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BacSeqer: Read simulator for bacterial RNA-Seq
Fialová, Adéla ; Sedlář, Karel
The RNA-Seq method has become a key tool in transcriptomics, providing deep insight into the genetic functioning of organisms. It is essential for understanding how genes are expressed, for discovering new gene variants and for understanding pathologies at the genetic level. RNA-Seq simulators are great for testing and validating bioinformatics tools, they offer a way to compare different computational algorithms and allow examining different sequencing protocols, parameter settings and sample sizes to ensure the most efficient use of resources. This study introduces BacSeqer, an RNA-Seq simulator specifically designed for bacterial transcriptomes with the aim of producing data that faithfully resembles those obtained in real experiments. It allows to take into account the specificities of the bacterial genome, especially an existence of only exons and their organization in operons that are not normally present in eukaryotes.
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Evaluating BPL Communication: A Simulation Approach
Baranyk, Matěj ; Benešl, Lukáš ; Rusz, Martin
In recent years BPL (Broadband over Power-line) technology is becoming more used. Despite the technology not needing any additional cable installation it is important to make sure that using the technology itself makes sense or what the needed requirements will be. Due to this reason, we opt to simulate almost real scenarios and compare them with outputs from network simulator ns-3. This way we can recognize the usefulness of our efforts even before we make any plans to install anything, which saves time and money. Furthermore, we can use the same simulator for diagnostics of already installed BPL routes.
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Design of 90 degree phase shift hybrid coupler
Ondrejka, Adam ; Kříž, Tomáš
This paper describes the design procedure for quadrature hybrid for UHF band. Circuits are based on distributed parameters with anticipated manufacturing on a PCB. Emphasis is put on a compact size, three methods are used for size reduction of transmission lines. All designs are simulated in electromagnetic simulation software. The best design using meandered lines is verified by measurement with no detectable deviation from target working frequency. Temperature simulation is conducted with the best design.
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Biophysical conditions triggering depolarization block in excitatory neurons.
Tobiáš, Marek ; Berling, David Maximilian (advisor) ; Korvasová, Karolína (referee)
Optogenetics is an increasingly popular neuronal stimulation technique used for study- ing neural circuits and controlling brain activity. However, when applied without suffi- cient knowledge, it can cause unintentional silencing of the targeted neurons by inducing a state termed depolarization block (DpB), in which neurons cease to fire action poten- tials. The susceptibility to silencing is not consistent among neurons, and the relationship between their biophysical properties and their vulnerability to DpB remains poorly un- derstood. In this thesis, we investigate how the densities of voltage-gated sodium (Nav) and potassium (Kv) channels, which are known to govern DpB dynamics, influence the neuron's ability to resist this phenomenon. We also examine the impact of neuronal size on DpB susceptibility. Using a computational model of a layer V pyramidal neuron, which we simplify to a single compartment to represent the behavior of a generic excita- tory neuron, we introduce an automatic classifier consistently identifying DpB through voltage trace analysis. This allows us to systematically assess the influence of varying Nav or Kv channel densities in the neuron's membrane. We discover that increasing these densities enhances the neuron's resistance to DpB. Contrary to previous studies, neu- ronal size...
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Application of Python programming language in image analysis and modeling of physical processes of graphene
Stehlíček, Kamil ; Képeš, Erik (referee) ; Bartošík, Miroslav (advisor)
In this thesis, we focus on evaluating experimental data using the Python programming language across three different physics problems dealing with graphene. The goals of the thesis are based on practical experiments that use gallium or gallium nitride to alter the electro-optical properties of graphene or experiments that require the simulation of charge propagation in graphene nanoelectronics. These tasks successively use image analysis and numerical simulations. The theoretical part of the thesis serves as a research and as an introduction to basic image processing algorithms and numerical simulation techniques. The practical part of the thesis then focuses on the evaluation of the success of each program, its implementation in practical evaluation and explanation of experimental results.
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Movement Planning of a Hexapod Robot
Hostačná, Kristína ; Šátek, Václav (referee) ; Rozman, Jaroslav (advisor)
Táto práca predstavuje riešenie na dosiahnutie autonómnej navigácie šesťnohých robotov k cieľu v zornom poli pomocou neurónových sietí. Toto riešenie bolo implementované na dvoch verziách robotov – jednoduchý dizajn s dvoma kĺbmi na každej nohe a zložitejší dizajn s tromi kĺbmi na každej nohe. Hlavná výzva tohto problému - tj. zložitosť ovládania viacerých kĺbov narástla, aby sa umožnil širší rozsah pohybov a tým aj zväčšenie možností využitia robota. Metodológia výskumu zahŕňa využitie experimentov v simulácii aj v reálnom svete na modelovanie a zber údajov. Údaje z rôznych senzorov, vrátane kamier a pozícií serv, sú využité na trénovanie modelov neurónových sietí schopných interpretovať senzorické vstupy a generovať riadiace signály pre aktuátory robota. Základná architektúra neurónovej siete bola spočiatku nasadená pre obe konfigurácie, zatiaľ čo sofistikovanejší prístup zahŕňajúci konvolučné a rekurentné neurónové siete bol použitý neskôr. Vo výsledku, trénované neurónové siete demonštrujú schopnosť navigácie k cieľu.
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Discrete modeling of transaction propagation in Bitcoin
Marek, Tomáš ; Marek, Marcel (referee) ; Zavřel, Jan (advisor)
Technologie blockchain je stěžejním bodem fungování Bitcoinu. Cílem teoretické části této práce je popsat principy, na kterých je technologie blockchain založena a zároveň shromáždit informace o tom, jak jsou transakce šířeny v síti Bitcoin. Cílem praktické části je vytvořit model velmi zjednodušeného Bitcoin Core klienta, který umožňí vytvářet, posílat a přijímat transakce na základě propagačního algoritmu využívaného v síti Bitcoin. Model je následně spouštěn v simulačním prostředí a výsledky simulace jsou analyzovány s cílem určit zdrojový uzel transakce.
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Analysis of the Impact of Problem Solving Strategies using UPPAAL STRATEGO
Karásek, Filip ; Žádník, Martin (referee) ; Strnadel, Josef (advisor)
This thesis analyzes and addresses the impact of strategies created using Uppaal Stratego. The implementation of four problems, counter, maze, bitmap, and intersection is demonstrated in this thesis. Experiments are conducted on these models, and strategies are formulated. For the first three problems, strategies with a positive impact on the given system were identified. However, for the last intersection model, it was not possible to find a strategy that demonstrably improved the system. This inability to demonstrate improvement is due to limitations in Uppaal Stratego and the complexity of the model.
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Design of a rotary pendulum with a flexible joint
Palát, Ondřej ; Formánek, Martin (referee) ; Dobossy, Barnabás (advisor)
This Bachelor thesis is focused on design of laboratory equipment with flexible joint. It describes construction, control electronics design, microcontroller programming and mathematical modelling describing flexible joint dynamics. Model parameters were estimated based on measurements. First part also describes market survey and brief description of algorithms used for numeric parameter estimation.
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