Sowohl in der Klinischen Labormedizin, der Klinischen Mikrobiologie als auch in der Pathologie ist die Massenspektrometrie (MS) ein bedeutender Bestandteil der Diagnostik geworden. Der Fortschritt in der Gerätetechnik ermöglicht in kurzer Zeit viele, hochaufgelöste Spektren zu generieren. Diese Informationsvielfalt macht die manuelle Auswertung durch den Anwender sehr kompliziert bis unmöglich. Aus diesem Grund ist die Unterstützung durch bioinformatische Programme notwendig. Für die Reproduzierbarkeit der Ergebnisse und die Qualitätskontrolle ist es essentiell, dass die verwendeten Algorithmen transparent und die Programme als Open Source Software (OSS) frei verfügbar sind (Aebersold and Mann, 2003). Das Ziel dieser Arbeit war die Entwicklung von MALDIquant, einer unter der GNU General Public License (GPL) stehenden, flexiblen OSS, die für die o.g. Anwendungsbereiche modernste Algorithmen für die komplette Analyse bietet und in der freien Programmiersprache R (R Core Team, 2014) geschrieben ist. Im Zusammenspiel mit dem dazugehörigen Paket MALDIquantForeign ist MALDIquant in der Lage die üblichen Dateiformate der verschiedenen MS-Geräte zu verarbeiten. Dadurch ist MALDIquant hersteller- und geräteunabhängig und eignet sich nicht nur für MALDI/TOF, sondern für alle zweidimensionalen MS-Daten. Angefangen vom Datenimport über die Prozessierung bis hin zur Analyse der Spektren bietet MALDIquant eine komplette Analyse-Pipeline und implementiert state-of-the-art Methoden. Neben weit verbreiteten Verfahren zur Baseline Correction und Peak Detection zeichnet sich MALDIquant besonders durch ein hervorragendes Peak Alignment aus. Dieses ist sehr genau und aufgrund des Fokus auf die Peaks schneller als die meisten anderen Verfahren und weitestgehend unabhängig von der Qualität der Intensitätenkalibrierung. Eine weitere Stärke von MALDIquant ist die Möglichkeit, eigene Algorithmen zu integrieren, sowie den Ablauf der Analyse den individuellen Bedürfnissen anzupassen. In der beispielhaften Analyse der Daten von Fiedler et al. (2009) konnten durch MALDIquant Peaks gefunden werden, die Patienten mit Pankreaskarzinom von nicht erkrankten Probanden unterscheiden. Einige dieser Peaks wurden bereits in anderen Publikationen beschrieben. Neben diesem Beispiel hat MALDIquant seine Nützlichkeit bereits in verschiedenen Anwendungsbereichen und Publikationen bewiesen, wie etwa in Ouedraogo et al. (2013) oder Jung et al. (2014).

South Africa has shown an increased interest and awareness of Open Source Software (OSS) in the past decade. One of the reasons for this was the support from the Shuttleworth Foundation for Open Source initiatives. Migrating to OSS is a difficult and time consuming activity that should not be underestimated by the migration team. Careful planning and roll-out procedures should be in place before one commence on this journey. Process reference models are used in different fields to capture the generic process flow of activities. For the OSS domain, no process reference models could be found for migration purposes. Therefore, this study has as aim the suggestion of an initial set of process reference models for an organisational OSS migration. These process reference models were identified by capturing the process models for a case study that entailed the migration of the CSIR software systems and desktops from proprietary to OSS. From this set of process models, the migration processes were identified and refined to a set of suggested process reference models for organisational OSS migrations. This set of process reference models are useful to determine the processes necessary for organisations considering migrating to OSS. The study is divided into four research questions, where the first focusses on use and value of process reference models and the second on what is already known about OSS migration processes. The third deals with key processes within an organisational open source migration (OOSM) and the last with process reference models for an OOSM. For the first research question, the use and value of process reference models and the usefulness of utilising process reference models is discussed as well as using process models as a modelling tool to identify and capture processes. For the second research question, a summary is provided of what we know about OSS migration processes and a description about what the researcher and others have learnt about OSS, OSS migrations, process reference models, the process and its structure. For the third research question, the key processes within an OOSM is discussed as well as all the processes that took place during the OSS migration project from basic administrative processes to complex processes, from the beginning of the project until its completion. Lastly, for the fourth research question, process reference models that are essential for an OOSM and possible generic migration process models bound to reoccur are identified by the researcher and validated using a focus group discussion. / M.Tech. (Information Technology)

Open source is growing outside the boundaries of hackers, amateurs and software development, creating a humongous potential in many different areas and aspects of society. The intrinsic and extrinsic motivations that drives open source have been in the subject of much research recently, but how they affect each other when paid and unpaid contributors come together is still hidden in obscurity. In this study I investigate how intrinsic and extrinsic motivation correlates with each other and how those correlations affect paid and unpaid open source software contributors. The literature synthesis is based on of systematic reviews through searches in library databases, identification of articles by searching on the Internet and by reading relevant books. My results indicate that intrinsic and extrinsic motivations continuously affect each other and that paid contributors are more vulnerable since their extrinsic motivation in terms of money is reached only when many other motivations are fulfilled. The paid contributor’s lower autonomy may result in a decrease in intrinsic motivation while social interaction may result in an increase of the same. The unpaid contributors are more likely to be intrinsically motivated than the paid contributors, resulting in higher psychological satisfaction, less stress, creativity and input of higher work effort among unpaid contributors.

The rapidly evolving technologies in the automotive industry have been defining new challenges, setting new goals and consenting to more complex systems. This steered the AUTOSAR community toward the independent development of the AUTOSAR Adaptive Platform with the intention of addressing and serving the demands defined by the new technology drivers. The use of an already existing software based on an open-source development - specifically GNU/Linux - was recognized as a matching candidate fulfilling the requirements defined by AUTOSAR Adaptive Platform as its operating system. However, this raises new challenges in addressing the safety aspect and the suitability of its implementation in safety-critical environments. As safety standards do not explicitly handle the use of open-source software development, this thesis proposes a tailoring procedure that aims to match the requirements defined by ISO 26262 for a possible qualification of GNU/Linux. And while very little is known about the behavior specification of GNU/Linux to appropriate its use in safety-critical environments, the outlined methodology seeks to verify the specification requirements of GNU/Linux leveraging its claimed compliance to the POSIX standard. In order to further use GNU/Linux with high pedigree of certainty in safety-critical applications, a software partitioning mechanism is implemented to provide control over the resource consumption of the operating system –specifically computation time and memory usage- between different criticality applications in order to achieve Freedom from Interference. The implementation demonstrates the ability to avoid interference concerning required resources of safety-critical applications.

ITC/USA 2009 Conference Proceedings / The Forty-Fifth Annual International Telemetering Conference and Technical Exhibition / October 26-29, 2009 / Riviera Hotel & Convention Center, Las Vegas, Nevada / Following-up on an ITC 2006 paper, "From RF to bits with Synthetic Beamforming", we follow the development and fielding of a Digital Beamforming (DBF) Antenna. This antenna, built for an airborne Telemetry application, supports 10 individual polarization-diverse beams and immediately converts RF to IF at the antenna element through a suite of LNBs. The IF is then digitized and all subsequent processing is performed through an array of 200+ FPGAs, including DBF, optimal combining, demodulation, and IF upconversion. We present our Model-Based Design approach, which allowed us to develop and test the system incrementally and rapidly, particularly during the transition from factory testing to flight operations, where several unexpected problems were discovered. Our software tool set enabled us to dissect the System behavior via post-mission replay, and our detailed simulations were instrumental in developing mitigation quickly. The System-level impacts and root causes of some of these issues are also discussed. We believe the flexibility of DBF and the modular software architecture were key in quickly mitigating many of these unforeseen real-world issues without hardware modification.

BACKGROUND: Some of the current software tools for comparative metagenomics provide ecologists with the ability to investigate and explore bacterial communities using α- & β-diversity. Feature subset selection - a sub-field of machine learning - can also provide a unique insight into the differences between metagenomic or 16S phenotypes. In particular, feature subset selection methods can obtain the operational taxonomic units (OTUs), or functional features, that have a high-level of influence on the condition being studied. For example, in a previous study we have used information-theoretic feature selection to understand the differences between protein family abundances that best discriminate between age groups in the human gut microbiome. RESULTS: We have developed a new Python command line tool, which is compatible with the widely adopted BIOM format, for microbial ecologists that implements information-theoretic subset selection methods for biological data formats. We demonstrate the software tools capabilities on publicly available datasets. CONCLUSIONS: We have made the software implementation of Fizzy available to the public under the GNU GPL license. The standalone implementation can be found at http://github.com/EESI/Fizzy.

International Telemetering Conference Proceedings / October 23-26, 2000 / Town & Country Hotel and Conference Center, San Diego, California / Since its debut, the Linux operating system has garnered much attention in the software development community. This paper discusses the open source operating system, Linux, and it’s application as the operating system powering a commercial off-the-shelf telemetry processing system. The paper begins by discussing what are the real-time requirements of the operating system in a telemetry processing system. A discussion to the Linux system is then presented. Soft real-time features of Linux are discussed which allow it to meet the telemetry processing requirements. Linux is compared with the more traditional operating system products and points are made as to why open source software is just as capable, if not preferable, of handling mission critical applications. The paper also presents the authors’ view of future of Linux and open source software in the telemetry marketplace. The paper concludes with a summary of products available for Linux that support telemetry processing and the data acquisition environment.

Inheritance is a salient feature of Object-Oriented (OO) paradigm which facilitates reuse and improves system comprehensibility in OO systems. The overall aim of inheritance is to model classes in a structured hierarchy where classes residing lower in the hierarchy (subclasses) can inherit the pre-existing functionality in the classes located higher up (superclasses) in the same line of hierarchy. Software maintenance and evolution are the process of making any modifications to a software system and upgrading its dynamic behaviour. In this Thesis, we empirically investigate the trends of evolution of eight Java Open-Source Systems (OSS) from an inheritance perspective and model the propensity for changes of inheritance in those systems. The systems used as testbed in this Thesis represent a variety of application domains with varying sizes and amount of inheritance employed. There are several levels of granularity for inheritance evolution that may manifest a particular trend. This starts from the highest level (package) to lower class, method an attribute levels; and each level may show a different and yet an important pattern of evolution. We empirically investigate the changes of inheritance in the form of increases (additions) and decreases (deletions) in number of classes, methods and attributes. Our analysis also includes the movement of classes within and across an inheritance hierarchy which is another compelling facet of evolution of inheritance and may not be extrapolated through incremental changes only. It requires a finer-grained scrutiny of evolutionary traits of inheritance. In addition, the Thesis also explores the trends of class interaction within and across an inheritance hierarchy and problems embedded in a system that may lead to faults, from an inheritance perspective. The results demonstrate how inheritance is used in practice, problems associated with inheritance and how inheritance hierarchies evolve as opposed to that of a ‘system’. Overall results informed our understanding of the trends in changes of inheritance in the evolution of Java systems.

This research provides a detailed account of Open Source Software (OSS) development in the context of developing countries (DCs) by exploring the specific case of Chinese indigenous Linux design and development. It builds an interdisciplinary, socio-technical, analytical framework from the perspective of science and technology studies (STS), in particular the social shaping of technology (SST), infrastructural studies and international technology transfer. It also covers the fields of economic analysis, policy studies and development studies. The research investigates the adaptation process of a unique OSS with infrastructural features – Linux in the context of China by conducting case studies on both embedded Linux and platform Linux products developed by two Chinese Linux providers. Drawing upon the concepts developed in the SST perspective and infrastructural studies, this research addresses both the dynamism and continuity of OSS. In order to avoid the shortcomings of existing social scientific study on OSS, we applied social and biography of artefacts (BoA) approaches to examine the evolution of Chinese Linux by mapping out the key actors, investigating the linkages between them, and probing deeply into the intricate interplays among these actors over time. A detailed longitudinal and contextual analysis has been undertaken through a qualitative historical case study of the evolution of both Chinese embedded Linux and platform Linux from 1998-2008. The empirical data reveals that the local adaptation and further innovation of Chinese Linux is a ‘generification’ process, i.e. a process of design and developing generic Linux solutions for diverse local users. Theoretically, the understanding of the socio-technical interfaces of the software (seeking, identifying, categorising local users/intermediaries, as well as collaborating with key players associated with the particular software) are central elements for software technology transfer and local technological capabilities building. The findings also throw the light on the crucial importance of government role in providing incentives and institutional measures for Linux adaptation in China. In particular, it highlights the challenges concerning the socio-technical specificities of infrastructural software, like Linux OS (operating system) and the particular relevance to DCs as technology adapters. Finally, this study throws light on the policy and practice for China’s future Linux development, and the implications for other DCs.

Releasing software is challenging. To decide when to release software, developers may consider a deadline, a set of features or quality attributes. Yet, there are many stories of software that is not released on time. In large-scale software development, release management requires significant communication and coordination. It is particularly challenging in Free and Open Source Software (FOSS) ecosystems, in which hundreds of loosely connected developers and their projects are coordinated for releasing software according to a schedule. In this work, we investigate the release management process in two large-scale FOSS development projects. In particular, our focus is the communication in the whole release management process in each ecosystem across multiple releases. The main research questions addressed in this dissertation are: (1) How do developers in these FOSS ecosystems communicate and coordinate to build and release a common product based on different projects? (2) What are the release management tasks in a FOSS ecosystem? and (3) What are the challenges that release managers face in a FOSS ecosystem? To understand this process and its challenges better, we used a multiple case study methodology, and colleced evidence from a combination of the following sources: documents, archival records, interviews, direct observation, participant observation, and physical artifacts. We conducted the case studies on two FLOSS software ecosystems: GNOME and OpenStack. We analyzed over two and half years of communication in each ecosystem and studied developers’ interactions. GNOME is a collection of libraries, system services, and end-user applications; together, these projects provide a unified desktop —the GNOME desktop. OpenStack is a collection of software tools for building and managing cloud computing platforms for public and private clouds. We catalogued communication channels, categorized coordination activities in one channel, and triangulated our results by interviewing key developers identified through social network analysis. We found factors that impact the release process in a software ecosystem, including a release schedule positively, influence instead of direct control, and diversity. The release schedule drives most of the communication within an ecosystem. To achieve a concerted release, a Release Team helps developers reach technical consensus through influence rather than direct control. The diverse composition of the Release Team might increase its reach and influence in the ecosystem. Our results can help organizations build better large-scale teams and show that software engineering research focused on individual projects might miss important parts of the picture. The contributions of this dissertation are: (1) an empirical study of release management in two FOSS ecosystems (2) a set of lessons learned from the case studies, and (3) a theory of release management in FOSS ecosystems. We summarize our theory that explains our understanding of release management in FOSS ecosystems as three statements: (1) the size and complexity of the integrated product is constrained by the release managers capacity, (2) release management should be capable of reaching the whole ecosystem, and (3) the release managers need social and technical skills. The dissertation discusses this theory in the light of the case studies, other research efforts, and its implications. / Graduate / 0984 / gpoo+proquest@calcifer.org