Aplikacija za analizu bioinformatičkih podataka pomoću vanjskih alata

undergraduate thesis

• Title (english): Application for Bioinformatic Analysis Using Outside Tools
• Author: Zvonimir Briševac
• Mentor: Krešimir Križanović (mentor)
• Committee member: Krešimir Križanović (predsjednik povjerenstva)
• Committee member: Mile Šikić (član povjerenstva)
• Committee member: Josip Marić (član povjerenstva)
• Granter: University of Zagreb; Faculty of Electrical Engineering and Computing; Zagreb
• Defense date and country: 2021-09-09, Croatia
• Scientific / art field, discipline and subdiscipline: TECHNICAL SCIENCES; Computing

Abstract

Cilj ovog rada je bio izrada desktop aplikacije s grafičkim sučeljem za pokretanje bioinformatičkih procesa pomoću vanjskih alata, te analiza rezultata tih procesa. Vanjski alati koji su korišteni u ovom radu su: Minimap2, Ram i Raven. Problem s navedenim alatima je što se pokreću preko naredbene linije, a procesi koje izvode mogu trajati danima. Aplikacija nudi korisniku mogućnost pokretanja navedenih alata preko grafičkih sučelja dizajniranih za svaku vrstu procesa koje korisnik želi pokrenuti. Procesi se pokreću neovisno o aplikaciji u pozadini računalnog sustava tako da aplikacija ne mora biti upaljena za vrijeme trajanja procesa. Korisnik može u bilo kojem trenutku provjeriti stanje svojih procesa, te je obavješten ukoliko je proces uspješno završen ili prekinut u izvođenju. Ukoliko je proces uspješno završen, korisnik može analizirati rezultate procesa.

Abstract (english)

The goal of this thesis was to develop a desktop application with graphical interface for running bioinformatic processes with the help of the external tools and analyzing the results of those processes. External tools which are being used in this thesis are: Minimap2, Ram and Raven. Problem with these tools is that they can only be runned through systems command line and the processes which they perform can last couple of days. Application offers the user an ability to run those processes by using its graphical interfaces specially designed for each type od process. Processes are being runned independently from application in the background of computers operating system which means that it is not necessary that the application is turned on during the whole process. User can check statuses of his/her processes at any moment. The user will also be informed when the process is finished or when it comes to an unexpected halt. If the process is succesfully finished, the user can run the analysis of its result.

• Keywords: bioinformatika; mapiranje; de novo; poravnanje; Minimap2; Raven; Ram; analiza; Java; Swing
• Keywords (english): bioinformatics; mapping; de novo; alignment; Minimap2; Raven; Ram; analysis; Java; Swing
• Language: croatian
• URN:NBN: urn:nbn:hr:168:972142
• Study programme: Title: Computing; Study programme type: university; Study level: undergraduate; Academic / professional title: sveučilišni/a prvostupnik/ prvostupnica (baccalaureus/baccalaurea) inženjer/inženjerka računarstva (sveučilišni/a prvostupnik/ prvostupnica (baccalaureus/baccalaurea) inženjer/inženjerka računarstva)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Closed access
• Created on: 2023-01-14 20:09:47