Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection

Permanent URI for this collectionhttps://hdl.handle.net/11147/7148

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20202

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Department: search.filters.department.İzmir Institute of Technology. Computer EngineeringPublisher: search.filters.publisher.PeerJ Inc.

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  • Article
    Citation - WoS: 1
    Creation of Mutants by Using Centrality Criteria in Social Network Analysis
    (PeerJ Inc., 2020) Takan, Savaş
    Mutation testing is a method widely used to evaluate the effectiveness of the test suite in hardware and software tests or to design new software tests. In mutation testing, the original model is systematically mutated using certain error assumptions. Mutation testing is based on well-defined mutation operators that imitate typical programming errors or which form highly successful test suites. The success of test suites is determined by the rate of killing mutants created through mutation operators. Because of the high number of mutants in mutation testing, the calculation cost increases in the testing of finite state machines (FSM). Under the assumption that each mutant is of equal value, random selection can be a practical method of mutant reduction. However, in this study, it was assumed that each mutant did not have an equal value. Starting from this point of view, a new mutant reduction method was proposed by using the centrality criteria in social network analysis. It was assumed that the central regions selected within this frame were the regions from where test cases pass the most. To evaluate the proposed method, besides the feature of detecting all failures related to the model, the widely-used W method was chosen. Random and proposed mutant reduction methods were compared with respect to their success by using test suites. As a result of the evaluations, it was discovered that mutants selected via the proposed reduction technique revealed a higher performance. Furthermore, it was observed that the proposed method reduced the cost of mutation testing.
  • Article
    Citation - WoS: 1
    Citation - Scopus: 1
    Dnmso; an Ontology for Representing De Novo Sequencing Results From Tandem-Ms Data
    (PeerJ Inc., 2020) Takan, Savaş; Allmer, Jens
    For the identification and sequencing of proteins, mass spectrometry (MS) has become the tool of choice and, as such, drives proteomics. MS/MS spectra need to be assigned a peptide sequence for which two strategies exist. Either database search or de novo sequencing can be employed to establish peptide spectrum matches. For database search, mzIdentML is the current community standard for data representation. There is no community standard for representing de novo sequencing results, but we previously proposed the de novo markup language (DNML). At the moment, each de novo sequencing solution uses different data representation, complicating downstream data integration, which is crucial since ensemble predictions may be more useful than predictions of a single tool. We here propose the de novo MS Ontology (DNMSO), which can, for example, provide many-to-many mappings between spectra and peptide predictions. Additionally, an application programming interface (API) that supports any file operation necessary for de novo sequencing from spectra input to reading, writing, creating, of the DNMSO format, as well as conversion from many other file formats, has been implemented. This API removes all overhead from the production of de novo sequencing tools and allows developers to concentrate on algorithm development completely. We make the API and formal descriptions of the format freely available at https://github.com/savastakan/dnmso.