Büyükaltay, Kaan
Microbiome studies mainly use two different approaches: metagenomic and amplicon analysis. The metagenomic analysis is based on a whole-genome shotgun approach. It is possible to acquire taxonomic resolution to species and strain level but requires high computational power and is expensive. In the amplicon analysis approach, marker genes like 16S, 18S, and ITS are used to identify the sequences. These genes are highly conserved but contain hypervariable regions, allowing researchers to acquire taxonomic resolution at the genus level. The downside of this approach is due to the biases introduced with PCR and its high error rate. QIIME 2 is a tool consisting of many plugins for amplicon analysis. QIIME 2 team has a decentralized development approach so that third parties can develop new plugins and share them with the community. Although there are different options for visualizations in QIIME 2, there is no tool for visualizing the contents of the features table for a single sample. On the other hand, Krona is a tool that visualizes hierarchical data as multi-layered pie charts. While this visualization is desired, it is not a straightforward task, as the QIIME 2 and Krona do not share the same data formats. This study aims to fill this gap by developing a plugin that will transfer QIIME2 outputs into Krona to ease the visualization of QIIME 2 analysis results with Krona without additional script or manipulation during amplicon analysis.


A strategic planning for a gypsum plasterboard producing company
Özaydın, Elif; Çağlar, Güven; Department of Industrial Engineering (2007)
This thesis creates a specific methodology for strategy development while drawing on approaches reported in the literature. The analysis is done at a company that produces gypsum, gypsum board, and related products. A sequential planning method is used where an environmental analysis is conducted in order to define the features of the environment that the company operates in. Then a capability analysis reveals the strengths and weaknesses of the company. For strategy development, this thesis introduces a po...
Shame-proneness vs guilt-proneness and their relationship to attributional styles, coping strategies and depressive symptom levels of university students
İnandılar Topaç, Hicran; Gençöz, Faruk; Department of Psychology (2010)
The purpose of the present study is to investigate the link between shame-proneness, guilt-proneness, attributional styles, and coping strategies, and then to determine which of these variables are significantly related to depressive symptomatology in the sample of Turkish undergraduates. Moreover, the association between shame-proneness, guilt-proneness and depressive symptomatology through attributional styles and coping strategies is examined. Four hundred undergraduates from different universities compl...
Development of a dynamic strategy map incorporating scenario analysis and system dynamics: a simulation test on an international construction company
Yıldız, Açelya Ecem; Dikmen Toker, İrem; Department of Civil Engineering (2018)
The balanced scorecard (BSC) and strategy map (SM) methods developed by Kaplan and Norton [1] are widely utilized both in academic studies and in practice to measure organizational performance. On the other hand, these methods are criticized in the literature due to their inability in quantifying bi-directional causalities among strategies, aggregating performance measures, reflecting dynamic nature of real-life behavior, and making simulations to understand implications of future scenarios to support strat...
Multi-criteria decision making with interdependent criteria using prospect theory
Bozkurt, Ahmet; Karasakal, Esra; Department of Industrial Engineering (2007)
In this study, an integrated solution methodology for a general discrete multi-criteria decision making problem is developed based on the well-known outranking method Promethee II. While the methodology handles the existence of interdependency between the criteria, it can also incorporate the prospect theory in order to correctly reflect the decision behavior of the decision maker. A software is also developed for the application of the methodology and some applications are performed and presented.
Towards an integrative perspective on the interplay between early maladaptive schemas and well-being: the role of early recollections, self-compassion and emotion regulation
Yakın, Duygu; Gençöz, Tülin; Department of Psychology (2015)
The present study was designed as a mixed method study, and was built upon two data sets, one of which was quantitative and the other qualitative. The first study aims to emphasize resourcefulness factors in schema theory from a positive psychology perspective, and emotion regulation and self-compassion were utilized as the indicators of the healthy adult mode. The data was gathered from 296 adults (179 female, 117 male). Accordingly, the mediator roles of self-compassion and emotion regulation were examine...
Citation Formats
K. Büyükaltay, “IMPLEMENTATION OF KRONA INTO QIIME 2,” M.S. - Master of Science, Middle East Technical University, 2022.