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Articles 1 - 8 of 8
Full-Text Articles in Computational Engineering
Hybrid Modelling For Stroke Care: Review And Suggestions Of New Approaches For Risk Assessment And Simulation Of Scenarios, Tilda Herrgårdh, Vince I. Madai, John Kelleher, Rasmus Magnusson, Mika Gustafsson, Lili Milani, Peter Gennemark, Gunnar Cedersund
Hybrid Modelling For Stroke Care: Review And Suggestions Of New Approaches For Risk Assessment And Simulation Of Scenarios, Tilda Herrgårdh, Vince I. Madai, John Kelleher, Rasmus Magnusson, Mika Gustafsson, Lili Milani, Peter Gennemark, Gunnar Cedersund
Articles
Stroke is an example of a complex and multi-factorial disease involving multiple organs, timescales, and disease mechanisms. To deal with this complexity, and to realize Precision Medicine of stroke, mathematical models are needed. Such approaches include: 1) machine learning, 2) bioinformatic network models, and 3) mechanistic models. Since these three approaches have complementary strengths and weaknesses, a hybrid modelling approach combining them would be the most beneficial. However, no concrete approach ready to be implemented for a specific disease has been presented to date. In this paper, we both review the strengths and weaknesses of the three approaches, and propose …
Computational Analysis And Prediction Of Intrinsic Disorder And Intrinsic Disorder Functions In Proteins, Akila I. Katuwawala
Computational Analysis And Prediction Of Intrinsic Disorder And Intrinsic Disorder Functions In Proteins, Akila I. Katuwawala
Theses and Dissertations
COMPUTATIONAL ANALYSIS AND PREDICTION OF INTRINSIC DISORDER AND INTRINSIC DISORDER FUNCTIONS IN PROTEINS
By Akila Imesha Katuwawala
A dissertation submitted in partial fulfillment of the requirements for the degree of Engineering, Doctor of Philosophy with a concentration in Computer Science at Virginia Commonwealth University.
Virginia Commonwealth University, 2021
Director: Lukasz Kurgan, Professor, Department of Computer Science
Proteins, as a fundamental class of biomolecules, have been studied from various perspectives over the past two centuries. The traditional notion is that proteins require fixed and stable three-dimensional structures to carry out biological functions. However, there is mounting evidence regarding a “special” class …
A Study Of Scalability And Cost-Effectiveness Of Large-Scale Scientific Applications Over Heterogeneous Computing Environment, Arghya K. Das
A Study Of Scalability And Cost-Effectiveness Of Large-Scale Scientific Applications Over Heterogeneous Computing Environment, Arghya K. Das
LSU Doctoral Dissertations
Recent advances in large-scale experimental facilities ushered in an era of data-driven science. These large-scale data increase the opportunity to answer many fundamental questions in basic science. However, these data pose new challenges to the scientific community in terms of their optimal processing and transfer. Consequently, scientists are in dire need of robust high performance computing (HPC) solutions that can scale with terabytes of data.
In this thesis, I address the challenges in three major aspects of scientific big data processing as follows: 1) Developing scalable software and algorithms for data- and compute-intensive scientific applications. 2) Proposing new cluster architectures …
Developing An Application For Evolutionary Search For Computational Models Of Cellular Development, Nicolas Scott Cornia
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 models …
Towards The Prediction Of Mutations In Genomic Sequences, Juan Carlos Martinez
Towards The Prediction Of Mutations In Genomic Sequences, Juan Carlos Martinez
FIU Electronic Theses and Dissertations
Bio-systems are inherently complex information processing systems. Furthermore, physiological complexities of biological systems limit the formation of a hypothesis in terms of behavior and the ability to test hypothesis. More importantly the identification and classification of mutation in patients are centric topics in today’s cancer research.
Next generation sequencing (NGS) technologies can provide genome-wide coverage at a single nucleotide resolution and at reasonable speed and cost. The unprecedented molecular characterization provided by NGS offers the potential for an individualized approach to treatment. These advances in cancer genomics have enabled scientists to interrogate cancer-specific genomic variants and compare them with the …
Algorithms For Library-Based Microbial Source Tracking, Aldrin Montana
Algorithms For Library-Based Microbial Source Tracking, Aldrin Montana
Master's Theses
Pyroprinting is a novel, library-based microbial source tracking method developed by the Biology department at Cal Poly, San Luis Obispo. This method consists of two parts: (1) a collection of bacterial fingerprints, called pyroprints, from known host species, and (2) a method for pyroprint comparison. Currently, Cal Poly Library of Pyroprints (CPLOP), a web-based database application, provides storage and analysis of over $10000$ pyroprints. This number is quickly growing as students and researchers continue to use pyroprinting for research. Biologists conducting research using pyroprinting rely on methods for partitioning collected bacterial isolates into bacterial strains. Clustering algorithms are commonly used …
Pathologyxgrid Implementation For The Interproscan Bioinformatics Software, Cody K. Bumgardner
Pathologyxgrid Implementation For The Interproscan Bioinformatics Software, Cody K. Bumgardner
Cody Bumgardner
SoftwareInterProScan is an essential step in the Epichloëfestucae genome project’s pipeline. Complete determination of the genome sequence for Epichloëfestucae, requires substantial programmatic and computing efforts. Due to the running time requirements the computational volume of some of its subtasks exceed the power of a traditional single processor computation and high performance approaches, such as grid computing, are needed.
The Personal Digital Assistant (Pda) As A Tool For Telementoring Endoscopic Procedures., Cody K. Bumgardner
The Personal Digital Assistant (Pda) As A Tool For Telementoring Endoscopic Procedures., Cody K. Bumgardner
Cody Bumgardner
Abstract: The telementoring of surgical procedures is currently achieved via a wired infrastructure that usually requires sophisticated videoconference systems. This project represents the first step in assessing the potential for using handheld computers as a mobile alternative to current telementoring systems. Specifically, this project compares a handheld computer to a standard CRT monitor regarding their capability to accurately display video images from an endoscopic procedure. Video images from two previously recorded endoscopic procedures were transmitted from a standard VCR to: 1) a handheld computer (iPAQ 3670 running Pocket PC) via a wireless LAN and 2) a standard CRT monitor via …