Journal of Telecommunications and Information Technology, 2012, nr 3

kwartalni

New Statistical Algorithms for the Analysis of Mass Spectrometry Time-Of-Flight Mass Data with Applications in Clinical Diagnostics

Mass spectrometry (MS) based techniques have emerged as a standard forlarge-scale protein analysis. The ongoing progress in terms of more sensitive machines and improved data analysis algorithms led to a constant expansion of its fields of applications. Recently, MS was introduced into clinical proteomics with the prospect of early disease detection using proteomic pattern matching. Analyzing biological samples (e.g. blood) by mass spectrometry generates mass spectra that represent the components (molecules) contained in a sample as masses and their respective relative concentrations. In this work, we are interested in those components that are constant within a group of individuals but differ much between individuals of two distinct groups. These distinguishing components that dependent on a particular medical condition are generally called biomarkers. Since not all biomarkers found by the algorithms are of equal (discriminating) quality we are only interested in a small biomarker subset that - as a combination - can be used as a fingerprint for a disease. Once a fingerprint for a particular disease (or medical condition) is identified, it can be used in clinical diagnostics to classify unknown spectra. In this thesis we have developed new algorithms for automatic extraction of disease specific fingerprints from mass spectrometry data. Special emphasis has been put on designing highly sensitive methods with respect to signal detection. Thanks to our statistically based approach our methods are able to detect signals even below the noise level inherent in data acquired by common MS machines, such as hormones. To provide access to these new classes of algorithms to collaborating groups we have created a web-based analysis platform that provides all necessary interfaces for data transfer, data analysis and result inspection. To prove the platform's practical relevance it has been utilized in several clinical studies two of which are presented in this thesis. In these studies it could be shown that our platform is superior to commercial systems with respect to fingerprint identification. As an outcome of these studies several fingerprints for different cancer types (bladder, kidney, testicle, pancreas, colon and thyroid) have been detected and validated. The clinical partners in fact emphasize that these results would be impossible with a less sensitive analysis tool (such as the currently available systems). In addition to the issue of reliably finding and handling signals in noise we faced the problem to handle very large amounts of data, since an average dataset of an individual is about 2.5 Gigabytes in size and we have data of hundreds to thousands of persons. To cope with these large datasets, we developed a new framework for a heterogeneous (quasi) ad-hoc Grid - an infrastructure that allows to integrate thousands of computing resources (e.g. Desktop Computers, Computing Clusters or specialized hardware, such as IBM's Cell Processor in a Playstation 3)

Konzepte zur interaktiven Entwurfsraum-Exploration im Tragwerksentwurf

Der Entwurfsraum für den Entwurf eines Tragwerks ist ein n-dimensionaler Raum, der aus allen freien Parametern des Modells aufgespannt wird. Traditionell werden nur wenige Punkte dieses Raumes durch eine numerische (computergestützte) Simulation evaluiert, meist auf Basis der Finite-Elemente-Methode. Mehrere Faktoren führen dazu, dass heute oft viele Revisionen eines Simulationsmodells durchlaufen werden: Zum einen ergeben sich oft Planungsänderungen, zum anderen ist oft die Untersuchung von Planungsalternativen und die Suche nach einem Optimum wünschenswert. In dieser Arbeit soll für ein vorhandenes Finite-Elemente-Framework die sequentielle Datei-Eingabeschnittstelle durch eine Netzwerkschnittstelle ersetzt werden, die den Erfordernissen einer interaktiven Arbeitsweise entspricht. So erlaubt die hier konzipierte Schnittstelle interaktive, inkrementelle Modelländerungen sowie Status- und Berechnungsergebnis-Abfragen durch eine bidirektionale Schnittstelle. Die Kombination aus interaktiver numerischer Simulation und Interoperabilität durch die Anwendung von Konzepten zur Bauwerks-Informations-Modellierung im Tragwerksentwurf ist Ziel dieser Dissertation. Die Beschreibung der Konzeption und prototypischen Umsetzung ist Gegenstand der schriftlichen Arbeit

On-demand distributed image processing over an adaptive Campus-Grid

This thesis explores how scientific applications, which are based upon short jobs (seconds and minutes) can capitalize upon the idle workstations of a Campus-Grid. These resources are donated on a voluntary basis, and consequently, the Campus-Grid is constantly adapting and the availability of workstations changes. Typically, to utilize these resources a Condor system or equivalent would be used. However, such systems are designed with different trade-offs and incentives in mind and therefore do not provide intrinsic support for short jobs. The motivation for creating a provisioning scenario for short jobs is that Image Processing, as well as other areas of scientific analysis, are typically composed of short running jobs, but still require parallel solutions. Much of the literature in this area comments on the challenges of performing such analysis efficiently and effectively even when dedicated resources are in use. The main challenges are: latency and scheduling penalties, granularity and the potential for very short jobs. A volunteer Grid retains these challenges but also adds further challenges. These can be summarized as: unpredictable re source availability and longevity, multiple machine owners and administrators who directly affect the operating environment. Ultimately, this creates the requirement for well conceived and effective fault management strategies. However, these are typically not in place to enable transparent fault-free job administration for the user. This research demonstrates that these challenges are answerable, and that in doing so opportunistically sourced Campus-Grid resources can host disparate applications constituted of short running jobs, of as little as one second in length. This is demonstrated by the significant improvements in performance when the system presented here was compared to a well established Condor system. Here, improvements are increased job efficiency from 60–70% to 95%–100%, up to a 99% reduction in application makespan and up to a 13000% increase in the efficiency of resource utilization. The Condor pool in use is approximately 1,600 workstations distributed across 27 administrative domains of Cardiff University. The application domain of this research is Matlab-based image processing, and the application area used to demonstrate the approach is the analysis of Magnetic Resonance Imagery (MRI). However, the presented approach is generalizable to any application domain with similar characteristics

Evolving an efficient and effective off-the-shelf computing infrastructure for schools in rural areas of South Africa

Upliftment of rural areas and poverty alleviation are priorities for development in South Africa. Information and knowledge are key strategic resources for social and economic development and ICTs act as tools to support them, enabling innovative and more cost effective approaches. In order for ICT interventions to be possible, infrastructure has to be deployed. For the deployment to be effective and sustainable, the local community needs to be involved in shaping and supporting it. This study describes the technical work done in the Siyakhula Living Lab (SLL), a long-term ICT4D experiment in the Mbashe Municipality, with a focus on the deployment of ICT infrastructure in schools, for teaching and learning but also for use by the communities surrounding the schools. As a result of this work, computing infrastructure was deployed, in various phases, in 17 schools in the area and a “broadband island” connecting them was created. The dissertation reports on the initial deployment phases, discussing theoretical underpinnings and policies for using technology in education as well various computing and networking technologies and associated policies available and appropriate for use in rural South African schools. This information forms the backdrop of a survey conducted with teachers from six schools in the SLL, together with experimental work towards the provision of an evolved, efficient and effective off-the-shelf computing infrastructure in selected schools, in order to attempt to address the shortcomings of the computing infrastructure deployed initially in the SLL. The result of the study is the proposal of an evolved computing infrastructure model for use in rural South African schools

XXIII Congreso Argentino de Ciencias de la Computación - CACIC 2017 : Libro de actas

Trabajos presentados en el XXIII Congreso Argentino de Ciencias de la Computación (CACIC), celebrado en la ciudad de La Plata los días 9 al 13 de octubre de 2017, organizado por la Red de Universidades con Carreras en Informática (RedUNCI) y la Facultad de Informática de la Universidad Nacional de La Plata (UNLP).Red de Universidades con Carreras en Informática (RedUNCI