Radni okvir za procjenu starosti koristeći knjižnicu epigenetičkih satova

master's thesis

• Title (english): Framework for Age Estimation Using Epigenetic Clocks Library
• Author: Luka Brečić
• Mentor: Klemo Vladimir (mentor)
• Committee member: Klemo Vladimir (predsjednik povjerenstva)
• Committee member: Marin Šilić (član povjerenstva)
• Committee member: Adrian Satja Kurdija (član povjerenstva)
• Granter: University of Zagreb; Faculty of Electrical Engineering and Computing; Zagreb
• Defense date and country: 2024-09-10, Croatia

Abstract

Ovaj rad bavi se razvojem i primjenom radnog okvira epygenetics za razvoj i laku integraciju epigenetičkih satova. U kratkom pregledu povijesnog razvoja epigenetičkih satova detaljno su opisane neki od postojećih epigenetičkih satova. Također su opisani matematički modeli na kojim počiva većina do sada otkrivenih epigenetičkih satova. Pregled do sada postojećih tehničkih implementacija koji na bilo koji način podržavaju rad s analizom DNK metilacije ili epigenetičkih satova, uvod je u detaljan opis implementacije radnog okvira u obliku Python knjižnice po uzoru na programski paket methylCIPHER pisanog u programskom jeziku R. Implementirani radni okvir imena epygenetics omogućuje jednostavnu i intuitivnu integraciju različitih epigenetičkih satova sa svrhom podržavanja i popularizacije rada s epigenetičkim satovima. Cilj rada bio je stvoriti alat koji je fleksibilan, lako proširiv, koji nije inertan na promjene i koji je jednostavan za korištenje, čime se olakšava rad s velikim skupovima podataka i omogućuje preciznija procjena biološke starosti. Na kraju rada opisane su korištene tehnologije prilikom razvoja ovog radnog okvira, kao i upute za korištenje radnog okvira. radni okvir ima ugrađenu potporu za automatsko testiranje čiji su rezultati iskorišteni za evaluiranje knjižnice čime je pokazana visoka usklađenost s rezultatima dobivenim korištenjem methylCIPHER programskog paketa.

Abstract (english)

This thesis focuses on the development and application of the epygenetics framework for the creation and easy integration of epigenetic clocks. A brief overview of the historical development of epigenetic clocks is provided, with detailed descriptions of some existing epigenetic clocks. The thesis also explores the mathematical models underlying most of the currently known epigenetic clocks. A review of existing technical implementations that support DNA methylation analysis or epigenetic clocks in any way serves as an introduction to a detailed description of the implementation of the framework in the form of a Python library modeled after the methylCIPHER package written in the R programming language. The implemented framework, named epygenetics, allows for simple and intuitive integration of various epigenetic clocks to support and popularize the use of epigenetic clocks. The goal of this work was to create a tool that is flexible, easily extensible, non-robust, and simple to use, thereby facilitating work with large datasets and enabling more accurate biological age estimation. The final section of the thesis describes the technologies used in the development of this framework, as well as instructions for its use. The framework includes built-in support for automated testing, the results of which were used to evaluate the library, demonstrating high consistency with results obtained using the methylCIPHER package.

• Keywords: CpG područje; DNK metilacija; nukleotid; dinukleotid; Python; epygenetics; methylCIPHER; Horvath; model; epigenetika; epigenetički sat; radni okvir
• Keywords (english): CpG site; DNA methylation; nucleotide; dinucleotide; Python; epygenetics; methylCIPHER; Horvath; model; epigenetics; epigenetic clock; framework
• Language: croatian
• URN:NBN: urn:nbn:hr:168:630877
• Study programme: Title: Computing; Study programme type: university; Study level: graduate; Academic / professional title: magistar/magistra inženjer/inženjerka računarstva (magistar/magistra inženjer/inženjerka računarstva)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Open access
• Created on: 2024-10-12 20:11:43