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Vulnerability Reports Analysis and Management
Domány, Dušan ; Toropila, Daniel (advisor) ; Galgonek, Jakub (referee)
Various vulnerabilities in software products can often represent a significant security threat if they are discovered by malicious attackers. It is therefore important to identify these vulnerabilities and report their presence to responsible persons before they are exploited by malicious subjects. The number of security reports about discovered vulnerabilities in various software products has grown rapidly over the last decade. It is becoming more and more difficult to process all of the incoming reports manually. This work discusses various methods that can be used to automate several important processes in collecting and sorting the reports. The reports are analyzed in various ways, including techniques of text mining, and the results of the analysis are applied in form of practical implementation.
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Czech text diacritization
Dušek, Boris ; Skopal, Tomáš (advisor) ; Galgonek, Jakub (referee)
The subject of this thesis is the implementation of an application that lls in accents to a Czech text from which the accents were removed. The application employs a dictionary and learning in order to predict the correct word. The application consists of a console mode, where the text is transformed automatically, and also of a GUI mode, that enables direct user feedback and points out conflicts to the user and proposes probable solutions.
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Intelligent flight ticket search engine
Hiekeová, Margaréta ; Skopal, Tomáš (advisor) ; Galgonek, Jakub (referee)
The subject of this thesis is implementation of an internet application for plane tickets searching in a form of a meta-searcher. In comparison with trivial functionality of commercial applications searching only flights between specific destinations, this application offers following kind of searching: "Flight begins up to 300 km from Prague and ends up to 500 km from Naples". Plane ticket information sources are integrated using modular architecture. Application retrieves the data from individual sources in parallel. Users can either wait for results or come pick them up later, because search history is persisted. The thesis comprises also programmer and user documentation.
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Query languages for the Semantic web
Galgonek, Jakub ; Yaghob, Jakub (advisor) ; Vojtáš, Peter (referee)
The idea of the Semantic Web brings new requirements such as to create and store metadata of documents or resources. Also ability to search in such metadata is needed. Existing query languages for the Semantic Web are unfortunately either too weak or have complicated syntax or semantics. The aim of this thesis is to compare existing Semantic Web query languages and to propose new one considering its expression strength. This comparison is done by juxtapositioning of their approaches to various issues in querying. Such issues are, for example, a basic selection of data, an ability to select data with recursively defined structure, creating data, a way of working with blank nodes, etc. On the basis of this comparison, the Tequila language is proposed. The Tequila is based on named pattern and provide general recursion. This thesis also shows the way how to use Tequila language and further, it compares the Tequila with other query languages.
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Data Profiling
Hladíková, Radka ; Kyjonka, Vladimír (advisor) ; Galgonek, Jakub (referee)
Title: Data Profiling Author: Radka Hladíková Department: Department of Software Engineering Supervisor: Ing. Vladimír Kyjonka Supervisor's e-mail address: Vladimir.Kyjonka@cze.sas.com Abstract: This thesis puts mind on problems with data quality and data profiling. This Work analyses and summarizes problems of data quality, data defects, process of data quality, data quality assessment and data profiling. The main topic is data profiling as a process of researching data available in existing data sources and creating of statistics and information about these data. There is a projected system for evaluating data status in term of its quality. Work is focused on measuring of general characteristic of data, following data defects and its analyses. With the help of data quality SW there is a projected and realized system for evaluation of data quality for real data. Keywords: data quality, data profiling, data quality metric, DataFlux
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WIWIL - social network for traverels
Ončo, Martin ; Vrána, Jakub (advisor) ; Galgonek, Jakub (referee)
Every day the number of people using social networks, where you create your network of friends from different areas of interest, is growing. They share experiences and valuable advice. The aim of this work is to implement a social network for travelers. The network enables travelers to create their own maps of visited localities. The users are able to write travel diaries corresponding these localities, which they can share with their friends or publish them. Social network is also designed for travel agencies. Tour offers will be sent from their profile to selected user inboxes. WIWIL - social network for travelers will be programmed in PHP and will use the services of existing network Facebook.
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Similarity Search in Protein Structure Databases
Galgonek, Jakub ; Skopal, Tomáš (advisor) ; Porto, Markus (referee) ; Svozil, Daniel (referee)
Proteins are one of the most important biopolymers having a wide range of functions in living organisms. Their huge functional diversity is achieved by their ability to fold into various 3D structures. Moreover, it has been shown that proteins sharing similar structure often share also other properties (e.g, a biological function, an evolutionary origin, etc.). Therefore, protein structures and methods to identify their similarities are so widely studied. In this thesis, we introduce a system allowing similarity search in pro- tein structure databases. The system retrieves, given a query structure, all database structures being similar to the query structure. It employs several key components. We have introduced a novel similarity measure assigning similarity scores to pairs of protein structures. We have designed specific access method based on LAESA metric indexing and using the proposed measure. The access method allows to search similar structures more effi- ciently than when a sequential scan of a database is employed. To achieve further speedup, the measure and the access method have been parallelized, resulting in almost linear speedup with the respect to the number of available cores. The last component is a web user interface that allows to accept a query structure and to present a list of...
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Similarity Search in Protein Structure Databases
Galgonek, Jakub
Proteins are one of the most important biopolymers having a wide range of functions in living organisms. Their huge functional diversity is achieved by their ability to fold into various 3D structures. Moreover, it has been shown that proteins sharing similar structure often share also other properties (e.g, a biological function, an evolutionary origin, etc.). Therefore, protein structures and methods to identify their similarities are so widely studied. In this thesis, we introduce a system allowing similarity search in pro- tein structure databases. The system retrieves, given a query structure, all database structures being similar to the query structure. It employs several key components. We have introduced a novel similarity measure assigning similarity scores to pairs of protein structures. We have designed specific access method based on LAESA metric indexing and using the proposed measure. The access method allows to search similar structures more effi- ciently than when a sequential scan of a database is employed. To achieve further speedup, the measure and the access method have been parallelized, resulting in almost linear speedup with the respect to the number of available cores. The last component is a web user interface that allows to accept a query structure and to present a list of...
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Use of residue-level annotations for structural prediction of protein-ligand binding sites
Břicháčková, Kateřina ; Hoksza, David (advisor) ; Galgonek, Jakub (referee)
The number of experimentally resolved protein structures in the Protein Data Bank has been growing fast in the last 20 years, which motivates the develop- ment of many computational tools for protein-ligand binding sites prediction. Binding sites prediction from protein 3D structure has many important applica- tions; it is an essential step in the complex process of rational drug design, it helps to infer the side-effects of drugs, it provides insight into proteins biological functions and it is helpful in many other fields, such as protein-ligand docking and molecular dynamics. As far as we know, there has not been a study that would systematically investigate general properties of known ligand binding sites on a large scale. In this thesis, we examine these properties using existing experimen- tal and predicted residue-level annotations of protein sequence and structure. We present an automated pipeline for statistical analysis of these annotations, based on hypothesis testing and effect size estimation. It is implemented in Python and it is easily extensible by user-defined annotations. The usage is demonstrated on 33 existing annotations and 4 different datasets. The practical significance of the results is tested with P2Rank prediction method. We hope that the results as well as the pipeline...
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Similarity Search in Protein Structure Databases
Galgonek, Jakub
Proteins are one of the most important biopolymers having a wide range of functions in living organisms. Their huge functional diversity is achieved by their ability to fold into various 3D structures. Moreover, it has been shown that proteins sharing similar structure often share also other properties (e.g, a biological function, an evolutionary origin, etc.). Therefore, protein structures and methods to identify their similarities are so widely studied. In this thesis, we introduce a system allowing similarity search in pro- tein structure databases. The system retrieves, given a query structure, all database structures being similar to the query structure. It employs several key components. We have introduced a novel similarity measure assigning similarity scores to pairs of protein structures. We have designed specific access method based on LAESA metric indexing and using the proposed measure. The access method allows to search similar structures more effi- ciently than when a sequential scan of a database is employed. To achieve further speedup, the measure and the access method have been parallelized, resulting in almost linear speedup with the respect to the number of available cores. The last component is a web user interface that allows to accept a query structure and to present a list of...
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