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Using Cellular Automata for Data Compression
Polák, Marek ; Trunda, Otakar (advisor) ; Mráz, František (referee)
In this thesis we research the possibilities of using cellular automata for lossless data compression. We describe the classification of cellular automata and their current usage. We study the properties of various types of elementary cellular automata (i.e. Wolfram rules), describe their equivalence classes, the ways of forward as well as backward simulation, we examine the rules with interesting behavior. The states provided by these rules are evaluated in terms of their orderliness (e.g. the ratio of living cells or approximation of entropy). We implement some standard compression algorithms and compare them in terms of usability for best rated states. By application of acquired knowledge we propose a new compression algorithm, test it on text and image data and compare the results with traditional compression algorithms. Powered by TCPDF (www.tcpdf.org)
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Development of MMORPG games in a decentralized environment
Polák, Marek ; Gemrot, Jakub (advisor) ; Kratochvíl, Miroslav (referee)
This thesis examines methods which could be used for developing MMORPG games so that there is no single entity that could arbitrarily control game mechanics, virtual assets or other game aspects. The theoretical part systematically analyzes the usual aspects of MMORPG games, then the principles of decentralized cryptocurrencies are presented, and one of them, Ethereum, is analyzed in more detail. Based on this theoretical knowledge, methods are proposed on how to use Ethereum to implement the identified aspects of MMORPG games, and the restrictions which must be imposed on these aspects are recognized. The practical part then introduces a specific implementation of MMORPG game on Ethereum, which demonstrates the above methods. In conclusion, the chosen approach is compared to the games with a common client-server architecture, especially in terms of complexity and gaming costs. 1
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Utilization of protein radical foootprinting for stuctural biology
Polák, Marek ; Novák, Petr (advisor) ; Junková, Petra (referee)
(In English) The reaction of highly reactive oxygen radicals with protein solvent-accessible residues can be utilized to map protein landscape. Fast photochemical oxidation of proteins (FPOP) is an MS- based technique, which utilizes highly reactive radical species to oxidize proteins and map protein surface or its interactions with their interaction partners. In this work, FPOP was employed to study protein-DNA interactions. First, a full-length of FOXO4-DBD was successfully expressed and purified. The ability of the protein to bind its DNA-response element was verified by electrophoretic and MS-based techniques, respectively. Optimal experimental conditions were achieved to oxidize the protein itself and in the presence of DNA, respectively. Oxidized samples were analyzed by bottom-up and top-down approach. In the bottom-up experiment, modification of individual residues was precisely located and quantified. Different extend of modification was observed for protein alone and in complex with DNA. To avoid experimental artifacts analyzing multiply oxidized protein, standard bottom up approach was replaced by a progressive top-down technology. Only a singly oxidized protein ion was isolated, and further fragmented by collision-induced dissociation (CID) and electron-capture dissociation (ECD),...
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The role of amino acids from the C-terminus of the insulin B chain in the selectivity towards insulin receptor isoforms.
Polák, Marek ; Žáková, Lenka (advisor) ; Obšilová, Veronika (referee)
The main function of insulin as a hormone is to control glucose homeostasis in the blood. This control takes place at different levels in different parts of the body. The complexity of the regulation of blood glucose levels is manifested through the insulin receptor (IR) and its two isoforms, IR-A and IR-B. IR-B is responsible for metabolic effects and the distribution in adipocytes, muscles and hepatic cells, whereas IR-A has, above all, mitogenic effects with lymphocytes, spleen, brain and cancer cells. Today's treatment of diabetes patients is focused on the use of insulin analogues, insulin replacemensts with a different IR-A and IR-B binding affinity. Today's patients use two different types of analogues, called fast-acting and basal, with a focus on the combination of these two types throughout the day. In 2011, prof. Belfiore from the Universtiry of Catanzzaro published a scientific article about the close relation between diabetes and some cancer types. This article triggered extensive debates about the impact of insulin or insulin analogues on the mitogenic isoform IR-A of the insulin receptor, and IR-A isoform on the insulin-like growth factor type 1. In the same year, two scientific groups from a Danish company Novo Nordisk, published the first hints at receptor isoform-selective insulin...
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Evolution and Adaptability of Complex Applications
Polák, Marek ; Holubová, Irena (advisor) ; Rahayu, Wenny (referee) ; Krátký, Michal (referee)
Evolution and Adaptability of Complex Applications Abstract In these days the applications become more complex that causes maintenance problems while evolving these applications. A change in one part of the applica- tion can significantly affect other parts of the application. The next aspect can be related systems which communicate with this application. They must be up- dated to satisfy their correct functionality. These problems can concern multiple domains, e.g., UML diagrams, XML schema diagrams, relational schemas, APIs, etc. We focus on this problem from the perspective of the MDA, which uses the platform independent model (PIM) for a general view of the problem and the platform specific model (PSM) for particular domains. Moreover, these models can be interconnected and related to each other. We propose novel PSM models from various widely used domains, operations over these models and algorithms for model transformations. Thanks to the MDA principle, it is possible to combine presented models and model a complex application. All models and related algorithms we present were experimentally implemented and tested in the DaemonX framework on real-world data for their verification. 1
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Using Cellular Automata for Data Compression
Polák, Marek ; Trunda, Otakar (advisor) ; Mráz, František (referee)
In this thesis we research the possibilities of using cellular automata for lossless data compression. We describe the classification of cellular automata and their current usage. We study the properties of various types of elementary cellular automata (i.e. Wolfram rules), describe their equivalence classes, the ways of forward as well as backward simulation, we examine the rules with interesting behavior. The states provided by these rules are evaluated in terms of their orderliness (e.g. the ratio of living cells or approximation of entropy). We implement some standard compression algorithms and compare them in terms of usability for best rated states. By application of acquired knowledge we propose a new compression algorithm, test it on text and image data and compare the results with traditional compression algorithms. Powered by TCPDF (www.tcpdf.org)
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Evolution and Adaptability of Complex Applications
Polák, Marek ; Holubová, Irena (advisor) ; Rahayu, Wenny (referee) ; Krátký, Michal (referee)
Evolution and Adaptability of Complex Applica- tions Abstract In these days the applications become more complex that causes maintenance problems while evolving these applications. A change in one part of the appli- cation can significantly affect other parts of the application. The next aspect can be related systems which communicate with this application. They must be updated to satisfy their functionality. These problems can concern multiple do- mains, e.g., UML diagrams, XML schema diagrams, relational schemas, etc. We focus on this problem from the perspective of the MDA, which uses the platform independent model (PIM) for a general view of the problem and the platform specific model (PSM) for particular domains. Moreover, these models can be in- terconnected. We propose novel PSM models from various widely used domains, operations over these models and algorithms for model transformations. Thanks to the MDA principle, it is possible to combine presented models and model a complex application. All models and related algorithms we present were experi- mentally implemented and tested in the DaemonX framework on real-word data for their verification. 1
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Web Data Extraction
Novella, Tomáš ; Holubová, Irena (advisor) ; Polák, Marek (referee)
Creation of web wrappers (i.e programs that extract data from the web) is a subject of study in the field of web data extraction. Designing a domain-specific language for a web wrapper is a challenging task, because it introduces trade-offs between expressiveness of a wrapper's language and safety. In addition, little attention has been paid to execution of a wrapper in restricted environment. In this thesis, we present a new wrapping language -- Serrano -- that has three goals in mind. (1) Ability to run in restricted environment, such as a browser extension, (2) extensibility, to balance the tradeoffs between expressiveness of a command set and safety, and (3) processing capabilities, to eliminate the need for additional programs to clean the extracted data. Serrano has been successfully deployed in a number of projects and provided encouraging results. Powered by TCPDF (www.tcpdf.org)
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Extension of the XML Check system
Hudeček, Petr ; Holubová, Irena (advisor) ; Polák, Marek (referee)
In this thesis, we improve the 2011 homework manager called XML Check. It is a web application used in the course XML Technologies at MFF UK and FEL ČVUT. Students and teachers have identified a number of deficiencies in the system that we are fixing. They have also suggested new functionality that we are implementing. Checking submissions for plagiarism is the most important new feature. This check is now applied to each new submission. We tried several different algorithms for this (Levenshtein distance, Greedy-String-Tiling algorithm and Zhang-Shasha tree edit distance) and we compare these algorithms. We determine their performance based on experiments on student submissions from the past four years. The improved system is now in active use.
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Generating of Synthetic XML Data
Rychnovský, Dušan ; Holubová, Irena (advisor) ; Polák, Marek (referee)
The aim of the thesis was to develop an algorithm to generate synthetic XML documents to cover the resolution of an XPath query with test cases, with a special emphasis on the ease of configuration. We have also implemented a prototype, optimized its performance and demonstrated its properties by running it on sample data. Powered by TCPDF (www.tcpdf.org)
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