The growing sophistication of version control systems, a class of tools employed in tracking and managing changes to documents, has had a transformative impact on the practice of programming. In recent years great strides have been made to improve these systems, but certain stubborn difficulties remain. For example, merging of concurrently introduced changes continues to be a labour-intensive and error-prone process. This thesis examines these difficulties by way of a critique of the conceptual framework underlying modern version control systems, arguing that many of their shortcomings are related to certain long-standing, open problems around identity. The research presented here casts light on how the challenges faced by users and designers of version control systems can be understood in those terms, ultimately arguing that future progress may benefit from a better understanding of the role of identity, representation, reference, and meaning in these systems and in computing in general.

Målet med min rapport har varit att undersöka de svårigheter och problem som utvecklare på Barnebys kan ställas inför under sitt dagliga arbete. För att begränsa mig har jag valt två stora områden att undersöka, det agila arbetssättet och versions hanteringssystem. Men det viktigaste fokuset i rapporten är vilka problem som uppstår som är relaterade att man jobbar flera utvecklare på samma projekt. Så kallade teams. Rapporten avhandlar en teoretisk bakgrund till de båda ämnena och sedan så genomför jag en undersökning bland de anställda på Barnebys teknikavdelning. Undersökningen görs medhjälp av Google Forms och här finns frågor kring dessa ämnen. Rapporten tar också upp förslag på lösningar och/eller förbättringar. Rapporten avslutas med en presentation av resultatet och egna reflektioner.

År 2015 ska alla avrinningsområden i EU-länderna vara fastställda. Anledningen till detta är att år 2000 trädde ett vattendirektiv i kraft. Syftet med direktivet är att skapa en helhetssyn för vattenresurserna i Europa och för att få en enhetlig och övergripande lagstiftning. I Sverige har SMHI redan bestämt vattendelare och avrinningsområden för ett stort antal områden i landet, men i och med direktivet har det blivit ett krav. En helhetssyn på vattenresurser tillsammans med kunskaper om geologi är en förutsättning för en hållbar utveckling och ett effektivt tillvaratagande av naturresurserna. Inom samhällsplaneringen spelar geologin en tämligen betydande roll. Vid exempelvis planering av nya bostadsområden är det av stor vikt att veta markens egenskaper. Syftet med detta examensarbete var att fastställa Kungsbäckens avrinningsområde samt att göra en geomorfologisk undersökning av området. Arbetet syftade även till att redogöra för några fluvialmorfologiska förekomster kring del av Kungsbäcken - från utloppet vid Gavleån vid Stora Vall till viadukten vid Regementsvägen. Genom att utföra studien som en kombination av naturgeografi och GIT påvisas möjligheterna att utföra olika typer av analyser och beräkningar utifrån de naturresurser som finns i ett område och den moderna tekniken. Vidare kommer resultatet från denna studie att delges SMHI. De kan därmed få nytta av materialet när de, på uppdrag av Naturvårdsverket, skall utföra en kartläggning av Kungsbäckens avrinningsområde. För att möjliggöra en geomorfologisk kartläggning av Kungsbäckens avrinningsområde och fastställa dess gränser studerades initialt tillgängligt material såsom tidigare studier, litteratur, terrängkarta, jord- och bergartskartor samt flygfotografier. Vid genomförandet av fastställningen av områdets gränser nyttjades bland annat SMHI:s tidigare gjorda gränser, en av oss gjord analog analys, utifrån tryckta terrängkartan 13H SV samt en flödesmodellering av en i studien gjord höjdmodell över området. Därefter gjordes fältstudier till tre stycken områden med osäkra områdesgränser, vilka framkom av ovan nämnda analyser. Med hjälp av flödesriktningsinstrument och okulär besiktning kunde gränserna då fastställas. Även fältstudier av geomorfologiskt intresse har utförts, såsom studie av ändmoräner och hällar. Med hjälp av genomförda fältstudier, analyser, digitalisering och litteraturgranskning har gränserna för Kungsbäckens avrinningsområde bestämts samt beräknats till en area av 105,4 km2. Områdets geomorfologiska kartläggning har resulterat i en karta där de olika förekomsterna finns redovisade (se bilaga 1, karta i A3-format). Förutom detta finns olika begrepp och naturfenomen beskrivna i rapporten samt nyttan med denna typ av studie. / In year 2000, the EU Water Framework Directive was adopted and by 2015, all European watersheds have to be established. The purpose with the directive is to create an overall view over the water resources in Europe and to get a comprehensive legislation. SMHI in Sweden has already established a few watersheds around the country. An overall view of the water resources together with knowledge of the geology is a requirement to a sustainable development and an effective taking care of the nature resources. Within the physical planning, the geology knowledge is very important. For example, it is vital to know the quality of the ground when planning new building complexes. The purpose with this bachelor thesis was to establish the watershed of Kungsbäcken and to do a geomorphologic survey of the area. The thesis also aimed to describe some of the fluvial morphologic presences, in a part of Kungsbäcken, i.e. from the outflow to Gavleån at Stora Vall, to the viaduct at Regementvägen. By doing the study as a combination of physical geography and GIT, the possibilities to do different types of analyses and calculations, on the basis of the nature resources in an area and the modern technique are pointed out. Furthermore, the result from this study will be given to SMHI. The result may be of benefit to SMHI, when mapping the watershed of Kungsbäcken later on. To make the geomorphologic survey of the watershed and to establish the boundaries of it, literature, earlier studies in the area, terrain- , rock, - soil maps and aerial photos were studied. Moreover, out of date-boundaries established by SMHI were used, together with an analogue analysis, based on the printed terrain map 13H SV. We also used a flow model, based on a digital elevation model over the area. The study also contained field trips. Three areas with uncertain boundaries were studied and with flow direction instruments and ocular examination, the boundaries were established. Field trips of geomorphologic interest were also made, like studies of recessional moraine and roch moutonnée. By field trips, analyses, digitizing and literature perusal, the boundaries of the watershed of Kungsbäcken has been established and the area is 105.4 km2. The result of the geomorphologic survey of the area can be seen in a map (appendix 1). Apart from that, concepts and nature phenomena are also described in the report along with observations of the benefits of studies like this one.

Many of us have encountered the discussion about which interface is better for working with Git, command-line or graphical. This thesis is an attempt to find out which user interface new Git users prefer for Git and what experienced Git users prefer. We aimed to find out if there’s anything significant which can be gained from using either of the interfaces in comparison to each other. Lastly we looked at what factors influences git users choice of user interface and how?. We have collected data through three interviews and a survey, which yielded approximately 370 responses. Based on our results we’ve found that the command-line interface is the more popular user interface, in general, amongst Git users. We’ve also found that most users stop using graphical user inter- faces, as their primary user interface, as they get more experience with Git. They usually change their primary user interface to a command- line interface or start using both the graphical user interface and the command-line interface together. The results from our study regard- ing why, is presented in this thesis.

In recent years, a new generation of distributed version control systems have taken the place of the aging centralized ones, with Git arguably being the most popular distributed system today. We investigate the potential of using Git commit history to predict files that are often changed together. Specifically, we look at the rename tracking heuristic found in Git, and the impact it has on prediction performance. By applying a data mining algorithm to five popular GitHub repositories we extract logical coupling – inter-file dependencies not necessarily detectable by static analysis – on which we base our change prediction. In addition, we examine if certain commits are better suited for change prediction than others; we define a bug fix commit as a commit that resolves one or more issues in the associated issue tracking system and compare their prediction performance. While our findings do not reveal any notable differences in prediction performance when disregarding rename information, they suggest that extracting coupling from, and predicting on, bug fix commits in particular could lead to predictions that are both more accurate and numerous. / De senaste åren har en ny generation av distribuerade versionshanteringssystem tagit plats där tidigare centraliserade sådana huserat. I spetsen för dessa nya system går ett system vid namn Git. Vi undersöker potentialen i att nyttja versionshistorik från Git i syftet att förutspå filer som ofta redigeras ihop. I synnerhet synar vi Gits heuristik för att detektera när en fil flyttats eller bytt namn, någonting som torde vara användbart för att bibehålla historiken för en sådan fil, och mäter dess inverkan på prediktionsprestandan. Genom att applicera en datautvinningsalgoritm på fem populära GitHubprojekt extraherar vi logisk koppling – beroenden mellan filer som inte nödvändigtvis är detekterbara medelst statisk analys – på vilken vi baserar vår prediktion. Därtill utreder vi huruvida vissa Gitcommits är bättre lämpade för prediktion än andra; vi definierar en buggfixcommit som en commit som löser en eller flera buggar i den tillhörande buggdatabasen, och jämför deras prediktionsprestanda. Medan våra resultat ej kan påvisa några större prestandamässiga skillnader när flytt- och namnbytesinformationen ignorerades, indikerar de att extrahera koppling från, och prediktera på, enbart bugfixcommits kan leda till förutsägelser som är både mer precisa och mångtaliga.

Estimates for 2017 indicate that 20% of cancers globally are gastrointestinal tract (GIT) cancers, with oesophageal cancer being the 8th most common cancer. Oesophageal squamous cell carcinoma (OSCC) occurs in the upper to mid oesophagus and is present at high incidence in developing countries including South Africa. There are no early symptoms, resulting in late diagnosis and poor prognosis. In this study, tumour and blood DNA was obtained from 35 OSCC patients and subjected to whole genome sequencing (WGS). Bioinformatics analysis pipelines were designed to identify the possibility of novel viral insertions, investigating Human Endogenous Retroviruses (HERV's) insertions alongside the presence of somatic mutations in patient samples. The aims being to identify integration of any foreign DNA, to investigate if there is any linkage between HERV insertion and somatic mutations, and to identify any somatic mutations of potential interest in the OSCC cohort. The novel virus investigations however, proved to be inconclusive and there appeared to be no link between HERV insertions and somatic mutations present in the patients. Very significantly, it was determined that numerous somatic mutations were present in the MUC3A gene of the patient cohort, an interesting observation as no such previous association with OSCC has been recorded. MUC3A is a membrane-bound glycoprotein component of mucous gels, and its aberrant expression has been correlated with invasion and metastasis in a variety of other cancers. However, due to the complexity of the particular gene sequence and the known inconsistencies of variant calling performed on complex data sets, these mutations should be viewed with extreme caution as they are likely to be false positives. Analysis of RNA-seq data showed a 4.6 log2 fold increase in MUC3A expression in the tumour samples of these OSCC patients, with a P-adjusted value of 7.05e-06, suggesting highly significant differential gene expression. Functional enrichment analysis further showed that MUC3A was significantly associated with one of the top 5 gene ontologies (extracellular matrix structural constituent) for molecular function ontology class together with a number of collagen (COL) and MMP genes known to play a role in oncogenic progression and membrane stiffness. GSEA and KEGG analysis indicated predominantly chemokine/cytokine pro-inflammatory enriched pathways. Immunohistochemistry staining showed 10 out of 13 of the samples had no detectable levels of MUC3A protein, suggesting that the production of a non-functional truncated protein may lead to the upregulation of MUC3A expression that could possibly play a role in downstream pro-oncogenic signalling.

Le travail en équipe est un des moyens pour développer les compétences transversales attendues dans l’industrie, en particulier dans le domaine informatique. Aussi, au cours d’une formation académique, c’est l’une des occasions où l’étudiant a l’opportunité de les développer. Cependant, la réussite d’un travail en équipe dépend entre autres du choix des outils facilitant le travail collaboratif, l’organisation, la collaboration et la gestion des conflits. La possibilité de pouvoir évaluer objectivement aussi bien le travail individuel que celui collaboratif des membres de l’équipe doit davantage faire partie de ce choix. Cette évaluation peut en l’occurrence être faite en termes de contributions. Parmi ces outils nous proposons de retenir le système de gestion de version Git. En effet, c’est un des systèmes les plus utilisés dans l’industrie et permet d’en tirer de nombreux avantages autant pour les étudiants que pour les enseignants, sans oublier les possibilités de minimisation des coûts reliés au matériel didactique. Aussi, l’utilisation de Git dans le cadre de travaux d’équipe, donne accès à toute l’information relative aux activités qui sont consignées dans son historique. En effet toute action est associée à son auteur, à la date à laquelle elle a été effectuée. En disposant de ces données, il s’agit alors de définir les critères à appliquer pour faire une analyse et établir un jugement. Nous proposons dans ce mémoire un inventaire des critères d’évaluation potentiels et identifions les plus pertinents en termes d’évaluation de la régularité et de contribution quantitative en tenant compte des biais qu’ils peuvent induire. Aussi, une des difficultés que peuvent rencontrer les enseignants au moment de produire une évaluation est non seulement de pouvoir évaluer les contributions, mais également de pouvoir en faire un suivi régulier, tout particulièrement lorsque les équipes sont nombreuses. Nous proposons alors un outil de support basé sur les critères que nous avons identifiés offrant un aperçu général et facilitant l’accès aux détails. Son évaluation dans le cadre d’un cours nous a permis d’identifier différents profils d’équipe ainsi que les limites d’utilisation d’un tel outil pour établir un jugement. / Teamwork is one of the ways to develop the transversal competencies expected in industry, especially in the field of Information Technology. However, the success of teamwork during programming courses depends on the choice of tools that facilitates collaborative work, organization and conflict management. Objectively evaluating both the individual and the collaborative work must be a great part of this choice. Among these tools, we propose to retain the version control system Git. Indeed, it is one of the most used systems in the industry and reaps many benefits for both students and teachers, including the minimization of cost of educational materials. Also, Git facilitates teamwork’s evaluation by giving access to information recorded in its history. It then becomes necessary to define the criteria to be applied to make an analysis and a judgment. We propose in this thesis an inventory of the potential evaluation criteria and identify the most relevant ones in terms of evaluation of the regularity and quantitative contribution considering the biases that they induce. Moreover, one of the difficulties that teachers may encounter when producing an assessment is not only to evaluate contributions, but also to be able to monitor them regularly, especially when teams are numerous. We then recommend a support tool based on the criteria we identified, offering a general overview and facilitating access to details. Its evaluation as part of a course allowed us to identify different team profiles as well as the limits to use of such a tool to make a judgment.

Command line and version control skills are vital to computer science students during their education and as they enter the software industry. These skills are commonly taught to undergraduate students via traditional lecturing methods and brief hands-on activities. Many students struggle with learning the Git version control system because they are not familiar with the command line, or they do not understand how Git works internally. Recent research highlights the effectiveness of using interactive visualizations to teach computer science concepts. Thus, we developed novel command line and Git exercises with interactive visualizations. These exercises integrate with learning management systems to automate grading. We tested the effectiveness of the exercises in a CS2 course at a large research institution by conducting pre-assessments before and post-assessments after the students completed the exercises. We found that students performed significantly better on both the command line and Git post-assessments than on the pre-assessments. Furthermore, we found that students with less experience with the command line and Git achieved a significantly greater improvement from the pre-assessments to the post-assessments. Additionally, we found that students with different levels of command line and Git experience did not perform differently on the exercises. Therefore, the exercises provide a novel tool for teaching command line and Git concepts to undergraduate computer science students with any level of command line and Git experience. / Master of Science / Command line is a term used to refer to a text-based user interface that allows users to interact with their computers by inputting commands. Git is a version control system typically used to track the stages of development for a computer program. Command line and Git skills are vital to computer science students during their education and as they enter the software industry. These skills are commonly taught to undergraduate students via traditional lecturing methods and brief hands-on activities. Many students struggle with Git because they are not familiar with the command line, or they do not understand how Git works internally. Recent research highlights the effectiveness of using interactive visualizations to teach computer science concepts. Thus, we developed novel command line and Git exercises with interactive visualizations. These exercises integrate with learning management systems to automate grading. We tested the effectiveness of the exercises in a CS2 course at a large research institution by conducting pre-assessments before and post-assessments after the students completed the exercises. We found that students performed significantly better on the post-assessments than on the pre-assessments. Furthermore, we found that students with less experience with the command line and Git achieved a significantly greater improvement from the pre-assessments to the post-assessments. Therefore, the exercises provide a novel tool for teaching command line and Git concepts to undergraduate computer science students with any level of command line and Git experience.

L'objet de cette thèse est l'étude de la structure symplectique des orbites coadjointes holomorphes, et de leurs projections.Une orbite coadjointe holomorphe O est une orbite coadjointe elliptique d'un groupe de Lie G réel semi-simple connexe non compact à centre fini provenant d'un espace symétrique hermitien G/K, telle que O puisse être naturellement munie d'une structure kählérienne G-invariante. Ces orbites coadjointes sont une généralisation de l'espace symétrique hermitien G/K.Dans cette thèse, nous prouvons que le symplectomorphisme de McDuff se généralise aux orbites coadjointes holomorphes, décrivant la structure symplectique de l'orbite O par le produit direct d'une orbite coadjointe compacte et d'un espace vectoriel symplectique. Ce symplectomorphisme est ensuite utilisé pour déterminer les équations de la projection de l'orbite O relative au sous-groupe compact maximal K de G, en faisant intervenir des résultats récents de Ressayre en Théorie Géométrique des Invariants. / This thesis studies the symplectic structure of holomorphic coadjoint orbits and the projection of such orbits.A holomorphic coadjoint orbit O is an elliptic coadjoint orbit which is endowed with a natural invariant Kählerian structure. These coadjoint orbits are defined for real semi-simple connected non compact Lie group G with finite center such that G/K is a Hermitian symmetric space, where K is a maximal compact subgroup of G. Holomorphic coadjoint orbits are a generalization of the Hermitian symmetric space G/K.In this thesis, we prove that the McDuff's symplectomorphism, available for Hermitian symmetric spaces, has an analogous for holomorphic coadjoint orbits. Then, using this symplectomorphism and recent GIT arguments from Ressayre, we compute the equations of the projection of the orbit O, relatively to the maximal compact subgroup K.

Cette thèse constitue un des éléments du projet de recherche EMOCAVI (Evolution des Modèles des Composants de puissance grand gAp au cours du VIeillissement). Elle porte sur l’étude de la fiabilité des transistors de puissance en Nitrure de Gallium (GaN) récemment apparus sur le marché. Ces travaux se focalisent sur la réalisation d’une méthodologie pour paramétrer le modèle du composant GaN GIT (Gate Injection Transistor) en fonction du vieillissement auquel il a été soumis. Pour atteindre cet objectif, nous sommes passés par plusieurs étapes. La première a été consacrée à la définition, la mise en place et la validation d’un banc de vieillissement et à la caractérisation de ces composants avant et en cours de vieillissement. Un banc de test de vieillissement en court-circuit répétitif à faible puissance a été conçu et mis en oeuvre. Ce banc a permis de valider l’hypothèse du vieillissement lié à l’énergie, d’identifier son niveau déterminant d’un point de vue fiabilité du composant et enfin mettre en évidence la dégradation progressive du composant afin d’identifier les paramètres du transistor les plus sensibles au vieillissement. La deuxième étape de nos travaux a été consacrée à l’établissement d’une méthodologie de création de modèle de vieillissement du composant GaN-GIT. En reproduisant le modèle COBRA présenté dans la littérature, nous avons réussi dans nos travaux à proposer une approche novatrice permettant d’intégrer les dépendances en température et en énergie subie par le composant pendant le stress (la durée d’impulsion Tsc et le nombre de pulse subi Nsc). La dernière étape de nos travaux a été dédiée à l’analyse physique de défaillance afin de confirmer les hypothèses faites sur les mécanismes de dégradation obtenus après vieillissement du composant. Pour réaliser ces analyses, nous avons commencé par la décapsulation du composant en combinant l’ouverture laser aux attaques chimiques de la résine constituant le packaging. Une fois le défaut localisé par photoluminescence, une analyse approfondie par des vues au microscope électronique à balayage MEB puis par découpe PFIB (Plasma Fouced Ion Beam) a été réalisée afin de déterminer le mécanisme de défaillance. Il s’agissait principalement de fissures situées dans le métal d’Al au niveau du drain ainsi que la présence de cavités dans la couche métallique qui sert à réaliser le contact ohmique au niveau de la source, ce qui explique l’augmentation de la résistance RDSON. / This thesis constitute one of the elements of the EMOCAVI research project (Evolution of the Large gAp Power Component Models during the VIeillissement). It deals with the study of the reliability of Gallium Nitride (GaN) power transistors which are recently appeared on the market. This work focuses on the realization of a methodology to parameterize the model of GaN GIT component (Gate Injection Transistor) according to the aging to which it has been subjected. To achieve this goal, it will be necessary to go through several steps. The first step was dedicated to the definition, implementation and validation of an aging bench for the component and the characterization of these components before and during aging. A low power repetitive short-circuit aging test bench was designed and implemented. This bench is used to validate the energy-related aging hypothesis, to identify its determining level from a point of view of the reliability of the component and finally to highlight the progressive degradation of the component in order to identify the parameters of the transistor which are the most sensitive to aging. The second step of our work was devoted to the establishment of a methodology to create the aging model for the GaN-GIT component. By reproducing the COBRA model presented in the literature, we have succeeded in our work in proposing an innovative approach to integrate the dependencies in temperature and energy suffered by the component during stress (the Tsc pulse duration and the number of pulse suffered Nsc). The last step of our work was dedicated to the physical failure analysis in order to confirm the hypothesis made on the degradation mechanisms obtained after aging of the component. To carry out these analyzes, we started with the de-capsulation of the component by combining the laser cutting with the chemical attacks of the resin constituting the packaging. Once the defect was localized by photoluminescence, an in-depth analysis by SEM scanning and then PFIB (Plasma Focused Ion Beam) scans was performed to determine the mechanism of failure. These were mainly cracks in the Al metal at the drain and the presence of cavities in the metal layer which is used to make the Ohmic contact at the source, which explains the increase in resistance RDSON.