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Big Data Proteogenomics And High Performance Computing: Challenges And Opportunities, Fahad Saeed 2015 Western Michigan University

Big Data Proteogenomics And High Performance Computing: Challenges And Opportunities, Fahad Saeed

Parallel Computing and Data Science Lab Technical Reports

Proteogenomics is an emerging field of systems biology research at the intersection of proteomics and genomics. Two high-throughput technologies, Mass Spectrometry (MS) for proteomics and Next Generation Sequencing (NGS) machines for genomics are required to conduct proteogenomics studies. Independently both MS and NGS technologies are inflicted with data deluge which creates problems of storage, transfer, analysis and visualization. Integrating these big data sets (NGS+MS) for proteogenomics studies compounds all of the associated computational problems. Existing sequential algorithms for these proteogenomics datasets analysis are inadequate for big data and high performance computing (HPC) solutions are almost non-existent. The purpose of ...


Stochastic Stability And Uncertainty Quantification Of Ring-Based Vibratory Gyroscopes, Soroush Arghavan 2015 The University of Western Ontario

Stochastic Stability And Uncertainty Quantification Of Ring-Based Vibratory Gyroscopes, Soroush Arghavan

Electronic Thesis and Dissertation Repository

Effect of stochastic fluctuations in angular velocity on the stability of two DOF ring-type MEMS gyroscopes is investigated. The governing Stochastic Differential Equations are discretized using the higher-order Milstein scheme in order to numerically predict the system response assuming the fluctuations to be white noise. Simulations via Euler scheme as well as a measure of Largest Lyapunov Exponents are employed for validation purposes due to lack of similar analytical or experimental data. The stability investigation predicts that the threshold fluctuation intensity increases nonlinearly with damping ratio. Under typical gyroscope operating conditions, nominal input angular velocity magnitude and mass mismatch appear ...


Software Metrics And Dashboard, Shilpika Shilpika, George K. Thiruvathukal, Saulo Aguiar, Konstantin Läufer, Nicholas J. Hayward 2015 Loyola University Chicago

Software Metrics And Dashboard, Shilpika Shilpika, George K. Thiruvathukal, Saulo Aguiar, Konstantin Läufer, Nicholas J. Hayward

Computer Science: Faculty Publications and Other Works

Software metrics are a critical tool which provide continuous insight to products and processes and help build reliable software in mission critical environments. Using software metrics we can perform calculations that help assess the effectiveness of the underlying software or process. The two types of metrics relevant to our work is complexity metrics and in-process metrics. Complexity metrics tend to focus on intrinsic code properties like code complexity. In-process metrics focus on a higher-level view of software quality, measuring information that can provide insight into the underlying software development process.

Our aim is to develop and evaluate a metrics dashboard ...


Optimization Of Blalock-Taussig Shunt And Anastomotic Geometry For Vascular Access Fistula Using A Genetic Algorithm, Guangyu Bao 2015 Washington University in St. Louis

Optimization Of Blalock-Taussig Shunt And Anastomotic Geometry For Vascular Access Fistula Using A Genetic Algorithm, Guangyu Bao

Engineering and Applied Science Theses & Dissertations

Blalock-Taussig (BT) shunts are used for defects that affect the flow of blood from the right ventricle, through the pulmonary artery, and to the lungs. Arteriovenous (AV) fistula is one type of vascular access which is a surgically created vein used to remove and return blood during hemodialysis. Plastic grafts used in the above two reconstructions may result in areas of non-physiologic flow in the grafts leading to risk of stenosis (blocked area) and thrombosis, which is the single major cause for access morbidity. The focus of this thesis is to study BT shunts and anastomoses models using Computational Fluid ...


Tetrahedral Mesh Optimization And Generation Via Topological Transformations And Gradient Based Node Perturbation, Christopher B. Hilbert 2015 University of Tennessee at Chattanooga

Tetrahedral Mesh Optimization And Generation Via Topological Transformations And Gradient Based Node Perturbation, Christopher B. Hilbert

Masters Theses and Doctoral Dissertations

A general tetrahedral mesh optimization scheme utilizing both topological changes (i.e. flips) and gradient-based vertex optimization (i.e. smoothing) is demonstrated. This scheme is used in the optimization of tetrahedral meshes created by third-party software as well as a grid generation methodology created for this work. The particular algorithms involved are explained in detail including, an explication of the primary optimization metric, weighted condition number. In addition, a thorough literature review regarding tetrahedral mesh generation is given.


A Parallel Algorithm For Compression Of Big Next-Generation Sequencing Datasets, Sandino N. Vargas Perez, Fahad Saeed 2015 Western Michigan University

A Parallel Algorithm For Compression Of Big Next-Generation Sequencing Datasets, Sandino N. Vargas Perez, Fahad Saeed

Parallel Computing and Data Science Lab Technical Reports

With the advent of high-throughput next-generation sequencing (NGS) techniques, the amount of data being generated represents challenges including storage, analysis and transport of huge datasets. One solution to storage and transmission of data is compression using specialized compression algorithms. However, these specialized algorithms suffer from poor scalability with increasing size of the datasets and best available solutions can take hours to compress gigabytes of data. In this paper we introduce paraDSRC, a parallel implementation of DSRC algorithm using a message passing model that presents reduction of the compression time complexity by a factor of O(1/p ). Our experimental results ...


Computational Fluid Dynamics Study Of Balloon System Tethered To A Stratosail, Jayakanth Loganathan, Kian-Meng Lim, Heow Pueh Lee, Boo Cheong Khoo 2015 National University of Signapore

Computational Fluid Dynamics Study Of Balloon System Tethered To A Stratosail, Jayakanth Loganathan, Kian-Meng Lim, Heow Pueh Lee, Boo Cheong Khoo

2015 Academic High Altitude Conference

In this paper, we present a numerical study of a stratospheric balloon system tethered to a passive device, known as the Stratosail, for station-keeping operation. For scientific applications, stratospheric balloons that operate at altitudes between 15 and 20 km will need to maintain station over a fixed point above the earth for a prescribed period of time. This is a challenging problem due to the limitation of payloads and lack of an energy source. The present study uses computational fluid dynamics (CFD) simulations to analyze the drift velocity of such a balloon-Stratosail system under typical wind conditions in the stratosphere ...


Cooperative 3-D Map Generation Using Multiple Uavs, Andrew Erik Lawson 2015 University of Connecticut - Storrs

Cooperative 3-D Map Generation Using Multiple Uavs, Andrew Erik Lawson

University Scholar Projects

This report aims to demonstrate the feasibility of building a global 3-D map from multiple UAV robots in a GPS-denied, indoor environment. Presented are the design of each robot and the reasoning behind choosing its hardware and software components, the process in which a single robot obtains a individual 3-D map entirely onboard, and lastly how the mapping concept is extended to multiple robotic agents to form a global 3-D map using a centralized server. In the latter section, this report focuses on two algorithms, Online Mapping and Map Fusion, developed to facilitate the cooperative approach. A limited selection of ...


Semi-Automated Test Generation With Spest, Adam Mozek 2015 California Polytechnic State University - San Luis Obispo

Semi-Automated Test Generation With Spest, Adam Mozek

Computer Science

Automated black box test generation is a useful tool for developers that allows them to

quickly generate a large number of tests with a wide range of values tested. The current most

popular tool for black box test generation in Java, JML, is lacking in a number of features.

SPEST aims to improve upon existing tools, and provide a black box test generation tool that

can create human readable tests from simple pre and post conditions added as comments to

the Java source code.


What Is The Right Context For An Engineering Problem: Finding Such A Context Is Np-Hard, Martine Ceberio, Vladik Kreinovich, Hung T. Nguyen, Songsak Sriboonchitta, Rujira Ouncharoen 2015 University of Texas at El Paso

What Is The Right Context For An Engineering Problem: Finding Such A Context Is Np-Hard, Martine Ceberio, Vladik Kreinovich, Hung T. Nguyen, Songsak Sriboonchitta, Rujira Ouncharoen

Departmental Technical Reports (CS)

In the general case, most computational engineering problems are NP-hard. So, to make the problem feasible, it is important to restrict this problem. Ideally, we should use the most general context in which the problem is still feasible. In this paper, we prove that finding such most general context is itself an NP-hard problem. Since it is not possible to find the appropriate context by utilizing some algorithm, it is therefore necessary to be creative -- i.e., to use some computational intelligence techniques. On three examples, we show how such techniques can help us come up with the appropriate context ...


Impact Responses Of Prestressing Tendons In Railway Concrete Sleepers In High Speed Rail Environments, Sakdirat Kaewunruen, Alex M. Remennikov 2015 University of Birmingham

Impact Responses Of Prestressing Tendons In Railway Concrete Sleepers In High Speed Rail Environments, Sakdirat Kaewunruen, Alex M. Remennikov

Sakdirat Kaewunruen

Prestressed concrete sleepers (or railroad ties) are designed in order to carry and transfer the wheel loads from the rails to the ground and are installed as the crosstie beam support in railway track systems. They are subjected to impact loading conditions that are resulted from train operations over wheel or rail abnormalities, such as flat wheels, dipped rails, crossing transfers, rail squats, corrugation, etc. The magnitude of the shock load relies on various factors such as axle load, types of wheel/rail imperfections, speeds of vehicle, track stiffness, etc.

This paper demonstrates the development of finite element modelling to ...


Three-Dimensional Ideal Gas Reference State Based Energy Function, Avdesh Mishra 2015 University of New Orleans

Three-Dimensional Ideal Gas Reference State Based Energy Function, Avdesh Mishra

University of New Orleans Theses and Dissertations

Energy functions are found to be a key of protein structure prediction. In this work, we propose a novel 3-dimensional energy function based on hydrophobic-hydrophilic properties of amino acid where we consider at least three different possible interaction of amino acid in a 3-dimensional sphere categorized as hydrophilic versus hydrophilic, hydrophobic versus hydrophobic and hydrophobic versus hydrophilic. Each of these interactions are governed by a 3-dimensional parameter alpha used to model the interaction and 3-dimensional parameter beta used to model weight of contribution. We use Genetic Algorithm (GA) to optimize the value of alpha, beta and Z-score. We obtain three ...


Adaptive Motion Pooling And Diffusion For Optical Flow, Naga Venkata Kartheek Medathati, Pierre Kornprobst, Guillaume Masson, Manuela Chessa, Fabio Solari 2015 INRIA

Adaptive Motion Pooling And Diffusion For Optical Flow, Naga Venkata Kartheek Medathati, Pierre Kornprobst, Guillaume Masson, Manuela Chessa, Fabio Solari

MODVIS Workshop

We study the impact of local context of an image (contrast and 2D structure) on spatial motion integration by MT neurons. To do so, we revisited the seminal work by Heeger and Simoncelli (HS) [4] using spatio-temporal filters to estimate optical flow from V1-MT feedforward interactions. However, the HS model has difficulties to deal with several problems encountered in real scenes (e.g., blank wall problem and motion discontinuities). Here, we propose to extend the HS model with adaptive processing by focussing on the role of local context indicative of the local velocity estimates reliability. We set a network structure ...


Secure And Reliable Routing Protocol For Transmission Data In Wireless Sensor Mesh Networks, Nooh Adel Bany Muhammad 2015 University of Southern Mississippi

Secure And Reliable Routing Protocol For Transmission Data In Wireless Sensor Mesh Networks, Nooh Adel Bany Muhammad

Dissertations

Abstract

Sensor nodes collect data from the physical world then exchange it until it reaches the intended destination. This information can be sensitive, such as battlefield surveillance. Therefore, providing secure and continuous data transmissions among sensor nodes in wireless network environments is crucial. Wireless sensor networks (WSN) have limited resources, limited computation capabilities, and the exchange of data through the air and deployment in accessible areas makes the energy, security, and routing major concerns in WSN. In this research we are looking at security issues for the above reasons. WSN is susceptible to malicious activities such as hacking and physical ...


Developing An Application For Evolutionary Search For Computational Models Of Cellular Development, Nicolas Scott Cornia 2015 Boise State University

Developing An Application For Evolutionary Search For Computational Models Of Cellular Development, Nicolas Scott Cornia

Boise State University Theses and Dissertations

VPEvolve is a free and open source application that utilizes a Visual Programming Environment (VPE) for the setup of the Genetic Algorithm (GA), for optimization of computational models. Specifically, the User Interface uses connected glyphs to represent the genetic operators of mutation, reproduction, fitness and selection. These glyphs give the user an intuitive way to set the parameters for the GA, and better visualization of the population's flow through these operators.

VPEvolve is currently being developed alongside research being done in Biocomputing to create models of cellular regeneration based on the regenerative properties of Planaria or flatworms. Since these ...


Disinfection And Advanced Oxidation Of Highly Absorbing Fluids By Uv/Vuv Light: Process Modeling And Validation, Ferdinando Crapulli 2015 The University of Western Ontario

Disinfection And Advanced Oxidation Of Highly Absorbing Fluids By Uv/Vuv Light: Process Modeling And Validation, Ferdinando Crapulli

University of Western Ontario - Electronic Thesis and Dissertation Repository

One of the limitations in treating highly absorbing fluids with ultraviolet photoreactors is the short light penetration into the fluid leading to the following issues: (a) if not engineered properly, ultraviolet photoreactors dealing with highly absorbing fluids are likely to be energy-inefficient due to a non-ideal use of emitted photons and non-uniform dose distribution (b) the quantification of photo-chemical rate constants could be a challenging task due to the severe mixing-limited conditions of the experimental apparatus used during the investigation. As a result, new lab-scale apparatus (alternative to the conventional collimated beam system) and modeling approaches are needed in order ...


Combination Of A Probabilistic-Based And A Rule-Based Approach For Genealogical Record Linkage, Pooja P. Shah 2015 Cal Poly SLO

Combination Of A Probabilistic-Based And A Rule-Based Approach For Genealogical Record Linkage, Pooja P. Shah

Master's Theses and Project Reports

Record linkage is the task of identifying records within one or multiple databases that refer to the same entity. Currently, there exist many different approaches for record linkage. Some approaches incorporate the use of heuristic rules, mathematical models, Markov models, or machine learning. This thesis focuses on the application of record linkage to genealogical records within family trees. Today, large collections of genealogical records are stored in databases, which may contain multiple records that refer to a single individual. Resolving duplicate genealogical records can extend our knowledge on who has lived and more complete information can be constructed by combining ...


Optimizing Harris Corner Detection On Gpgpus Using Cuda, Justin Loundagin 2015 California Polytechnic State University - San Luis Obispo

Optimizing Harris Corner Detection On Gpgpus Using Cuda, Justin Loundagin

Master's Theses and Project Reports

ABSTRACT

Optimizing Harris Corner Detection on GPGPUs Using CUDA

The objective of this thesis is to optimize the Harris corner detection algorithm implementation on NVIDIA GPGPUs using the CUDA software platform and measure the performance benefit. The Harris corner detection algorithm—developed by C. Harris and M. Stephens—discovers well defined corner points within an image. The corner detection implementation has been proven to be computationally intensive, thus realtime performance is difficult with a sequential software implementation. This thesis decomposes the Harris corner detection algorithm into a set of parallel stages, each of which are implemented and optimized on the ...


Visualizing Relationships Between Related Variables: Improving Physics Education Through D3.Js Network Visualizations, Stephanie Friend 2015 California Polytechnic State University - San Luis Obispo

Visualizing Relationships Between Related Variables: Improving Physics Education Through D3.Js Network Visualizations, Stephanie Friend

Liberal Arts and Engineering Studies

phiMap is a web application started by Cal Poly professors and students to aid professors in teaching physics. I developed Javascript visualizations for phiMap that serve to simplify the processes of both teaching and learning physics. These visualizations aim to present relationships between physics variables in an easy to understand manner, and they could eventually have a huge impact on physics education.


Tematyka Prac Doktorskich, Wojciech M. Budzianowski 2015 Wroclaw University of Technology

Tematyka Prac Doktorskich, Wojciech M. Budzianowski

Wojciech Budzianowski

No abstract provided.


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