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Mining novel terpene synthases from large-scale repositories
Čalounová, Tereza ; Pluskal, Tomáš (advisor) ; Štáfková, Jitka (referee)
Terpenes and terpenoids represent the largest and most structurally diverse group of natural products, with applications across many fields, including the pharmaceutical industry. These molecules are synthesized in nature by enzymes known as terpene synthases. This thesis conducted a bioinformatic analysis of a curated database containing all 1125 experimentally characterized terpene synthases, focusing on identifying patterns in sequence lengths and domain architectures of these enzymes across different kingdoms of life. Based on this analysis's knowledge, sequence-guided mining was conducted to identify possible new terpene synthases. Using nearly 5.5 billion protein sequences from various large-scale sequence repositories, the mining resulted in the identification of more than 600 thousand putative terpene synthases. These putative terpene synthases mainly originate from Bacteria and metagenomes, sources that had historically been less explored. The resulting dataset, accompanied by a phylogenetic tree, sequence similarity network, and two prioritization scores, offers a valuable resource for the discovery of novel terpenes. Keywords: terpene synthase, TPS, mining, Pfam, SUPERFAMILY, domain, terpene
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The comparison of animal species determination (barcoding) methods
Maťátková, Jana ; Vaněk, Daniel (advisor) ; Sember, Alexandr (referee)
Species identification is the key element in many scientific fields, from diversity studies to forensic science and the food industry. Traditional morphological methods based on the visual distinction of anatomical features often encounter limits associated with distinguishing morphologically similar animals. However, with the rise of molecular methods, a new perspective has emerged, namely DNA analysis, which offers higher accuracy and independence from external factors. This bachelor's thesis presents a detailed overview and a comparsion of various molecular methods used to identify animals. It focuses on a thorough evaluation of the principles of these methods and their effectiveness. Special attention is paid to target sequences associated with DNA barcoding, its universal use and limitations that may arise depending on specific animal species. An important element of successful identification is the existence and use of databases that serve as a source of reference data to compare sequences from unknown samples.
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Modelovací úlohy - Role strategií při procesu transformace mentální představy do formální reprezentace
GEYER, Jakub
Modeling tasks, consisting in the transformation of a mental image into the formal representation, very often occur in the study of computer science, mathematics, but also in other technical and non-technical fields. From the didactic point of view, it is interesting in modeling tasks (among others), which methods/procedures solvers (students) use to manage more demanding complex tasks. It is often possible to encounter students, who have significant problems solving complex tasks (or they are not able to solve them satisfactorily at all), even though they did not have any problems with similar simpler tasks before during the course. A possible explanation can be seen in the suboptimal use of modeling strategies (e.g. divide&conquer, iterative approach, etc.) or their total absence. This research is focused on the analysis of the role of strategies in modeling tasks, the possibilities of their support/development and teaching methods. The study is conducted, which aimed to analyze the possible impact of strategies in the procedures of university students in solving modeling tasks in the areas of 3D modeling and databases. The goal of the research was also to analyze the possibility of generalization of modeling strategies and their transferability between domains with different type of model.
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Database Design
Vasmanský, Lukáš ; Kříž, Jiří (referee) ; Luhan, Jan (advisor)
This bachelor's thesis focuses on the design of a relational database system for data storage and subsequent analysis within a specific catering establishment. The thesis proposes an efficient database structure that enables the collection of data about diners and their orders. The database is designed to reduce the costs of the entity and streamline the operation of the canteen.
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A Service for Querying Aliases of Malicious Software
Julina, Tomáš ; Regéciová, Dominika (referee) ; Zobal, Lukáš (advisor)
The main goal of this bachelor's thesis is to design and develop service, which would deal with the problem of existence of malware aliases by providing mapping of each alias to specific family. The specific family would be set as canonical in advance. This thesis also presents several ways of obtaining data automatically for such mapping. The created service is meant to help malware researchers in their research. It can also be used in existing services, that currently don't take malware aliases into account, which could have caused some duplicity in their data.
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System for monitoring of technical parameters of gamma ray emitters
Šulc, Michal ; Králík, Martin (referee) ; Mézl, Martin (advisor)
The thesis "System for Monitoring the Technical Condition of Irradiators" focuses on developing a system that simplifies the display, interpretation, and subsequent processing of data obtained from stability tests on linear accelerators. The thesis is divided into theoretical and practical parts. The theoretical part deals with radiotherapy and the technical tests conducted. The practical part describes the development and implementation of the system. The resulting product will be used in clinical practice at the Radiation Oncology Clinic of the Masaryk Memorial Cancer Institute.
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Use of Business Intelligence Tools in a Small Enterprise
Siakhel, Luther Thawng ; Luhan, Jan (referee) ; Kříž, Jiří (advisor)
The bachelor's thesis focuses on the selection and application of suitable Business Intelligence tools through Microsoft Power BI Desktop. The thesis contains a theoretical introduction that defines the key terms, that are necessary to understand the following parts of the thesis. This is followed by a section to analyze the current state of the company. The final part is focused on data processing using BI tools and the presentation of results in the form of visualization reports to support the company's strategic decisionmaking.
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Plugins for Efficient Datastore in the Sysrepo Library
Kušnírik, Ondrej ; Martínek, Tomáš (referee) ; Matoušek, Jiří (advisor)
This work concerns an introduction to the sysrepo library and its datastore plugins, problems with storing data to files and solving these problems by connecting a database to the sysrepo library. In short, this library serves as a complex repository for configuration YANG data on Unix/Linux systems. Data, which the default plugin stores in files, cannot be managed fast and efficiently enough causing overall slowdown of data management. A database connected to the sysrepo library via a datastore plugin could however solve this issue. After comparing different databases, two were selected (MongoDB and Redis) based on work efficiency with YANG data and other qualities. The datastore plugins were then implemented for these databases, optimized and tested for performance at the end. In comparison to the original plugin based on files, the plugins based on databases primarily excel at management of low amounts of data, where for instance the loading of an element from one hundred thousand is faster by up to three orders of magnitude.
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Optimization of Data Collection
Martynek, David ; Klusák, Aleš (referee) ; Kříž, Jiří (advisor)
This bachelor's thesis deals with the design and creation of a database for the company ABC. It comprises a theoretical part, an analysis of the current state, and a practical part. The theoretical part provides necessary information for understanding databases. The analysis of the current state presents the company ABC. The practical part focuses on the actual solution proposal. After completing this part, an evaluation follows.
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Proposal of Part of Information System as a Support for Managerial Tasks
Krejčová, Gabriela ; Kindlová, Dita (referee) ; Luhan, Jan (advisor)
The goal of this bachelor thesis is to create a proposal for a part of company's information system. Based on the current state analysis of the company's information system and the SWOT analysis, the requirements for the new information system were defined. Using data and functional modeling, the design of a partial part of the information system for solving managerial tasks is presented in order to unify the analyzes and outputs performed by sales representatives, to increase their work efficiency and facilitate the manager's control over the performance of his co-workers.
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