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Multiple sequence alignment
Ferenc, Matej ; Pangrác, Ondřej (advisor) ; Bálek, Martin (referee)
Title: Multiple Sequence Alignment Author: Matej Ferenc Department: Department of Applied Mathematics Supervisor: RNDr. Ondřej Pangrác, Ph.D. Supervisor's e-mail address: pangrac@kam.mff.cuni.cz Abstract: In this work we study multiple sequence alignment problem, for aligning protein or DNA sequences. There is a lot of ways how to solve this problem. Some of them are optimized for speed, while others are optimized for quality of the produced alignment. We implement two methods - progressive and iterative, which are based on creating a phylogeny tree and align sequences according to it. We will also provide a few distance methods. Our aim is to compare the methods and their parameters for creating best alignments and to find out, when to use which methods. Keywords: bioinformatics, alignment, sequences
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Possible improvements of global optimization methods inspired by nature
Pátek, Zdeněk ; Rytíř, Pavel (advisor) ; Bálek, Martin (referee)
This study focuses on the global optimization of functions of real variables using methods inspired by nature. It contains a description of selected global optimization techniques (Differential Evolution, Self-Organizing Migrating Algorithm, Steady-State Evolutionary Algorithm, Particle Swarm Optimization, Gregarious Particle Swarm Optimizer a Hybrid Particle Swarm with Differential Evolution Operator). I have found four improvements of these techniques, discovered their suitable parameter configurations and compared them on chosen trial functions. Experimental results proved that described improvements can increase performance of the optimization techniques inspired by nature.
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Spectrogram generation and their synthesis
Krajíček, Jan ; Bálek, Martin (advisor) ; Pangrác, Ondřej (referee)
The thesis describes generation of time-frequency-intensity graphs (spectrograms) of audio recordings using the Fourier transform. The theoretical possibilities and limitations of spectrogram synthesis (audio reconstruction of a given spectrogram) are discussed and two practical synthesis methods are described, based on reconstruction using pure tones and random noise. Spectrogram generation and both described synthesis methods are implemented in the form of a computer program with a graphical user interface, allowing straightforward configuration of relevant parameters.
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Music manager
Sixta, Martin ; Bílý, Tomáš (advisor) ; Bálek, Martin (referee)
This Bachelor thesis describes a music manager program "Yamp"from the perspective of a software developer. The program Yamp is a graphical user interface application which can play audio files, view and edit metada information stored inside audio files, and enables to view additional information not stored inside audio files. The Yamp application can be categorized as a music player with collection management capabilities. The program is written in C++ programming language (with some parts written in plain C). It uses software libraries from the GNOME Desktop Platform, for audio playback is used the GStreamer library. The graphical user interface uses the gtkmm library. The application was tested by the author of the program. The thesis is split up in 5 chapters. The first chapter explains motivation behind the work along with summary of technologies and libraries used to develop the application. Chapter 2 presents overview of the most important technology used to develop the program. Chapter 3 describes installation process and usage of the application. Chapter 4 describes details of implemention and finally Chapter 5 sumps up experience obtained during development of the programn. The work also containes the software application itself, user's guide and application programming interface documentation...
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Planar drawings of graphs
Macošek, Jan ; Pangrác, Ondřej (advisor) ; Bálek, Martin (referee)
This text and the enclosed program focuses on the planar drawings of graphs: It first sums up the basics of this domain, then describes the planarity testing, finding of the planar embedding and the straight-line planar drawing of graph using Schnyder's grid embedding algorithm. It also explores the effect of different triangulation strategies and the impact of the selection of the outer face on the planar drawing in several criteria. It also uses pictures made with the enclosed program to show the planar drawings. Powered by TCPDF (www.tcpdf.org)
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Music effects
Marko, Matej ; Bálek, Martin (advisor) ; Valla, Tomáš (referee)
Title: Music effects Author: Matej Marko Department: Department of applied mathematics Supervisor: Mgr. Martin Bálek Supervisor's e-mail address: Martin.Balek@mff.cuni.cz Abstract: The effects have crucial position in the proccess of creating music. They enrich song's arrangement and make it all more colorful. Aim of the work is to create application that allows the user to play a sound file and apply chosen effets on it's content in real-time. All changes in effects' settings are imidiatelly transformed into the hearable results. Certain settings can be applied on the whole file and the results afterwards exported to the file. Part of the application is naturally implementation of chosen effects. Main topic of the work's text are methods used to implement the effects. Keywords: effects, music, sound
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Effective group elevator scheduling
Bartoš, Michal ; Černý, Jakub (advisor) ; Bálek, Martin (referee)
This work deals with effectiveness of planing algorithms controlling group of elevators. For comparing planing algorithms was created simulation software, which test its properties with regarding to setting of parameters of elevator system and building where is elevator system placed. Results of testing are compared by measured values and determinate pertinence of use of particular planing algorithm in dependency on setting of parameters. Capabilities of planing algorithm also depend on informations which can elevator system provide to it. For this reason this work also deals with elevator system itself and suggest its changes allowing planing algorithms work more effective.
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Graph Visualisation
Kratochvíl, Jakub ; Pergel, Martin (advisor) ; Bálek, Martin (referee)
This thesis concentrates on drawing graphs in 3D. In the first part of the text, we concentrate on orthogonal layouts of graphs with maximum degree 6. We show how to draw graphs using high dimensional embedding (HDE) and propose a new fast algorithm based upon sampling of the HDE. Further, we developed an application for Win32 that allows the user to translate, zoom and rotate the graph drawing, thus taking full advantage of the 3D layout.
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Sociomap Visualization
Höschl, Cyril ; Bálek, Martin (advisor) ; Černý, Jakub (referee)
In this work we study algorithms for visualization of sociomaps. We focus on surface-fitting method which converts bitmap picture into a sequence of closed spline curves. For curve-fitting, we describe tracing algorithm that for a given level of height in a smooth surface finds a contour as a closed Bézier curve. Further we describe algorithm that draws hierarchy of clusters into a 2D plane. We first create a skeleton of the cluster analysis which we then project into a plane using curve-fitting method. We describe methods of interpolation of surface based on inverse distances weights and also we present a linear interpolation based on Delanauy triangulation. We apply these methods on sociomappig analysis. Sociomapping is a data-mining method for visualization of relations among objects as well as analyzing statistical data. The result of sociomapping analysis is an easy-to-read picture - a sociomap. We explain cluster analysis for model of a sociomap and also we describe statistical test based on fuzzy approach.
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