Dans ce mémoire, je présenterai les outils que nous avons développés dans le cadre de ma maîtrise. Tout d'abord, je présenterai un outil d'analyse de données génomiques nommé Versatile Aggregrate Profiler (VAP). Ensuite, je présenterai un outil d'identification de profils agrégés similaires nommé vap_sim ainsi que la méthodologie utilisée afin d'obtenir un paramétrage adéquat de l'outil pouvant s'adapter assez facilement aux différents profils agrégés. Au troisième chapitre, je présenterai un outil de validation de formats génomiques nommé Genomic Format Validator (GFV) permettant d'identifier simplement et rapidement les erreurs de structure et de logique dans un fichier de données génomiques. Finalement, au dernier chapitre, je présenterai trois outils complémentaires à VAP.

IFMIF sera constitué de deux accélérateurs de deutons délivrant des faisceaux continus de 125mA et d’énergie 40MeV qui bombarderont une cible de lithium liquide. Face à cette très haute puissance faisceau de 10 MW, de nouveaux défis doivent être relevés pour le développement de tels accélérateurs. C’est pour cette raison qu’a été prise la décision de construire un accélérateur prototype, LIPAc (Linear IFMIF Prototype Accelerator) ayant les mêmes caractéristiques faisceau qu’IFMIF, mais avec une énergie limitée à 9MeV. Dans le cadre de cette thèse, des instruments de diagnostics faisceau ont été développés pour IFMIF et LIPAc. Ces diagnostics concernent des moniteurs de pertes faisceau ainsi que des profileurs transverse de faisceau travaillant en mode intercepteur ou non.Pour la surveillance des pertes faisceau, des chambres à ionisation et des détecteurs au diamant ont été testés et calibrés en neutrons et en γ dans la gamme en énergie de LIPAc. Lors de ces expériences, pour la première fois des diamants ont été testés avec succès à des températures cryogéniques. Pour les profileurs interceptant le faisceau, des simulations thermiques ont été réalisées afin d’assurer leur bon fonctionnement. Pour les profileurs n’interceptant pas le faisceau, des moniteurs basés sur l’ionisation du gaz résiduel (IPM) contenu dans le tube faisceau ont été développés. Un prototype a été construit et testé, puis s’inspirant de ce retour d’expérience les IPMs finals ont été conçus et construits. Pour contrecarrer la charge d’espace générée par le faisceau, un algorithme a été élaboré afin de reconstruire le profil réel du faisceau. / The IFMIF accelerator will accelerate two 125mA continuous wave (cw) deuteron beams up to 40MeV and blasts them onto a liquid lithium target to release neutrons. The very high beam power of 10MW pose unprecedented challenges for the accelerator development. Therefore, it was decided to build a prototype accelerator, the Linear IFMIF Prototype Accelerator (LIPAc), which has the very same beam characteristic, but is limited to 9 MeV only. In the frame of this thesis, diagnostics devices for IFMIF and LIPAc have been developed. The diagnostics devices consist of beam loss monitors and interceptive as well as non-interceptive profile monitors. For the beam loss monitoring system, ionization chambers and diamond detectors have been tested and calibrated for neutron and γ radiation in the energy range expected at LIPAc. During these tests, for the first time, diamond detectors were successfully operated at cryogenic temperatures. For the interceptive profilers, thermal simulations were performed to ensure safe operation. For the non-interceptive profiler, Ionization Profile Monitors (IPMs) were developed. A prototype has been built and tested, and based on the findings, the final IPMs were designed and built. To overcome the space charge of accelerator beam, a software algorithm was written to reconstruct the actual beam profile.

Detta examensarbete beskriver i detalj hur ICC-profiler fo¨r utskriftsmedier, i detta fall fo¨r storformatskrivare, skapas. Examensarbetet omfattade framtagande av ICC-profiler fo¨r substrat till storformatskrivaren Mutoh Toucan PJ-1614NXE (Mutoh Toucan) hos BEMI REKLAM AB (BEMI), Borla¨nge. Fo¨retaget har tidigare anva¨nt en standardlinja¨risering till samtliga substrat fo¨r storformatskrivaren, dock utan att applicera na°gon ICC-profil fo¨r utenheter. Samtliga substrat till Mutoh Toucan a¨r avsedda fo¨r utomhusbruk.

Most dynamic program analysis techniques such as profile-driven compiler optimizations, software testing and runtime property checking infer program properties by profiling one or more executions of a program. Unfortunately, program profiling does not come for free. For example, even the most efficient techniques for profiling acyclic, intra-procedural paths can slow down program execution by a factor of 2. In this thesis, we propose techniques that significantly lower the overheads of profiling paths, enabling the use of path-based dynamic analyzes in cost-sensitive environments. Preferential path profiling (PPP) is a novel software-only path profiling scheme that efficiently profiles given subsets of paths, which we refer to as interesting paths. The algorithm is based on the observation that most consumers of path profiles are only interested in profiling a small set of paths known a priori. Our algorithm can be viewed as a generalization of the Ball-Larus path profiling algorithm. Whereas the Ball-Larus algorithm assigns weights to the edges of a given CFG such that the sum of the weights of the edges along each path through the CFG is unique, our algorithm assigns weights to the edges such that the sum of the weights along the edges of interesting paths is unique. Furthermore, our algorithm attempts to achieve a minimal and compact encoding of the interesting paths; such an encoding significantly reduces the overheads of path profiling by eliminating expensive hash operations during profiling. Interestingly, we find that both the Ball-Larus algorithm and PPP are essentially a form of arithmetic coding. We use this connection to prove that the numbering produced by PPP is optimal. We also propose a programmable, non-intrusive hardware path profiler (HPP). The hardware profiler consists of a path detector that detects paths by monitoring the stream of retiring branch instructions emanating from the processor pipeline. The path detector can be programmed to detect various types of paths and track architectural events that occur along paths. The second component of the hardware profiling infrastructure is a Hot Path Table (HPT), that collects accurate hot path profiles. Our experimental evaluation shows that PPP reduces the overheads of profiling paths to 15% on average (with a maximum of 26%). The algorithm can be easily extended to profile inter-procedural paths at minimal additional overheads (average of 26%). We modeled HPP using a cycle-accurate superscalar processor simulator and find that HPP generates accurate path profiles at extremely low overheads (0.6% on average) with a moderate hardware budget. We also evaluated the use of PPP and HPP in a realistic profiling scenarios. We find that the profiles generated by HPP can effectively replace expensive profiles used in profile-driven optimizations. We also find that even well-tested programs tend to exercise a large number of untested paths in the field, emphasizing the need for efficient profiling schemes that can be deployed in production environments.

The construction of fish passes has been a longstanding measure to improve river ecosystem status by ensuring the passability of weirs, dams and other in- channel structures for migratory fish. Many fish passes have a low biological effectiveness because of unsuitable hydrodynamic conditions hindering fish to rapidly detect the pass entrance. There has been a need for techniques to quantify the hydrodynamics surrounding fish pass entrances in order to identify those passes that require enhancement and to improve the design of new passes. This PhD thesis presents the development of a methodology for the rapid, spatially continuous quantification of near-pass hydrodynamics in the field. The methodology involves moving-vessel Acoustic Doppler Current Profiler (ADCP) measurements in order to quantify the 3-dimensional water velocity distribution around fish pass entrances. The approach presented in this thesis is novel because it integrates a set of techniques to make ADCP data robust against errors associated with the environmental conditions near engineered in-channel structures. These techniques provide solutions to (i) ADCP compass errors from magnetic interference, (ii) bias in water velocity data caused by spatial flow heterogeneity, (iii) the accurate ADCP positioning in locales with constrained line of sight to navigation satellites, and (iv) the accurate and cost-effective sensor deployment following pre-defined sampling strategies. The effectiveness and transferability of the methodology were evaluated at three fish pass sites covering conditions of low, medium and high discharge. The methodology outputs enabled a detailed quantitative characterisation of the fish pass attraction flow and its interaction with other hydrodynamic features. The outputs are suitable to formulate novel indicators of hydrodynamic fish pass attractiveness and they revealed the need to refine traditional fish pass design guidelines.

Le transport sédimentaire contrôle l'évolution morphologique des rivières, l'érosion du littoral et l'équilibre des écosystèmes. Il constitue également un facteur de risque pour les populations et les infrastructures. Le sheet-flow, ou charriage intense, est un régime de transport sédimentaire qui s'établi lors de crues dans les fleuves et les rivières ou lors du déferlement des vagues littorales sur les plages sableuses. Le fort taux de transport associé à ce régime le rend très morphogène et une bonne compréhension des processus physiques impliqués est fondamentale pour prédire la morphodynamique. Cependant, les interactions granulaires et les fluctuations turbulentes, qui sont les principaux mécanismes à l'œuvre dans ce phénomène, constituent des verrous scientifiques pour la modélisation du régime de sheet-flow. Cette déficience s'explique essentiellement par le manque de données expérimentales haute résolution. Partant de ce constat, l'objectif de la thèse est de proposer un modèle diphasique et un dispositif expérimental haute résolution permettant de mieux caractériser les mécanismes impliqués. indent Dans un premier temps, le modèle diphasique est présenté et les résultats obtenus sont confrontés aux données de la littérature. L'analyse des résultats montre que la rhéologie des écoulements granulaires denses ($mu(I)/phi(I)$) et l'approche de longueur de mélange utilisées sont des fermetures appropriées pour reproduire les principales caractéristiques du régime de sheet-flow pour une large gamme d'écoulements et de propriétés sédimentaires. La deuxième partie de la thèse est consacrée à la mise en place d'un dispositif expérimental capable de fournir des mesures instantanées de vitesse et de concentration en régime de sheet-flow uniforme. Dans la troisième partie les grandeurs moyennes sont analysées pour décrire la structure verticale de l'écoulement. Les résultats obtenus montrent qu'une formulation en longueur de mélange et un profil de Rouse permettent de décrire la contrainte turbulente et le profil de concentration dans la suspension à condition de fortement modifier le paramètre de von Karman ($kappa approx 0.2$) et le nombre de Schmidt ($sigma_s=0.44$). La rhéologie frictionnelle ($mu(I)/phi(I)$) et la théorie cinétique des écoulements granulaires prédisent qualitativement le comportement observé, mais échoue à reproduire quantitativement les mesures. Le lien étroit existant entre les structures cohérentes turbulentes et la dynamique du lit sédimentaire illustre l'importance des fluctuations et de l'intermittence de l'écoulement. Ce couplage pourrait expliquer l'écart observé entre le comportement prédit par les modèles de contraintes inter-granulaires et les mesures expérimentales. Finalement, la comparaison des analyses statistiques en régime de sheet-flow et en écoulement sur fond fixe rugueux permet de montrer que l'énergie cinétique turbulente est peu affectée par la présence des sédiments mais que le niveau de corrélation entre fluctuations horizontales et verticales est sensiblement diminué, impliquant une diminution de la longueur de mélange et de la viscosité turbulente. Une augmentation significative de la rugosité équivalente induite par le lit mobile est aussi observée. / Sediment transport controls river morphological evolution, coastal erosion and ecosystem equilibrium. It represents a risk factor for populations and infrastructures. The sheet-flow, or intense bed-load, is a regime of sediment transport occurring during river floods or in the coastal wave breaking region above sandy beaches. The large amount of sediment transported in this regime is the main source for morphological evolution in our natural systemswater bodies. A good understanding of the underlying physical processes is a pre-requisite for accurate morphodynamic predictions. However, particle-particle interactions and turbulent flow interactions, which are the main driving mechanisms in this problem, constitute the scientific bottlenecks for sheet-flow modelling. This deficiency is mainly caused by the lack of high resolution experimental data. Based on this observation, the objective of the present thesis is to propose a novel two-phase model and to generate a new set of high resolution experiment data to improve process based sheet-flow modelling. indent First, the two-phase flow model is presented and the obtained results are compared with data from the literature. The result analysis has shown that the dense granular flow rheology ($mu(I)/phi(I)$) combined with a turbulent mixing length concept predicts the main sheet flow characteristics over a wide range of flow and sediment properties. Secondly, the experimental set up providing high-rate measurements of velocity and concentration under a uniform sheet-flow regime is presented. Third, the measured mean flow quantities are analysed to describe the vertical structure of the flow. The obtained results show that a mixing length formulation and a Rouse profile allow to describe the turbulent stress and the concentration profiles in the turbulent suspension layer, provided that the von Karman parameter and the Schmidt number are modified ($kappa approx 0.2$ and $sigma_s=0.44$). The frictional rheology ($mu(I)/phi(I)$) and the kinetic theory of granular flows predict qualitatively the observed behaviour but fail to reproduce measurements quantitatively. The observed link between the turbulent coherent structures and the bed dynamic illustrates the importance of flow fluctuations and intermittency. This coupling could be responsible for the discrepancy found between the predictions from the intergranular stresses models and the measurements. Finally, the comparison between the statistical analysis performed for a sheet-flow regime and for a clear water flow over a rough fixed bed demonstrates that the turbulent kinetic energy is weakly affected by the presence of sediments whereas the turbulent correlation level between horizontal and vertical fluctuations is significantly reduced, leading to a decrease of both the mixing length and the turbulent eddy viscosity. An increase of the equivalent roughness height induced by the moving bed is also observed.

The diploma thesis focuses especially on a design of a way for evaluating roughness in road profile, which affects driving characteristics of a car and a ride. In the theoretical part of the thesis are mentioned the most used methods and tools for road roughness analysis in the world. For the purposes of this thesis an experimental measuring were undertaken in order to obtain data for the own design of a road profile analysing system.

Research has shown that university students are extra vulnerable to experiencing loneliness because of the social, structural, and behavioral changes associated with starting to study at university. Studies have also shown that different attachment profiles can have an impact on an individual's experience of loneliness. A lot of earlier research has investigated loneliness as one whole concept, so the aim of the present study was to look into both emotional and social loneliness in university students and to understand their relationship with adult attachment. One-hundred and twenty-six university students over 18 years old answered De Jong-Gierveld Loneliness Scale (DJGLS) and Attachment Style Questionnaire (ASQ) through an online survey. A quantitative between groups design was used to explore the specific aims of the study. For the statistical analysis the participants were divided into four groups based on type and amount of loneliness. The results of the study showed that emotional loneliness was associated with insecure-ambivalent attachment and social loneliness associated with insecure-avoidant attachment. Those with high levels of emotional loneliness had significantly higher levels of insecure-ambivalent attachment compared with those with high levels of social loneliness. Individuals with low levels of both loneliness types, had significantly higher levels of secure attachment and lower levels of insecure attachment compared with the other groups, which indicates that the more securely attached an individual is the less lonely he or she is. / Forskning har visat att universitetsstudenter är extra sårbara vad gäller upplevd ensamhet på grund av de sociala, strukturella och beteendemässiga förändringarna som är associerade med att börja studera på universitet. Studier har även visat att olika typer av anknytnings profiler kan ha en påverkan på en individs upplevda ensamhet. Mycket av den tidigare forskningen har undersökt ensamhet som ett enda koncept, så syftet med denna studie var att undersöka både emotionell och social ensamhet hos universitetsstudenter och förstå deras relation till vuxenanknytning. Deltagarna bestod av 126 universitetsstudenter över 18 år som svarade på De Jong-Gierveld Loneliness Scale (DJGLS) och Attachment Style Questionnaire (ASQ) genom en webb-baserad enkät. En kvantitativ mellangruppsdesign användes för att undersöka studiens specifika syften. För den statistiska analysen delades deltagarna in i fyra grupper baserat på typ och mängd av ensamhet. Resultatet av studien visade att emotionell ensamhet var associerat med otrygg-ambivalent anknytning och social ensamhet var associerat med otrygg-undvikande anknytning. De med höga nivåer av emotionell ensamhet hade signifikant högre nivåer av otrygg-ambivalent anknytning jämfört med de som hade höga nivåer av social ensamhet. Individer som hade låga nivåer av båda typerna av ensamhet, hade signifikant högre nivåer av trygg anknytning och lägre nivåer av otrygg anknytning jämfört med de andra grupperna, vilket tyder på att ju tryggare anknytning man har desto mindre ensam känner man sig.

Network functions (NFs) hold a key role in networks, offering in-network services, such as enhanced performance, policy enforcement, and security. Traditionally, NFs have been implemented in specialized, thus expensive hardware. To lower the costs of deploying NFs, network operators have adopted network functions virtualization (NFV), by migrating NFs from hardware to software running in commodity servers. Several approaches to NFV have shown that commodity network stacks and drivers (e.g., Linux-based) struggle to keep up with increasing hardware speed. Despite this, popular networking services still rely on these commodity components. Moreover, chaining NFs (also known as service chaining) is challenging due to redundancy in the elements of the chain. This licentiate thesis addresses the performance problems of NFV service chains.The first contribution is a framework that (i) profiles NFV service chains to uncover performance degradation reasons and (ii) leverages the profiler’s data to accelerate these chains, by combining multiplexing of system calls with scheduling strategies. These accelerations improve the cache utilization and thereby the end-to-end latency of chained NFs is reduced by a factor of three. Moreover, the same chains experience a multi-fold latency variance reduction; this result improves the quality of highly-interactive services.The second contribution of this thesis substantially revises the way NFV service chains are realized. NFV service chains are synthesized while eliminating redundant input/output and repeated elements, providing consolidated stateful cross layer packet operations across the chain. This software-based synthesis achieves line-rate 40 Gbps throughput for stateful and long service chains. This performance is 8.5x higher than the performance achieved by the software-based state of the art FastClick framework. Experiments with three example Internet Service Provider-level service chains show that this synthesis approach operates at 40 Gbps, when the classification of these chains is offloaded to an OpenFlow switch. / Nätverksfunktioner (NF) har en nyckelroll i nätverk. De erbjuder tjänster i nätverken som förbättrad prestanda, policy övervakning och säkerhetsfunktioner. Vanligtvis så har NF implementerats med hjälp av specialiserad, och därmed kostsam, hårdvara. Detta har lett till att nätverksoperatörer har börjat använda nätverksfunktionsvirtualisering (NFV) för att minska kostnaden. NFV implementeras genom att NF flyttas från specialiserad hårdvara till mjukvara som kör på vanliga servrar. Flera försök med NFV har visat att vanliga nätverksstackar och drivrutiner (exempelvis Linux baserade) har svårt att erbjuda samma prestanda som hårdvaran gör. Trots detta bygger flera populära nätverkstjänster på NFV. Dessutom är det en utmaning att koppla samman NFV i kedjor, då redundanta operationer utförs. I den här avhandlingen försöker vi lösa prestanda problem kopplade till kedjor av NFV. Det första bidraget i den här avhandlingen är ett ramverk som (i) profilerar NFV kedjor för att hitta orsaker till prestanda problem samt (ii) använder profileringsdata för att förbättra prestandan i kedjorna. Detta görs genom att kombinera multiplexing av systemanrop med planläggningsstrategier. Tillsammans förbättrar dessa lösningar cache användningen och minskar därmed end-to-end latensen i kedjade NFV med en faktor tre. Dessutom minskar vår metod variansen i latens, något som är viktigt för tjänstekvalitén i interaktiva tjänster.Det andra bidraget i den här avhandlingen är en omarbetning av hur kedjade NFV konstrueras. Vi syntetiserar NFV service kedjor genom att ta bort redundanta element och konsoliderar paketoperationer som sträcker sig över flera lager i nätverksstacken. Vår mjukvarubaserade lösning klarar av 40 Gbps genomströmning i en lång kedja. Detta är 8.5 ggr mer än vad som uppnåtts med den tidigare standard lösningen för mjukvara, ramverket FastClick. Vi presenterar experiment med tre servicekedjor för nätverksleverantörer där vår syntetiserade lösning klarar 40 Gbps, när klassificeringen av kedjan görs med hjälp av en OpenFlow switch. / <p>QC 20161103</p> / European Union Horizon 2020 BEhavioural BAsed forwarding (BEBA) / European Research Council (ERC) PROPHET

The Vision for eHealth infers that Sweden should be best in the world to utilize the opportunities of the digitization by 2025. One of three particularly important areas of action to realize the vision is standardization of e.g. exchange of information. HL7 FHIR is a modern standard for interoperability within e-health. HL7 FHIR enables the exchange of information between different healthcare information systems in an easy way. The basic building blocks in HL7 FHIR are called resources. These represent healthcare entities of some kind, e.g. Patient, Medication, Care plan, and Device. A base set of resources should either together, or by themselves, be able to satisfy the most common use cases in healthcare. A set of rules about a resource's content is called a profile, which is used for defining extensions and constraints on a resource. Profiles can be used to customize the standard to everything from a small local use-case to characteristics common for a whole country, so-called national profiles. This master thesis project sought to investigate the opportunities and restrictions with HL7 FHIR profiling by mapping the outlook of e-health stakeholders in Sweden. The project conducted a mixed method approach. Surveys were sent out to regions, county councils and private caregivers and interviews were held with national stakeholders, industry suppliers, HL7 Sweden and subject experts. The qualitative data was processed through a thematic analysis and the quantitative data was processed through a descriptive analysis. The results showed that there were positive views on governing and maintaining HL7 FHIR and FHIR profiling on a national level and to the establishment of national FHIR profiles. However, questions remain on how it shold be done. Among caregivers there were in general positive attitudes towards HL7 FHIR as a standard for interoperability and towards a possible implementation. However, the implementation level was low and specific knowledge of HL7 FHIR profiles is yet needed. / Vision e-Hälsa 2025 innebär att Sverige ska vara bäst i världen på att utnyttja möjligheterna med digitaliseringen år 2025. Ett av tre särskilt viktiga handlingsområden för att förverkliga visionen är standardisering, t.ex. av utbyte av information. HL7 FHIR är en modern standard för interoperabilitet inom e-hälsa och möjliggör utbyte av information mellan olika hälsoinformationssystem på ett enkelt sätt. De grundläggande byggstenarna i HL7 FHIR kallas resurser. Dessa representerar hälso- och sjukvårdsentiteter av något slag, t.ex. Patient, Medicin, Vårdplan och Apparat. En basuppsättning av resurser ska antingen tillsammans eller i sig själva kunna tillgodose de vanligaste användningsfallen inom hälso- och sjukvård. En uppsättning regler om en resurs innehåll kallas för profil och används för att definiera tillägg och begränsningar på en resurs. Profiler kan användas för att anpassa standarden till allt från ett litet lokalt användningsfall till egenskaper som är gemensamma för ett helt land, så kallade nationella profiler. Detta masterexamensarbete ämnade undersöka möjligheter och begränsningar med HL7 FHIR-profilering genom att kartlägga utsikterna för ehälso-aktörer i Sverige. I projektet genomfördes en mixad metodinriktning, i vilken enkäter skickades ut till regioner, landsting och privata vårdgivare och intervjuer hölls med nationella intressenter, leverantörer, HL7 Sverige och ämnesexperter. Kvalitativ data genomgick en tematisk analys och kvantitativ data genomgick en deskriptiv analys. Resultatet visade på en generellt positiv attityd gentemot ett framtagande och förvaltande av HL7 FHIR och FHIR-profiler på nationell nivå och införande av nationella FHIR-profiler. Däremot kvarstår frågor om hur det ska realiseras. Bland vårdgivare var det generellt positiva attityder gentemot HL7 FHIR som en standard för interoperabilitet och en eventuell implementation. Däremot var den generella implementationsnivån låg och ytterligare kunskap om HL7 FHIR-profiler behövs.