Browsing by Author "Murrell, Hugh Crozier."

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An analysis of algorithms to estimate the characteristics of the underlying population in Massively Parallel Pyrosequencing data.
(2011) Ragalo, Anisa.; Murrell, Hugh Crozier.
Massively Parallel Pyrosequencing (MPP) is a next generation DNA sequencing technique that is becoming ubiquitous because it is considerably faster, cheaper and produces a higher throughput than long established sequencing techniques like Sanger sequencing. The MPP methodology is also much less labor intensive than Sanger sequencing. Indeed, MPP has become a preferred technology in experiments that seek to determine the distinctive genetic variation present in homologous genomic regions. However there arises a problem in the interpretation of the reads derived from an MPP experiment. Specifically MPP reads are characteristically error prone. This means that it becomes difficult to separate the authentic genomic variation underlying a set of MPP reads from variation that is a consequence of sequencing error. The difficulty of inferring authentic variation is further compounded by the fact that MPP reads are also characteristically short. As a consequence of this, the correct alignment of an MPP read with respect to the genomic region from which it was derived may not be intuitive. To this end, several computational algorithms that seek to correctly align and remove the non-authentic genetic variation from MPP reads have been proposed in literature. We refer to the removal of non-authentic variation from a set of MPP reads as error correction. Computational algorithms that process MPP data are classified as sequence-space algorithms and flow-space algorithms. Sequence-space algorithms work with MPP sequencing reads as raw data, whereas flow-space algorithms work with MPP flowgrams as raw data. A flowgram is an intermediate product of MPP, which is subsequently converted into a sequencing read. In theory, flow-space computations should produce more accurate results than sequence-space computations. In this thesis, we make a qualitative comparison of the distinct solutions delivered by selected MPP read alignment algorithms. Further we make a qualitative comparison of the distinct solutions delivered by selected MPP error correction algorithms. Our comparisons between different algorithms with the same niche are facilitated by the design of a platform for MPP simulation, PyroSim. PyroSim is designed to encapsulate the error rate that is characteristic of MPP. We implement a selection of sequence-space and flow-space alignment algorithms in a software package, MPPAlign. We derive a quality ranking for the distinct algorithms implemented in MPPAlign through a series of qualitative comparisons. Further, we implement a selection of sequence-space and flow-space error correction algorithms in a software package, MPPErrorCorrect. Similarly, we derive a quality ranking for the distinct algorithms implemented in MPPErrorCorrect through a series of qualitative comparisons. Contrary to the view expressed in literature which postulates that flowspace computations are more accurate than sequence-space computations, we find that in general the sequence-space algorithms that we implement outperform the flow-space algorithms. We surmise that flow-space is a more sensitive domain for conducting computations and can only yield consistently good results under stringent quality control measures. In sequence-space, however, we find that base calling, the process that converts flowgrams (flow-space raw data) into sequencing reads (sequence-space raw data), leads to more reliable computations.
Computer simulation of the two body abrasive wear process.
(2002) Naicker, Theo.; Murrell, Hugh Crozier.
New computer technologies are applied to the classical material engineering two-body abrasive wear process. The computer simulation provides an interactive and visual representation of the wear process. The influence of grit size, grit tip radius and load (at constant workpiece hardness and tool path) on the wear rate, wear coefficient and wear surface topography is predicted. The simulation implements microcutting and microploughing with material displacement to the sides of the groove. The validation of the simulation is demonstrated by comparing with the previous modelling literature and with experiments.
The development of a swarm intelligent simulation tool for sugarcane transport logistics systems.
(2008) McDonald, Brendon Clyde.; Dube, Erick.; Murrell, Hugh Crozier.
Transport logistics systems typically evolve as networks over time, which may result in system rigidity and cause changes to become expensive and time consuming. In this study a logistics model, named TranSwarm, was developed to simulate sugarcane harvesting, transport and mill-yard activities for a mill supply area. The aim was to simulate produce flow, and allow individual working entities to make decisions, driven by rules and protocols, based on their micro-environments. Noodsberg mill was selected as a case study because of low current levels of synchronization. Growers were assumed to operate independent harvesting and transport systems causing inconsistent convergences at the mill. This diverse and fragmented system provided a suitable environment to construct a model that would consider interactions between individual growers and their respective transport systems. Ideally, by assessing the micro-decisions of individuals and how they influence the larger holistic supply chain, TranSwarm quantifies the impacts of different types of transport practices, such as staggering shift changes, transport scheduling, core sampling and consortium-based logistics. TranSwarm is visual, mechanistic and represents key entities, such as roads, farm groupings and the mill. The system uses discrete events to create a dynamic and stochastic environment from which observations and conclusions can be drawn. This approach potentially allows stakeholders to identify key components and interactions that may jeopardize overall efficiency and to use the system to test new working protocols and logistics rules for improving the supply chain.
Investigation of techniques for automatic polyphonic music transcription using wavelets.
(2009) McGuiness, John C.; Murrell, Hugh Crozier.
It has been said (although sadly I have no source) that music is one of the most useful yet useless phenomena known to mankind. Useless in that it has, apparently, no tangible or immediately practical function in our lives, but extremely useful in that it is a truly universal language between human beings, which transcends boundaries and allows us to express ourselves and experience emotions in rather profound ways. For the majority of us, music exists to be listened to, appreciated, admired (sometimes reviled) but generally as some sort of stimulus for our auditory senses. Some of us feel the need to produce music, perhaps simply for our own creative enjoyment, or maybe because we crave the power it lends us to be able to inspire feelings in others. For those of us who love to know “the reason why” or “how things work” and wish to discover the secrets of music, arguably the greatest of all the arts, there can surely be no doubt that a fascinating world of mathematics, harmony and beauty awaits us. Perhaps the reason why music is able to convey such strong emotions in us is because we are (for whatever strange evolutionary reason or purpose) designed to be innately pattern pursuing, sequence searching and harmony hungry creatures. Music, as we shall discover in this research, is chock-a-block full of the most incredible patterns, which are just waiting to be deciphered.
Modelling with mathematica.
(1994) Murrell, Hugh Crozier.; Sartori-Angus, Alan G.
In this thesis a number of mathematical models are investigated with the aid of the modelling package Mathematica. Some of the models are of a mechanical nature and some of the models are laboratories that have been constructed for the purpose of assisting researchers in a particular field. In the early sections of the thesis mechanical models are investigated. After the equations of motion for the model have been presented, Mathematica is employed to generate solutions which are then used to drive animations of the model. The frames of the animations are graphical snapshots of the model in motion. Mathematica proves to be an ideal tool for this type of modelling since it combines algebraic, numeric and graphics capabilities on one platform. In the later sections of this thesis, Mathematica laboratories are created for investigating models in two different fields. The first laboratory is a collection of routines for performing Phase-Plane analysis of planar autonomous systems of ordinary differential equations. A model of a mathematical concept called a bifurcation is investigated and an animation of this mathematical event is produced. The second laboratory is intended to help researchers in the tomography field. A standard filtered back-projection algorithm for reconstructing images from their projections is implemented. In the final section of the thesis an indication of how the tomography laboratory could be used is presented. Wavelet theory is used to construct a new filter that could be used in filtered back-projection tomography.
A real time, system independent, secure, Internet based auctioning system.
(2000) Brown, Cuan.; Murrell, Hugh Crozier.; Swart, Hendrika Cornelia Scott.
This thesis outlines the creation of a secure, real time, system independent, Internet based auctioning application. The system has been developed to meet the needs of today's stringent reqUirements on secure Internet based applications. To attain this goal, the latest cryptographic algorithms and development platforms have been used. The result is a JAVA based server and client auctioning application. The client application is designed to run In any common web browser, and the server to execute on any JAVA enabled operating system with a web server and Internet connection. The real time system uses a relatively secure hybrid cryptosystem for communication. This involves the use of RSA for secure key exchange, and RC6 and MARS for secure communication.
Relieving the cognitive load of constructing molecular biological ontology based queries by means of visual aids.
(2007) O'Neill, Kieran.; Murrell, Hugh Crozier.; Jacobson, Daniel.; Garcia-Castro, Alexander.
The domain of molecular biology is complex and vast. Bio-ontologies and information visualisation have arisen in recent years as means to assist biologists in making sense of this information. Ontologies can enable the construction of conceptual queries, but existing systems to do this are too technical for most biologists. OntoDas, the software developed as part of this thesis work, demonstrates how the application of techniques from information visualisation and human computer interaction can result in software which enables biologists to construct conceptual queries.