Microarrays are now an established tool for biological research and have a wide range of applications. In this thesis I investigate the BeadArray microarray technology developed by Illumina. The design of this technology is unique and gives rise to many computational and statistical challenges. However, I show how knowledge from other microarray technologies can be used to our advantage. I describe the beadarray software package, which is now used by researchers around the world. The development of this software was motivated by the fact that Illumina's software (BeadStudio) gives a summarised view of Illumina data and does not gives users any control over several processing steps that were found to be crucial for other microarray technologies. A main feature of beadarray is the ability to access raw data. The advantages of such data include the ability to perform more detailed quality assessment and greater control over the analysis at all stages. The analysis of a control experiment shows that the processing steps used in BeadStudio can be improved. In particular, utilising variances calculated from the raw data can increase the ability to detect genes which have different expression levels between samples, a common goal for microarray studies. The data from the control experiment are made available for other researchers to use and validate their own analysis methods. One issue discovered during the analysis of the control experiment was that only half of the intended genes could be reliably measured due to problems in the design of the probes targetting particular genes. By considering a large set of publicly available Illumina arrays, I show how such unreliable measurements can affect the analysis of Illumina data. I also show how potential problems can be identified in advance of an experiment and incorporated into an analysis pipeline.

Libraries share a number of core values with the Open Source Software (OSS) movement, suggesting there should be a natural tendency toward library participation in OSS projects. However, Dale Askey's 2008 Code4Lib column entitled We Love Open Source Software. No, You Can't Have Our Code, claims that while libraries are strong proponents of OSS, they are unlikely to actually contribute to OSS projects. He identifies, but does not empirically substantiate, six barriers that he believes contribute to this apparent inconsistency. The goal of this thesis is to empirically investigate not only Askey's central claim but also the six barriers he proposes. Additionally, we will utilize statistical methods and machine learning algorithms to identify barriers encountered by libraries as they grapple with whether or not to release their code as open source. We will offer insights into possible correlations between a library's engineering, talent management and innovation policies and practices and its propensity to initiate open source software projects.

Open source software is becoming a credible and realistic alternative to proprietary software in municipalities. The aim of this thesis is to explore the strategies and logical issues that inspire and motivate municipalities to migrate into or integrate use of open source software. The research approach used in the study is an explorative, comparative case study performed in the three Swedish municipalities of Falköping, Alingsås and Kungälv, which considers implementation and use of OpenOffice in administration. The methodologies used in the case study were in-depth interviews with Chief Information Officers in the municipalities and document analysis. The interviews were combined with the tool of SWOTanalysis to further focus on the reasons for choosing OpenOffice as an application program. There is certainly not a unique strategy to migrate into or integrate use of Free/Open Source Software. Since each municipality is autonomous in the process of decision-making, various strategic planning or guidelines are use in different municipalities. In the municipalities of Alingsås and Kungälv the strategic planning is used for leading the processes of implementation of new software applications. However, in Falköping municipality, the procedures are guided by a set of guidelines. The lower Total Cost of Ownership and the Free/Open Source Software’s freedoms besides many other advantages, make the municipalities stimulated to migrate into use of OpenOffice suite. In contrast, there are some drawbacks and barriers, such as shortage of internal and external standardization and lack of user knowledge and familiarity, which demotivate the municipalities to take this decision. To lower costs of IT administration seems to be the most significant factor in motivating municipalities to migrate into use of OpenOffice. More research is needed in order to find out the consequences of implementation of OpenOffice in municipalities as well as to investigate if Total Cost of Ownership really is decreased by the use of Open Office.

Using design patterns is a widely accepted method to improve software development. There are many benefits of the application of patterns claimed in the literature. The most cited claim is that design patterns can provide a common design vocabulary and therefore improve greatly communication between software designers. Most of the claims are supported by experiences reports of practitioners, but there is a lack of quantitative research concerning the actual application of design patterns and about the realization of the claimed benefits. In this paper we analyze the development process of over 1000 open source software projects using version control information. We explore this information to gain an insight into the differences of software development with and without design patters. (author's abstract) / Series: Working Papers on Information Systems, Information Business and Operations

Thesis (M.S.)--Mississippi State University. Department of Computer Science and Engineering. / Title from title screen. Includes bibliographical references.

Thesis (Ph. D.)--University of California, San Diego, 2003. / Vita. Includes bibliographical references (leaves 227-238).

This thesis investigates the following research questions: (1) What is open source project governance and how can it be conceptualized? (2) What is the relationship between the dimensions of OSS governance and the specific purposes that governance is hypothesized to serve in open source projects? (3) How do the major configurations of governance dimensions affect the performance of open source projects? Two studies were conducted to answer these questions: an exploratory qualitative study and a survey study. In the qualitative study, we clearly defined, developed, and validated the various dimensions of OSS governance. This allowed for the identification of a limited number of configurations of governance dimensions that most frequently occur in open source projects. We found that a patterning in governance dimensions takes place because dimensions are in fact interdependent. Therefore, only a fraction of the theoretically conceivable configurations of governance dimensions appear to be viable and were observed among a range of open source projects. This provided us with a preliminary understanding of how these dimensions configure to create three distinct configurations of project governance which were labeled as follows: Open Communities, Managed Communities, and Defined Communities. In the quantitative survey, we first validated these configurations of governance using cluster analysis and then tested the relationships between these configurations (clusters) and the specific purposes that governance is hypothesized to serve in open source projects, namely solve collective action dilemmas, solve coordination problems, and create a climate for project excellence, while assessing their influence on the performance of projects. The results confirmed the presence of three main governance configurations (clusters) and also showed that open source projects that adopt a Defined Community approach to governance were the most successful. In these types of projects, the combination of a tightly managed software development process with a decentralized community management structure was found to create a balance between anarchy and control that allows these projects to benefit from one of the virtues of open source development, the open contribution and participation of a wide variety of talented developers, while avoiding the pitfalls of an uncontrolled and scattered development process. / Thesis (Ph.D, Management) -- Queen's University, 2012-04-11 16:00:02.186

Thesis (M.S.)--Oregon State University, 2008. / Printout. Includes bibliographical references (leaves 82-84). Also available on the World Wide Web.

Thesis (M.S.)--Northwest Missouri State University, 2006. / The full text of the thesis is included in the pdf file. Title from title screen of full text.pdf file (viewed on January 25, 2008) Includes bibliographical references.

Univ., Diss.--Freiburg (Breisgau), 2007.