requirements from various stakeholders is presented and a strategy that addresses these requirements is synthesised. A study on the appropriate computer graphics methods and technologies is outlined and limitations of current technologies are assessed. Systems that solve these limitations are described and the result of usability and user acceptance testing are offered as evidence.

Usability Evaluation Of Modeling Languages, Christian Schalles

Theses

Over the last two decades more and more companies started to recognize the importance of graphical modeling as a way to meet their business goals. In order to describe a business case such as a business process or an application system, information in various different formats has to be integrated within a graphical model. Graphical models are developed using modeling languages such as the Unified Modeling Language (UML) and Event Driven Process Chains (EPC). The usability of graphical modeling languages has not been explicitly considered in past research. Most usability evaluation surveys are mainly focusing on applications, websites, software and …

The Identification And Reduction Of Energy Streams Within The Pharmaceutical Sector Using Software Algorithms, Raymond Corbett

Theses

Pharmaceutical companies are under increasing financial pressure to optimise production costs, due to a growing number of products coming off patent, research and development costs increasing exponentially and the difficulty of bringing genuinely innovative products to market. Generic drug manufacturers are not exempt from these pressures; costs must be driven down by all drug manufacturers due to the increasingly competitive healthcare market.

The operating costs of a modern Pharmaceutical Plant run to several Million Euros per annum. Complex process’s involving the consumption of large amounts of energy, and hence costs, are a necessity. Any increase in the efficiency of a …

Ontology Management For Universities, Roland Böving

Theses

What is the 'knowledge' of a university? It is the sum of all experiences and all contributions of students and staff. Knowledge ultimately exists, among other things, in the form of theses, articles, lectures and research reports. The largest knowledge pool of a university is made up, however, of the knowledge and expertise of every single member of the university. As a result of the high rate of turnover of people, knowledge and expertise are on the one hand constantly being lost, but this is replaced by a fresh intake of upcoming young students and lecturers reflecting the spirit of …

Morality In The Virtual Space: Applying Moral Philosophy To Digital Worlds, James O'Sullivan

Theses

Since the turn of the century and the dawn of the digital age, online communities have witnessed significant growth in their importance. Significant numbers of virtual environments now exist, within which millions of individuals interact socially and economically, engaged fully in what is equivalent to a physical encounter, the only differences being the virtual representations through which they interact, and the physical security that this representation affords them. Though physically absent, individuals are fully engaged psychologically, and thus open to the same ethical dilemmas presented through reality. Application of real-world moral codes is encumbered by the existence of what 1 …

Ranking Single Nucleotide Polymorphisms With Support Vector Regression In Continuous Phenotypes, Seif Shahidain

Theses

Support vector machines (SVM) have been used to improve the ranking of single nucleotide polymorphisms (SNPs) over traditional chi-square tests in disease case studies [2]. In this investigation, ranking SNPs with support vector regression (SVR) was compared to the Wald test in predicting continuous phenotypes. SVR-ranked SNPs consistently outperformed the Wald test-ranked SNPs to provide a more accurate prediction of the phenotype with fewer SNPs across several methods of prediction.

Dynamic-Parinet (D-Parinet) : Indexing Present And Future Trajectories In Networks, Mou Nandi

Theses

While indexing historical trajectories is a hot topic in the field of moving objects (MO) databases for many years, only a few of them consider that the objects movements are constrained. DYNAMIC-PARINET (D-PATINET) is designed for capturing of trajectory data flow in multiple discrete small time interval efficiently and to predict a MO’s movement or the underlying network state at a future time.

The cornerstone of D-PARINET is PARINET, an efficient index for historical trajectory data. The structure of PARINET is based on a combination of graph partitioning and a set of composite B+-tree local indexes tuned for a given …

Fast Program For Sequence Alignment Using Partition Function Posterior Probabilities, Meera Prasad

Theses

The key requirements of a good sequence alignment tool are high accuracy and fast execution. The existing Probalign program is a highly accurate tool for sequence alignment of both proteins and nucleotides. However, the time for execution is fairly high. The focus is therefore, to reduce the running time of the existing version of Probalign, maintaining its current accuracy level.

The thesis conducts a detail analysis of the performance of Probalign to bring down the running time of the existing code. A modified version of Probalign, Version 1.4 is released. A new program for sequence alignment with faster computation is …

Aminormotiffinder - A Graph Grammar Based Tool To Effectively Search A Minor Motifs In 3d Rna Molecules, Ankur Malhotra

Theses

RNA Motifs are three dimensional folds that play important role in RNA folding and its interaction with other molecules. They basically have modular structure and are composed of conserved building blocks dependent upon the sequence. Their automated in silico identification remains a challenging task. Existing motif identification tools does not correctly identify motifs with large structure variations. Here a “graph rewriting” based method is proposed to identify motifs in real three dimensional structures. The unique encoding of A Minor Searcher takes into consideration the non canonical base pairs and also multipairing of RNA structural motifs. The accuracy is demonstrated by …

Semi-Automatic Management Of Knowledge Bases Using Formal Ontologies, Andreas Textor

Theses

This thesis presents an approach that deals with the ever-growing amount of data in knowledge bases, especially concerning knowledge interoperability and formal representation of domain knowledge. There arc multiple issues that must be addressed with current systems. A multitude of different formats, sources and tools exist in a domain, and it is desirable to develop their use further towards a standardised environment. Such an environment should support both the representation and processing of data from this domain, and the connection to other domains, where necessary. In order to manage large amounts of data, it should be possible to perform whatever …