Construction of a global map of human gene expression : the process, tools and analysis

This thesis studies human gene expression space using high throughput gene expression data from DNA microarrays. In molecular biology, high throughput techniques allow numerical measurements of expression of tens of thousands of genes simultaneously. In a single study, this data is traditionally obtained from a limited number of sample types with a small number of replicates. For organism-wide analysis, this data has been largely unavailable and the global structure of human transcriptome has remained unknown. This thesis introduces a human transcriptome map of different biological entities and analysis of its general structure. The map is constructed from gene expression data from the two largest public microarray data repositories, GEO and ArrayExpress. The creation of this map contributed to the development of ArrayExpress by identifying and retrofitting the previously unusable and missing data and by improving the access to its data. It also contributed to creation of several new tools for microarray data manipulation and establishment of data exchange between GEO and ArrayExpress. The data integration for the global map required creation of a new large ontology of human cell types, disease states, organism parts and cell lines. The ontology was used in a new text mining and decision tree based method for automatic conversion of human readable free text microarray data annotations into categorised format. The data comparability and minimisation of the systematic measurement errors that are characteristic to each lab- oratory in this large cross-laboratories integrated dataset, was ensured by computation of a range of microarray data quality metrics and exclusion of incomparable data. The structure of a global map of human gene expression was then explored by principal component analysis and hierarchical clustering using heuristics and help from another purpose built sample ontology. A preface and motivation to the construction and analysis of a global map of human gene expression is given by analysis of two microarray datasets of human malignant melanoma. The analysis of these sets incorporate indirect comparison of statistical methods for finding differentially expressed genes and point to the need to study gene expression on a global level.

Measuring and tracking quality factors in Free and Open Source Software projects

Free and Open Source Software (FOSS) has gained increased interest in the computer software industry, but assessing its quality remains a challenge. FOSS development is frequently carried out by globally distributed development teams, and all stages of development are publicly visible. Several product and process-level quality factors can be measured using the public data. This thesis presents a theoretical background for software quality and metrics and their application in a FOSS environment. Information available from FOSS projects in three information spaces are presented, and a quality model suitable for use in a FOSS context is constructed. The model includes both process and product quality metrics, and takes into account the tools and working methods commonly used in FOSS projects. A subset of the constructed quality model is applied to three FOSS projects, highlighting both theoretical and practical concerns in implementing automatic metric collection and analysis. The experiment shows that useful quality information can be extracted from the vast amount of data available. In particular, projects vary in their growth rate, complexity, modularity and team structure.

Free/Open Source Software Development : Results and Research Methods

Free and open source software development is an alternative to traditional software engineering as an approach to the development of complex software systems. It is a way of developing software based on geographically distributed teams of volunteers without apparent central plan or traditional mechanisms of coordination. The purpose of this thesis is to summarize the current knowledge about free and open source software development and explore the ways on which further understanding on it could be gained. The results of research on the field as well as the research methods are introduced and discussed. Also adapting software process metrics to the context of free and open source software development is illustrated and the possibilities to utilize them as tools to validate other research are discussed.

Kuviteltu aatelismies : Aateluus viholliskuvana ja itseymmärryksenä 1800-luvun Suomessa

An imagined nobleman Nobility as an enemy image and in-group identity in nineteenth-century Finland The focal point of this study is the difficult relationship between two seemingly very different 19th-century elite groups, the upwardly mobile bourgeois intelligentsia and the slowly declining traditional nobility. In the thinking of the bourgeois contender the two emerged as exact opposites, styled as conflicting ideal types: an outdated, exclusive, degenerate hereditary aristocracy versus a dynamic and progressive new force in society, recruited solely on the basis of personal merit, originating from the common people and representing the nation. The appearance of an important 19th-century novelty, print publicity, coincided with the emergence of the bourgeois intelligentsia. The institutions of the developing publishing industry were manned by the aspiring new group. The strengthening flow of progressive, democratic, nationalist ideas distributed via the printing presses carried an undercurrent of self-promotion. It transmitted to the developing readership the self-image of the new cultural bourgeoisie as the defender and benevolent educator of the nation. Having won the contest over the media, the intelligentsia was free to present its predecessor and rival as an enemy of the people. In its politics the nobility emerged as an ideal scapegoat, represented as the source for existing social evils, all if which would promptly go away after its disappearance. It also served as a black backcloth, against which the democratic, national, progressive bourgeois intelligentsia would shine more brightly. In order to shed light on the 19th-century process of (re)modelling the image of nobility as a public enemy I have used four different types of source materials. These include three genres of print publicity, ranging from popular historical and contemporary fiction to nonfictional presentations of national history and the news and political commentaries of the daily papers, complemented by another, originally oral type of publicity, the discussion protocols of the Finnish four-estate parliament. To counterpoint these I also analysed the public self-image of the nobility, particularly vis-à-vis the nationalist and democratic ethos of the modernising politics.