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Benchmark of the Computational Tools for the Prediction of the Effect of Mutations on Protein Stability
Berezný, Matej ; Martínek, Tomáš (referee) ; Musil, Miloš (advisor)
Návrh proteínov vyžaduje informáciu o tom ako mutácie ovplyvňujú celkovú stabilitu proteinu. Pre tento prípad existuje mnoho verejne dostupných nástrojov avšak ich kolektívne používanie či porovnávanie je veľmi pracné. Presne pre tento prípad som vyvinul BenchStab; konzolovú aplikáciu/Python knižnicu navrhnutú pre rýchlu a priamočiaru manipuláciu s 18 prediktormi, umožňujúc hromadné získavanie mutačných výsledkov. Zároveň som vytvoril novú unikátnu dátovú sadu, získanú z FireProtDB. Tento dataset som použil na porovnanie 24 rôznych predikčných metód pomocou rôznych metrík.
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***???
Kopřiva, Radim ; Vašíček, Ondřej (referee) ; Fiedor, Jan (advisor)
This bachelor thesis presents the development and implementation of a web client for the Unite tool. It focuses on the design and implementation of a user interface that allows users to run analyses and view their results using analytics tools transformed by Unite. The thesis provides a basic overview of OSLC and Unite technologies, as well as a summary of the design, implementation and testing of the web client.
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Simulation scenarios in NS2 demonstrating knowledge obtained in the MPKT course
Mašek, Jan ; Mlýnek, Petr (referee) ; Jeřábek, Jan (advisor)
The aim of the bachelor´s thesis is to develop simulation tasks for modeling of data networks. The tasks will be used in the course Modern communication technique (MKPT). The networks are simulated in the environment of Network Simulator 2 (NS2). A brief description of program environment NS2, as well as basics of Tcl language is mentioned in the introduction. Described is the possibility of simulation HTTP protocol in NS2 using OTcl PagePool classes. Totally six proposed tasks form the core of the thesis. The first task uses PagePool/Math and displays the simplest communication between client, server and cache. Next task uses PagePool/CompMath and it shows the communication between client, cache, Web server, FTP server and FTP client. The task, that uses PagePool/WebTraf class, simulates communication between two clients and three servers. The last three tasks are of different topologies and course of communication using PagePool/ProxyTrace. The exercises of this class are the most complicated and their input files allow defining whole communication. The outputs of exercises are given in graphs, log files of HTTP communication and the last task contains detailed instructions.
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Simulation scenarios in NS2 demonstrating knowledge obtained in the MPKT course
Mašek, Jan ; Mlýnek, Petr (referee) ; Jeřábek, Jan (advisor)
The aim of the bachelor´s thesis is to develop simulation tasks for modeling of data networks. The tasks will be used in the course Modern communication technique (MKPT). The networks are simulated in the environment of Network Simulator 2 (NS2). A brief description of program environment NS2, as well as basics of Tcl language is mentioned in the introduction. Described is the possibility of simulation HTTP protocol in NS2 using OTcl PagePool classes. Totally six proposed tasks form the core of the thesis. The first task uses PagePool/Math and displays the simplest communication between client, server and cache. Next task uses PagePool/CompMath and it shows the communication between client, cache, Web server, FTP server and FTP client. The task, that uses PagePool/WebTraf class, simulates communication between two clients and three servers. The last three tasks are of different topologies and course of communication using PagePool/ProxyTrace. The exercises of this class are the most complicated and their input files allow defining whole communication. The outputs of exercises are given in graphs, log files of HTTP communication and the last task contains detailed instructions.
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