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Acceleration of Open vSwitch
Vodák, David ; Orsák, Michal (referee) ; Martínek, Tomáš (advisor)
Virtual switch is a program, which is used for connecting virtual machines to network and that is why it is a crucial part of server virtualization. However virtual switch is consuming too much performance of the server which it is running on. A measurement of Open vSwitch (OvS) indicates that for data speed of 10 Gb/s, approximately 4 cores of the processor are fully occupied. As the consumption of performance is directly proportional to transmission speed, it may eventually get to the point where the consumption of performance cannot be handled. This bachelor thesis is about acceleration of the Open vSwitch with the help of the DPDK Poll Mode Driver extended by support of the SR-IOV virtualization technology as well as the interface for offloading classification rules to hardware called RTE flow. In the scope of this thesis the SR-IOV is implemented and then tested on OvS. Furthermore, the RTE flow support was designed and partially implemented.
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Hardware Accelerating of Encryption Algorithm
Hradil, David ; Martínek, Tomáš (referee) ; Kořenek, Jan (advisor)
The goal of this thesis is to design a hardware realization of circuit which will implement the AES algorithm. A motivation was to make an acceleration against the classic software encryption. The acceleration is achieved by special designed parts of the circuit, which correspond to particular operations of the AES algorithm. First, there was necessary to design the circuit. In the next step there was a need to describe the designed circuit by the VHDL language. Then the circuit was simulated and synthesized. Due to comparing the circuit with software processing a software implementation was created. Both implementations were created for the FITKit platform. The hardware implementation is made by the FPGA technology and the software implementation is realized in a microcontroller. The result of the thesis is almost one thousandfold acceleration against the classic software encryption.
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Detection of Genome Variations
Beluský, Tomáš ; Vogel, Ivan (referee) ; Martínek, Tomáš (advisor)
An influence of variations in human genome is perceptible at a first glance on human itself to see differences between the individuals and entire populations. Also, behavior or probability of certain diseases are influenced in large way by differences at genome's level. This work presents methods for detecting variations in the human genome that were developed after an arose of the second-generation sequencing technologies. A new tool that combines read pair and split read methods, with information about a depth of coverage was also designed and implemented. The tool was tested on simulated and real data and compared with a reference outputs.
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Analysis of DNA Structure Elements
Knytl, Marek ; Burgetová, Ivana (referee) ; Martínek, Tomáš (advisor)
The aim of this master's thesis is the design and implementation of tool trackAnalysis for statistical analysis of DNA structure elements. The positions of individual elements in genome are obtained in the form of the track, and with these positions the tool performs a set of analyzes, including randomness test of track, test examining distances between track and genes, detection of clusters and overlaps. The indivudual tests results can be linked together. The results will be displayed in the form of a list, a graph or a new annotation track. An important part of this thesis is also testing the resulting tool on a set of real data.
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Detection of Enzymes in Metagenomic Data
Smatana, Stanislav ; Martínek, Tomáš (referee) ; Hon, Jiří (advisor)
This thesis presents specification and implementation of a system for detection of enzymes in metagenomic data. The detection is based on a provided enzyme sequence and its goal is to search the metagenomic sample for its novel variants. In order to guarantee that found enzymes truly have the desired catalytic function, the system employs a number of catalytic function verification methods. Their specification, implementation and evaluation is one of the main contributions of this thesis. Experiments have shown, that proposed methods reach sensitivity as high as 89%, specificity of 95%, values of AUC metric above 0.9 and average throughput of 1,203 verifications per second on regular personal computer. Evaluation of the system also led to discovery of a partial sequence of novel haloalkane dehalogenase enzyme in a metagenomic sample from soil. The implementation is able to work on a personal computer as well as on a grid computing environment.
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DNA Sequence Classification
Heczková, Petra ; Burgetová, Ivana (referee) ; Martínek, Tomáš (advisor)
The work deals with DNA sequence classification. The first part summarizes information about existing methods a their characteristics. In the second part there are description of implementation and experiments. Average sensitivity of method was 65% and specificity 92%.
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Fast Regular Expression Matching Using FPGA
Kaštil, Jan ; Martínek, Tomáš (referee) ; Kořenek, Jan (advisor)
The thesis explains several algorithms for pattern matching. Algorithms work in both software and hardware. A part of the thesis is dedicated to extensions of finite automatons. The second part explains hashing and introduces concept of perfect hashing and CRC. The thesis also includes a suggestion of possible structure of a pattern matching unit based on deterministic finite automatons in FPGA. Experiments for determining the structure and size of resulting automatons were done in this thesis.
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Random Numbers Generator with Selected Distribution
Kajan, Michal ; Martínek, Tomáš (referee) ; Kořenek, Jan (advisor)
This thesis describes random numbers generating techniques. First part focuses on methods of obtaining pseudorandom numbers and presents typical examples of random numbers generators. This part also contains description of distribution transformation methods of random numbers and briefly deals with testing of statistical properties of random numbers generators. Following part describes LFSR generator in detail as one of most widely used generators for hardware applications. In addition, description of transformation process and implementation of circuit calculating transformation to the exponential distribution is included. Last part contains resources requierements of designed circuits for implementation in FPGA.
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Clustering of Biological Sequences
Kubiš, Radim ; Burgetová, Ivana (referee) ; Martínek, Tomáš (advisor)
One of the main reasons for protein clustering is prediction of structure, function and evolution. Many of current tools have disadvantage of high computational complexity due to all-to-all sequence alignment. If any tool works faster, it does not reach accuracy as other tools. Further disadvantage is processing on higher rate of similarity but homologous proteins can be similar with less identity. The process of clustering often ends when reach the condition which does not reflect sufficient quality of clusters. Master's thesis describes the design and implementation of new tool for clustering of protein sequences. New tool should not be computationally demanding but it should preserve required accuracy and produce better clusters. The thesis also describes testing of designed tool, evaluation of results and possibilities of its further development.
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