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Analysis of horizontal transfer of genetic components using static network analysis
Labanava, Anastasiya ; Jurečková, Kateřina (referee) ; Schwarzerová, Jana (advisor)
The bachelor's thesis focuses on the issue of horizontal genetic elements transfer between bacteria of different strains and the software analysis implementation that enables horizontally transferred genes identification. The packages and tools used were tested on a dataset of bacterial genomes from several strains. The thesis’ theoretical part provides a detailed description of the genetic components transfer between bacteria and describes modern laboratory techniques that enable genome sequencing in various ways. In the practical part, the thesis deals with the preprocessing of genomic files to obtain suitable data for annotation. To detect the horizontal transfer of genetic elements between bacteria, a script is introduced, which organizes annotated bacteria to tables and searches for the same genes in their genomes that, under theoretical assumptions, were horizontally transferred. Furthermore, the gene transfer is visualized using tools that graphically represent phylogenetic relations between bacteria. In the final step, bacterial genomes are connected into networks, and based on their static analysis, a discussion is conducted on the results accuracy and the success of the proposed analysis.
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Annotations editor for WYSIWYG JavaScript-Based Text Editors
Kleban, Martin ; Schmidt, Marek (referee) ; Dytrych, Jaroslav (advisor)
This master's thesis deals with analysis of plugins development possibilities for WYSIWYG JavaScript-based text editors (TinyMCE, CKEditor, NicEdit, jWYSIWYG) and it describes design of annotations editor as a plugin for chosen editors. Structured annotations editor was implemented for TinyMCE and it includes own user interface implementation without usage of any complex universal libraries. Gained pieces of knowledge from WYSIWYG editors analysis and annotations editor implementation are to be found in the enclosure.
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Knowledge Discovery from Time Series
Krutý, Peter ; Burget, Radek (referee) ; Bartík, Vladimír (advisor)
This thesis is focused on the field of knowledge discovery from data, specifically from time series. Main objective is to research Python programming language support in this area and then design and implement an application that will allow to demonstrate and compare selected methods. Methods are demonstrated in experiments using appropriate data set. The output of the thesis is a comparison of methods for specific tasks and the application implementing selected methods.
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Searching Semantically Annotated Texts
Grešová, Katarína ; Smrž, Pavel (referee) ; Dytrych, Jaroslav (advisor)
This thesis deals with the issue of semantic searching over indexes of big text data. The aim of this thesis is to design and implement a search engine with web user interface enabling dynamical configuration of access to indexes and editing annotations in the text. The thesis analyzes the current search engine solution and its shortcomings, which results in a specification of requirements for a search engine that is suitable for common use and fulfils the potential of all search engine related tools. The thesis also describes the design, implementation and testing of the resulting system, which also includes an extension in a form of global constraints, which increases the accuracy of the requested search result description.
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Semantic Enrichment Component
Doležal, Jan ; Otrusina, Lubomír (referee) ; Dytrych, Jaroslav (advisor)
This master's thesis describes Semantic Enrichment Component (SEC), that searches entities (e.g., persons or places) in the input text document and returns information about them. The goals of this component are to create a single interface for named entity recognition tools, to enable parallel document processing, to save memory while using the knowledge base, and to speed up access to its content. To achieve these goals, the output of the named entity recognition tools in the text was specified, the tool for storing the preprocessed knowledge base into the shared memory was implemented, and the client-server scheme was used to create the component.
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Image annotation using deep learning
Zarapina, Natalya ; Rajnoha, Martin (referee) ; Burget, Radim (advisor)
This semester thesis describes the design and implementation of the client-server program for classification and localization of certain elements which are present in provided images. This program loads a set of images and use deep learning, especially deep convolution neural network perform a classification. First part describes the architecture, basic principles of operations in convolution network and chosen machine learning algorithms for classification. Second part contains a description of created program.
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Annotation Addon for Internet Explorer
Pěnkava, Pavel ; Kouřil, Jan (referee) ; Dytrych, Jaroslav (advisor)
This thesis deals with the creation of the Internet Explorer browser extension for annotation creation. It describes the extension concept and the consequent implementation of solution. It also includes the evaluation of other applicable technologies for extension creation, along with their advantages and disadvantages. Addon is designed to cooperate with the annotation server of 4A Framework (Annotations Anywhere, Annotations Anytime) project. The communication format between them is therefore based on the project specifications.
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Annotations in WYSIWYG Text Editors
Loukota, Petr ; Kouřil, Jan (referee) ; Dytrych, Jaroslav (advisor)
This bachelor's thesis deals with the design of fixes and improvements of available annotations editor and their implementation. The annotations editor for WYSIWYG text editors is created in JavaScript language and developed in the environment of TinyMCE editor. It is independent on a web browser and it will be possible to use it with other WYSIWYG editors like CKEditor or Aloha in future. The design is focused on manipulation with attributes of types but it also deals with the new concept of settings of annotations editor. The processing of suggested annotations that are sent by a server is also part of the solution. This thesis describes the design and implementation of mentioned improvements and pay attention to the possible ways of another development at its end.
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Annotation Addon for Firefox
Trhlík, Jiří ; Schmidt, Marek (referee) ; Dytrych, Jaroslav (advisor)
This bachelor's thesis aims to analyse annotations and process of creating a Mozzila Firefox addon. It provides a brief description of both problems and focuses on a design and an implementation of a Mozilla Firefox addon, which can create and store structured annotations.
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Web Tool for Playing and Anotation of BAG Files
Omacht, Martin ; Bambušek, Daniel (referee) ; Kapinus, Michal (advisor)
This work deals with the design and implementation of a web application for playback and annotation of multimedia data from files in BAG format. The created annotations are intended for training artificial intelligence in robotic systems. The resulting application is implemented with the help of React library for creating the user interface and framework Django for the server-side REST API. The entire application is containerized using Docker. This work describes the BAG format, analyzes modern libraries for creating web applications and introduces existing solutions for data annotation or playback of BAG files. Furthermore, the design of the application is presented and its implementation is described. A separate library rosbag_pyreader, which is used to read BAG files with random access, was created as part of this work. The resulting application allows user to display and annotate 2D and 3D data from multiple robotic sensors at the same time and then export the annotations in JSON format.
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