This theses deals with flow of two immisible fluid in horizontal pipeline. First part teoretically describes immisible flow. What follows is experimental measurement in wich experimental track was adjusted for inlet of oil from the top. Water and corn germ oil were used as fluids. There were observed many modes of flow on the track. After that PIV was described and measured. PIV was done for measurement of values of velocity vectors. Simulation of one chosen mode was developed in the last chapter. This simulation was done in Ansys Fluent with help of VOF method. Simulation was done both in 3D and 2D pipeline. In the end these simulation were compared with experiment measurement and were critically evaluated.

The current trend towards large-scale research projects with big quantities of data from multiple sources require robust and efficient data handling. This thesis explores techniques for automatizing research data pipelines. Specifically, two tasks related to automation within a long-term research project in cognitive neuroscience are addressed. The first task is to develop a tool for automatic transcribing of paper-based questionnaires using computer vision. Questionnaires containing continuous scales, so called visual analog scales (VASs), are used extensively in e.g. psychology. Despite this, there currently exists no tool for automatic decoding of these types of questionnaires. The resulting computer vision system for automatic questionnaire transcribing we present, called "VASReader", reliably detects VAS marks with an accuracy of 98%, and predicts their position with a mean absolute error of 0.3 mm when compared to manual measurements. The second task addressed in this thesis project is to investigate whether machine learning can be used to detect anomalies in Magnetic Resonance Imaging (MRI) data. An implementation of the unsupervised anomaly detection technique Isolation Forest shows promising results for the detection of anomalous data points. The model is trained on image quality metric (IQM) data extracted from MRI. However, it is concluded that the site of scanning and MRI machine model used affect the IQMs, and that the model is more prone to classify data points originating from machines and institutions that have less support in the database as anomalous. An important conclusion from both tasks is that automation is possible and can be a great asset to researchers, if an appropriate level and type of automation is selected.

Introductory part of this thesis is aimed on theoretical description, principle and building of biogas stations, which require solution of many different problems. A specific group of the problems concern transport of mixed substrates of different concentrations both in and outside the area of biogas station. A major part of the substrate transport is done by pumping it in pressure pipeline. Experimental work consists of design and description of a measuring circuit. Graphic characteristics for water and gas loss levels are drawn from the measured readings. Multiples of pressure losses by flowage of substrates with different levels of dry basis are graphically expressed with a help of correction coefficients.

The subject of this thesis is strength design of pipe connecting furnace of continuous catalytic reforming with reactor. First is realize analytical design of individual parts according to ASME VIII, ČSN EN 12952-3 a ČSN EN 13480-3. It is also design and optimize supporting pipe using Caesar II. At the end of work is creating isometric documentation.

La technologie CMOS a contribué au développement de l'industrie des semi-conducteurs. Cependant, au fur et à mesure que le noeud technologique est réduit, la technologie CMOS fait face à des défis importants liés à la dissipation dûe aux courants de fuite et aux effets du canal court. Pour résoudre ce problème, les chercheurs se sont intéressés à la spintronique ces dernières années, compte tenu de la possibilité de fabriquer des dispositifs de taille réduite et d'opérations de faible puissance. La jonction tunnel magnétique (MTJ) est l'un des dispositifs spintroniques les plus importants qui peut stocker des données binaires grâce à la Magnétorésistance à effet tunnel (TMR). En dehors des applications de mémoire non volatile, la MTJ peut également être utilisée pour combiner ou remplacer les circuits CMOS pour implémenter un circuit hybride, de façon à combiner une faible consommation d'énergie et des performances à grande vitesse. Cependant, le problème de la conversion fréquente de charge en spin dans un circuit hybride peut entraîner une importante consommation d'énergie, ce qui obère l'intérêt pour des circuits hybrides. Par conséquent, le concept ASL qui repose sur un pur courant de spin comme support de l'information est proposé pour limiter les conversions entre charge et spin, donc pour réduire la consommation d'énergie. La conception de circuits à base de dispositif ASL entraîne de nombreux défis liés à l'hétérogénéité qu'ils introduisent et à l'espace de conception étendu à explorer. Par conséquent, cette thèse se concentre sur l'écart entre les exigences d'application au niveau du système et la fabrication des nanodispositifs. Au niveau du dispositif, nous avons développé un modèle compact intégrant le STT, la TMR, les effets d'injection/accumulation de spin, le courant de breakdown des canaux et le délai de diffusion de spin. Validé par comparaison avec les résultats expérimentaux, ce modèle permet d'explorer les paramètres du dispositif liés à la fabrication, tels que les longueurs de canaux et les tailles de MTJ, et aide les concepteurs à éviter leur destruction. De plus, ce modèle, décrit avec Verilog-A sur Cadence et divisé en plusieurs blocs : injecteur, détecteur, canal et contact, permet une conception indépendante et une optimisation des circuits ASL qui facilitent la conception de circuits hiérarchiques et complexes. En outre, les expressions permettant le calcul de l'injection/accumulation de spin pour le dispositif ASL utilisé sont dérivées. Elles permettent de discuter des phénomènes expérimentaux observés sur les dispositifs ASL. Au niveau circuit, nous avons développé une méthodologie de conception de circuit/système, en tenant compte de la distribution des canaux, de l'interconnexion des portes et des différents rapports de courant d'injection provoqués par la diffusion de spin. Avec les spécifications et les contraintes du circuit/système, les fonctions booléennes du circuit sont synthétisées en fonction de la méthode de synthèse développée et des paramètres de niveau de fabrication : longueur des canaux, et tailles MTJ sont spécifiées. Basé sur cette méthodologie développée, les circuits combinatoires de base qui forment une bibliothèque de circuits sont conçus et évalués en utilisant le modèle compact développé. Au niveau du système, un circuit DCT, un circuit de convolution et un système Intel i7 sont évalués en explorant les problèmes d'interconnexion : la répartition de l'interconnexion entre les portes et le nombre de tampons inséré. Avec des paramètres théoriques, les résultats montrent que le circuit/système ASL peut surpasser le circuit/système basé sur CMOS. De plus, le pipeline du circuit basé sur ASL est discuté avec MTJ comme tampons insérés entre les étapes. La reconfigurabilité provoquée par les polarités/valeurs du courant d'injection et les états des terminaux de control des circuits ASL sont également discutés avec l'exploration reconfigurable des circuits logiques de base. / The CMOS technology has tremendously affected the development of the semi-conductor industry. However, as the technology node is scaled down, the CMOS technology faces significant challenges set by the leakage power and the short channel effects. To cope with this problem, researchers pay their attention to the spintronics in recent years, considering its possibilities to allow smaller size fabrication and lower power operations. The magnetic tunnel junction (MTJ) is one of the most important spintronic devices which can store binary data based on Tunnel MagnetoResistance (TMR) effect. Except for the non-volatile memory, MTJ can be also used to combine with or replace the CMOS circuits to implement a hybrid circuit, for the potential to achieve low power consumption and high speed performance. However, the problem of frequent spin-charge conversion in a hybrid circuit may cause large power consumption, which diminishes the advantage of the hybrid circuits. Therefore, the ASL concept which uses a pure spin current to transport the information is proposed for fewer charge-spin conversions, thus for less power consumption. The design of ASL device-based circuits leads to numerous challenges related to the heterogeneity they introduce and the large design space to explore. Hence, this thesis focus on filling the gap between application requirements at the system level and the device fabrication at the device level. In device level, we developed a compact model integrating the STT, the TMR, the spin injection/accumulation effects, the channel breakdown current and the spin diffusion delay. Validated by comparing with experimental results, this model allows exploring fabrication-related device parameters such as channel lengths and MTJ sizes and help designers to prevent from device damages. Moreover, programmed with Verilog-A on Cadence and divided into several blocks: injector, detector, channel and contact devices, this model allows the independent design and cross-layer optimization of ASL-based circuits, that eases the design of hierarchical, complex circuits. Furthermore, the spin injection/accumulation expressions for the used ASL device are derived, enabling to discuss the experimental phenomena of the ASL device. In circuit level, we developed a circuit/system design methodology, taking into account the channel distribution, the gate interconnection and the different injection current ratios caused by the spin diffusion. With circuit/system specifications and constraints, the boolean functions of a circuit are synthesized based on the developed synthesis method and fabrication-level parameters: channel lengths, MTJ sizes are specified. Based on this developed methodology, basic combinational circuits that form a circuit library are designed and evaluated by using the developed compact model. In system level, a DCT circuit, a convolution circuit and an Intel i7 system are evaluated exploring the interconnection issues: interconnection distribution between gates and inserted buffer count. With theoretical parameters, results show that ASL-based circuit/system can outperform CMOS-based circuit/system. Moreover, the pipelining schema of the ASL-based circuit is discussed with MTJ as latches inserted between stages. The reconfigurability caused by the injection current polarities/values and the control terminal states of ASL-based circuits are also discussed with the reconfigurable exploration of basic logic circuits.

Non-coding RNAs are the most abundant class of RNAs found throughout genomes. These RNAs are key players of gene regulation and thus, the func- tion of whole organisms. Numerous methods have been developed so far for detecting novel classes of ncRNAs or finding homologs to the known ones. Because of their abundance, the sequence availability of these RNAs is rapidly increasing, as is the case for example for microRNAs. However, for classes of them, still only incomplete information is available, invertebrates 7SK snRNA for instance. Consequently, a lot of false positive outputs are produced in the former case, and more accurate annotation methods are needed for the latter cases to improve derivable knowledge. This makes the accuracy of gathering correct homologs a challenging task and it leads directly to a not less important problem, the curation of these data. Finding solutions for the aforementioned problems is more complex than one would expect as these RNAs are characterized not only by sequences informa- tion but also structure information, in addition to distinct biological features. In this work, data curation methods and sensitive homology search are shown as complementary methods to solve these problems. A careful curation and annotation method revealed new structural information in the invertebrates 7SK snRNA, which pushes the investigation in the area forward. This has been reflected by detecting new high potential 7SK RNA genes in different invertebrates groups. Moreover, the gaps between homology search and well- curated data on the one side, and between experimental and computational outputs on the other side, are closed. These gaps were bridged by a curation method applied to the microRNA data, which was then turned into a com- prehensive workflow implemented into an automated pipeline. MIRfix is a microRNA curation pipeline considering the detailed sequence and structure information of the metazoan microRNAs, together with biological features related to the microRNA biogenesis. Moreover, this pipeline can be integrated into existing methods and tools related to microRNA homology search and data curation. The application of this pipeline on the biggest open source microRNA database revealed its high capacity in detecting wrong annotated pre-miRNA, eventually improving alignment quality of the majority of the available data. Additionally, it was tested with artificial datasets highlighting the high accuracy in predicting the pre-miRNA components, miRNA and miRNA*.:Chapter 1: Introduction Chapter 2: Biological and Computational background 2.1 Biology 2.1.1 Non-coding RNAs 2.1.2 RNA secondary structure 2.1.3 Homology versus similarity 2.1.4 Evolution 2.2 The role of computational biology 2.2.1 Alignment 2.2.1.1 Pairwise alignment 2.2.1.2 Multiple sequence alignment (MSA) 2.2.2 Homology search 2.2.2.1 Sequence-based 2.2.2.2 Structure-based 2.2.3 RNA secondary structure prediction Chapter 3: Careful curation for snRNA 3.1 Biological background 3.2 Introduction to the problem 3.3 Methods 3.3.1 Initial seeds and models construction 3.3.2 Models anatomy then merging 3.4 Results 3.4.1 Refined model of arthropod 7SK RNA 3.4.1.1 5’ Stem 3.4.1.2 Extension of Stem A 3.4.1.3 Novel stem B in invertebrates 3.4.1.4 3’ Stem 3.4.2 Invertebrates model conserves the HEXIM1 binding site 3.4.3 Computationally high potential 7SK RNA candidate . 3.4.4 Sensitivity of the final proposed model 3.5 Conclusion Chapter 4: Behind the scenes of microRNA driven regulation 4.1 Biological background 4.2 Databases and problems 4.3 MicroRNA detection and curation approaches Chapter 5: Initial microRNA curation 5.1 Introduction 5.2 Methods 5.2.1 Data pre-processing 5.2.2 Initial seeds creation 5.2.3 Main course 5.3 Results and discussion 5.4 Conclusion Chapter 6: MIRfix pipeline 6.1 Introduction 6.2 Methods 6.2.1 Inputs and Outputs 6.2.2 Prediction of the mature sequences 6.2.3 The original precursor and its alternative 6.2.4 The validation of the precursor 6.2.5 Alignment processing 6.3 Results and statistics 6.4 Applications 6.4.1 Real life examples and artificial data tests 6.4.2 miRNA and miRNA* prediction 6.4.3 Covariance models 6.5 Conclusion Chapter 7: Discussion

This diploma thesis deals with the history and the development of the gas industry in Czechoslovakia, namely the construction of the transit gas pipeline and development of the gas transit system. One of the part of this thesis is a history of the coal gas and the reasons for its gradual replacement by a natural gas. The metodology of this thesis is based mainly on interviews based on the method of oral history, on archival records, and contemporary literature. Primarily it is focused on oral history fieldwork, particularly on the personal experiences of narrators who were direct participants in the construction. This work is also focused on the circumstances of the negotiations of the construction of a transit gas pipeline and further expansion of the transit system from the seventies to the nineties of the 20th century. Keywords Transit pipeline, natural gas, gas industry, economy, energetics, coal gas, normalization

Examiners of programming assignments in higher education and people in the software industry both need to test and review code. However, the assessing techniques used are often quite different. The IT industry often uses agile work methods like continuous integration and automated tests, while examiners either do manual assessments or rely on code grading tools. The students will most likely become developers and work using agile processes. Therefore, there are possible benefits of universities trying to imitate the work processes of the software industry. The purpose of this study was to develop a workflow for programming assignments inspired by continuous integration, Scrum, and GitLab flow. The workflow was developed based on the requirements of Linnaeus University and tested on one of their programming assignments. It showed that a simplified agile work process is suitable for programming assignments since the demonstration fulfilled all of the predefined requirements. However, examiners might miss some of the workflow’s benefits if the programming assignment can not be tested automatically since it will require more manual work while grading.

In the world of software development, there is an increasing demand for software to keep up with rapid changes in its real-world context. A Resilient Digital Twin of an Organization is a type of software whose purpose is to digitally represent an organization or a component of an organization - as a Digital Twin -, and to keep doing so accurately throughout the real-world organization’s changes - a Resilient Digital Twin. An architectural pattern, called the EA Blueprint Pattern, has recently been proposed as a pattern to use for developing Resilient Digital Twins that can change together with the changes in the organization. However, software architecture is not the only factor that enables continuous change and adaptability in software. For software development teams to be able to deliver software rapidly and reliably, the software development process itself must be adapted to allow for frequent and fast changes. From this need, the Agile methodology and subsequently the set of work practises called DevOps has emerged. DevOps leverages automation and fast feedback as tools to facilitate a shorter system development life cycle and continuous delivery. The usage of DevOps is becoming increasingly popular in the software development field. It stands to reason that there is a need to ensure that the EA Blueprint Pattern is appropriate even in a DevOps context, where different tools and routines may be used than in traditional development. To complete this project, a use case of the EA Blueprint Pattern has been moved from a traditionally developed and deployed setting to a DevOps setting that includes essential DevOps tools such as Infrastructure as Code, a cloud environment, and a CI/CD pipeline that enables automatic deployment and therefore a shorter system development life cycle. By doing this, it can be gauged how well the EA Blueprint Pattern is adapted to a modern software development process which utilises the advantages of DevOps.

Statens veterinärmedicinska anstalt, SVA, is a government agency that works for better animal and human health with a primary focus on infectious animal diseases. One of their projects involves tracking the spread of Campylobacter infection in broilers and the occurrence of antimicrobial resistance in these bacteria. A pipeline was developed to contribute to making the analysis of Whole Genome Sequencing (WGS) data from Campylobacter more effective. This was done by changing the currently used pipeline’s programming language from Perl to Python and adding the possibility to run multiple analyses in parallel. With parallelization, the time for running multiple analyses was reduced compared to running them sequentially, even if it was not as fast in practice as in theory. It also did not work as well when running parallel analyses of different strains compared to identical strains. Furthermore, different attributes of the pipeline were changed or added to improve the pipeline and a database comparison was performed in order to suggest the best ones for future use. VFDB, CARD, and MEGARes were suggested as appropriate databases to use in future WGS analysis of Campylobacter. Due to a lack of resources and technical difficulties, some of the requested attributes for the pipeline could not be implemented, such as the tool Pilon and the inclusion of MLST and cgMLST analysis. Nonetheless, the pipeline is well structured, has most of the requested tools, and is easy to run. With some minor improvements, the pipeline will be a useful tool for SVA and their project.