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Interactive environment for flow-cytometry data analysis
Molnárová, Soňa ; Kratochvíl, Miroslav (advisor) ; Pacovský, Jan (referee)
Pr·toková cytometrie je metoda pro měření chemických vlastností jed- notlivých buněk v roztoku, s aplikacemi v biologickém a klinickém výzkumu. Nedávny pokrok technologií pr·tokové cytometrie umožňuje mimořádně snadně vyrobit větší soubory dat, které popisují další zajímavé jevy, které vytváří nové výzvy pro zpracování dat a softwaru pro analýzu. Tato práce popisuje a implementuje prototyp softwaru, který zjednodušuje zpracování dat im- plementací interaktivního pipeline editoru pro analýzu, který je navržen tak, aby efektivně zpracovával obrovské soubory dat. Funkcionalita soft- waru je demonstrována implementací nejnovějšího algoritmu analýzy dat a porovnáním efektivity zdroj· s typickým nástrojem pro analýzu v pro- gramu R. Budoucí využití softwaru biology a lékaři je usnadněno poskytnutím jednoduchého rozhraní pro přidávání nových algoritm·, čímž se rozšiřuje funkčnost. 1
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High-performance exploration and querying of selected multi-dimensional spaces in life sciences
Kratochvíl, Miroslav ; Bednárek, David (advisor) ; Glaab, Enrico (referee) ; Svozil, Daniel (referee)
This thesis studies, implements and experiments with specific application-oriented approaches for exploring and querying multi-dimensional datasets. The first part of the thesis scrutinizes indexing of the complex space of chemical compounds, and details a design of high-performance retrieval system for small molecules. The resulting system is then utilized within a wider context of federated search in heterogeneous data and metadata related to the chemical datasets. In the second part, the thesis focuses on fast visualization and exploration of many-dimensional data that originate from single- cell cytometry. Self-organizing maps are used to derive fast methods for analysis of the datasets, and used as a base for a novel data visualization algorithm. Finally, a similar approach is utilized for highly interactive exploration of multimedia datasets. The main contributions of the thesis comprise the advancement in optimization and methods for querying the chemical data implemented in the Sachem database cartridge, the federated, SPARQL-based interface to Sachem that provides the heterogeneous search support, dimensionality reduction algorithm EmbedSOM, design and implementation of the specific EmbedSOM-backed analysis tool for flow and mass cytometry, and design and implementation of the multimedia...
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Development of MMORPG games in a decentralized environment
Polák, Marek ; Gemrot, Jakub (advisor) ; Kratochvíl, Miroslav (referee)
This thesis examines methods which could be used for developing MMORPG games so that there is no single entity that could arbitrarily control game mechanics, virtual assets or other game aspects. The theoretical part systematically analyzes the usual aspects of MMORPG games, then the principles of decentralized cryptocurrencies are presented, and one of them, Ethereum, is analyzed in more detail. Based on this theoretical knowledge, methods are proposed on how to use Ethereum to implement the identified aspects of MMORPG games, and the restrictions which must be imposed on these aspects are recognized. The practical part then introduces a specific implementation of MMORPG game on Ethereum, which demonstrates the above methods. In conclusion, the chosen approach is compared to the games with a common client-server architecture, especially in terms of complexity and gaming costs. 1
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Firmware for CzechLight optical measurement and calibration device
Oboňová, Ivona ; Kratochvíl, Miroslav (advisor) ; Aschenbrenner, Vojtěch (referee)
The goal of this thesis is to implement firmware for the Optical Mea- surement and Calibration Device, which was designed and constructed in CESNET. The purpose of the device is to simplify the calibration of various fiber-optical networking devices, used in CESNET infrastructure. The thesis includes an overview of the internal structure and communication interfaces within the device, which is then used for designing and implementing the firmware. The results are demonstrated on created unit tests, implemented simulator and then on realistic hardware, by running the measurement on an existing optical component. The produced firmware will serve as a basis for the development of more advanced devices in CESNET. 1
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Type inference and polymorphism for C
Klepl, Jiří ; Kratochvíl, Miroslav (advisor) ; Šefl, Vít (referee)
The C language, despite its age, is one of the main languages in systems development. It is valued for giving the user almost complete control over the memory management and the computations the program written in it performs. However, a large portion of criticism of C arises from the lack of generic programming features. C compensates that by utilizing preprocessor macros, which are prone to user errors. This problem has been addressed in the early stages of the development of the C++ language, but many systems developers refuse C++ because of its complexity and non-transparency of the code. We propose a simpler solution by applying the Hindley-Milner type sys- tem extended by Haskell type classes and type constructors. We will show that this approach is viable even with minimal changes to the syntax of C, but giving it much higher expressiveness. 1
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Tokenization-aware Diff and Patch
Antoniewicz, Arkadiusz Martin ; Kratochvíl, Miroslav (advisor) ; Horký, Vojtěch (referee)
File comparison algorithms and utilities 'diff', 'patch' and 'diff3' are widely used in programming for the purpose of code comparison, and in many version control systems. Despite the usefulness, the differences and patches produced by the tools are strictly line-oriented, which complicates processing of differently formatted data, such as free flowing text, markup, and various other formats where line breaks are not crucial. This thesis de- scribes and implements a customizable version of these tools, which allows the user to specify an arbitrary tokenization of the input, thus allowing easy diffing, patching and change-merging of content not supported by the tradi- tional diff. Additionally, the thesis describes a newly appearing challenge of managing the whitespace in the patches, and demonstrates the functional- ity on a practical use-case that can not be performed with the current diff utilities. 1
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C++ linter based on linear types
Beneš, Jiří ; Kratochvíl, Miroslav (advisor) ; Šefl, Vít (referee)
Low-level programming requires careful management of system resources, most notably memory. In C++ programmers are encouraged to follow idioms like RAII and smart pointers to handle resources correctly as violating them leads to unsafe code. Typed functional programming languages guarantee safe automatic mem- ory management, but are often sub-optimal in handling system resources. A nice, formal solution to handling resources naturally is linear types. Unfortu- nately, existing languages that support linearity are cumbersome and require explicit, complicated annotations from the programmer. We bridge the two worlds by exploring a novel combination of C++ and linear types. We describe a new type system with linearity for C++ by using constrained qualified types, while requiring no additional input from the programmer. The applied result of our work is called Lily, a static analysis tool for C++ using the Clang compiler infrastructure. Lily can statically detect large, general classes of issues, some of which are not detected by common state-of-the-art tools for C++. 1
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Scalable addressing and routing protocol for ad-hoc networks
Drozdík, Tomáš ; Kratochvíl, Miroslav (advisor) ; Kliber, Filip (referee)
Ad hoc networks are dynamic networks with no pre-existing structure or centralized administration, where all the devices participate equally in the routing of packets. The lack of established structure complicates the effi- ciency of routing in such networks, and makes many address allocation meth- ods unsuitable. The thesis proposes a new routing and addressing protocol SARP, which works as a distance-vector routing protocol, but optimizes the sizes of the routing tables on the individual nodes by automatically approxi- mating the routes into groups where possible. Most importantly, SARP does not require any pre-established network structure nor unique router identi- fiers, and works only by exchanging the entries in routing tables. We show that SARP is a scalable routing protocol on networks where the addresses can be grouped well. Additionally, we show that SARP can, to some extent, use the reduced information for successful address assignment. However, a fully working address assignment in general settings will require further re- search in methods to globally detect address collisions without unique router identification. 1
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GPU-accelerated Mahalanobis-average hierarchical clustering
Šmelko, Adam ; Kratochvíl, Miroslav (advisor) ; Hric, Jan (referee)
Hierarchical clustering algorithms are common tools for simplifying, exploring and analyzing datasets in many areas of research. For flow cytometry, a specific variant of agglomerative clustering has been proposed, that uses cluster linkage based on Mahalanobis distance to produce results better suited for the domain. Applicability of this clustering algorithm is currently limited by its relatively high computational complexity, which does not allow it to scale to common cytometry datasets. This thesis describes a specialized, GPU-accelerated version of the Mahalanobis-average linked hierarchical clustering, which improves the algorithm performance by several orders of magnitude, thus allowing it to scale to much larger datasets. The thesis provides an overview of current hierarchical clustering algorithms, and details the construction of the variant used on GPU. The result is benchmarked on publicly available high-dimensional data from mass cytometry.
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Firmware for CzechLight optical measurement and calibration device
Oboňová, Ivona ; Kratochvíl, Miroslav (advisor) ; Aschenbrenner, Vojtěch (referee)
The goal of this thesis is to implement firmware for the Optical Measurement and Calibration Device, which was designed and constructed in CESNET. The purpose of the device is to simplify the calibration of various fibre-optical networking devices, used in CESNET infrastructure. The thesis includes an overview of the internal structure and communication interfaces within the device, which is than used for designing and implementing the firmware. The results are demonstrated on realistic hardware, by running the measurement on an existing optical component. The produced firmware will serve as a basis for the development of more advanced devices in CESNET.
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