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Browsing by Author "Takan, Savaş"

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    Master Thesis
    A common representation, standardization, analysis for de novo sequencing results
    (Izmir Institute of Technology, 2012-12) Takan, Savaş; Aytaç, İsmail Sıtkı
    Proteomics is the study of the proteins that can be derived from a genome. For the identification and sequencing of proteins mass spectrometry has become the tool of choice. Within mass spectrometry-based proteomics proteins can be identified or sequenced by either database search or de novo sequencing. Both methods have certain advantages and drawbacks but in the long run we envision de novo sequencing to become the predominant tool. Currently, there is no a general solution to store and share de novo sequencing results which diminishes the usefulness of these results. Hence, they need to be integrated and further analyzed and cannot be used directly as evidence for peptide identification and protein sequencing at present. In order to make improvements the field of de novo sequencing a standard is vitally important. In an attempt to overcome the standardization problem, the de novo markup language (DNML) and De Novo MS Ontology (DNMSO) are developed. These standards provide many-to-many relationships between spectra and predictions, exchange and merging functions, showing all results, PTMs, compact, no using proprietary formats. Next, a programming interface is developed since it is thought that the missing of proper APIs as another obstacle, introducing a needlessly high learning curve for developers. It is standard, compact, modular, easily extensible and also have read, write, create, convert, supports current standards facilities. In order to allow the experimental proteomics community to analyze data stored in the DNMSO standard, Graphical User Interface is developed , DNMSO Analyzer, to provide some facilities such as reading of various spectra file formats, reading, viewing, summarizing of DNMSO, and several conversions from existing de novo results to DNMSO in DNMSO Analyzer.
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    Doctoral Thesis
    Fourier analysis based testing of finite state machines
    (Izmir Institute of Technology, 2019-03) Takan, Savaş; Ayav, Tolga
    Finite state machine (FSM) is a widely used modeling technique for circuit and software testing. FSM testing is a well-studied topic in the literature and there are several test case generation methods such as W, Wp, UIO, UIOv, DS, HSI and H. Despite the existing methods, there is still a need for alternative techniques with better performance in terms of test suite size, fault detection ratio and test generation time. In this thesis, two new test case generation methods, F and Fw have been proposed. The proposed test generation methods are based on Fourier analysis of Boolean functions. Fourier transformations have been studied extensively in mathematics, computer science and engineering. The proposed F method only tests outputs whereas Fw method also tests the next state with the outputs. In this context, the proposed methods are compared with UIO andWmethods in terms of characteristic, cost, fault detection ratio and effectiveness. The evaluation data are analyzed using T-Test and Hedges’ g. Results show that F and Fw methods outperform the existing methods in terms of the fault detection ratio per test.