Aplikacija za organizaciju velikih bioinformatičkih podataka

master's thesis

• Title (english): Application for Organizing Big Bioinformatics Data
• Author: Fran Andrija Arbanas
• Mentor: Krešimir Križanović (mentor)
• Committee member: Krešimir Križanović (predsjednik povjerenstva)
• Committee member: Marko Subašić (član povjerenstva)
• Committee member: Igor Mekterović (član povjerenstva)
• Granter: University of Zagreb; Faculty of Electrical Engineering and Computing; Zagreb
• Defense date and country: 2022-07-13, Croatia
• Scientific / art field, discipline and subdiscipline: TECHNICAL SCIENCES; Computing

Abstract

Sve pristupačnije metode sekvenciranja koje dolaze do bržih rezultata jeftinije povećavaju količinu očitanja. S očitanjima povećavati će se i količina analiza tih podataka i količina projekata koji se u bioinformatici obrađuju. Sve to rezultira povećanjem količine datoteka koje korisnik koji se bavi bioinformatikom mora negdje spremiti i organizirati. Predloženo rješenje nudi mogućnost organizacije tih podataka za bioinformatičare. Radi se o upravljačkom sučelju napisanom u Djangu, Pythonovom mrežnom okviru. U upravljačkom sučelju korisnici mogu objavljivati datoteke i stavljati ih u odgovarajuće tipove podataka te uređivati dodatna polja koja određeni tip podataka nudi. Ovo rješenje omogućuje da korisnici na jednostavan način drže svoje podatke organizirane po tipu podataka i da unutar tog tipa imaju funkcionalnosti poput pretraživanja unosa i sortiranja. Dodatno ovo rješenje nudi pregledavanje vlastitog direktorija sa podacima za podatke koji nisu uneseni u sustav. Takvi podaci se onda prebacuju u neraspoređene podatke i korisnik ih treba obraditi, odnosno dodijeliti im njihov tip podataka i dodatna polja ako je potrebno. Ovo rješenje nema najbolje iskustvo za korisnika, bolje bi bilo kada bi se napravilo zasebno korisničko sučelje jer Djangovo upravljačko sučelje ima određena ograničenja. Unatoč tome, ovo rješenje bi trebalo biti dobar početak razvoja kompleksnijeg sustava za organizaciju bioinformatičkih podataka.

Abstract (english)

With sequencing methods that produce results faster and cheaper becoming more and more accessible, we see an increase in the amount of reads. With the amount of reads rising, the amount of data analyses and the number of projects regarding bioinformatics will rise. All of that results in an increase of the number of files that a user in bioinformatics has to store and organize. The suggested solution offers a possibility of organizing that data. Suggested solution is an admin site that's written in Django, Python's web framework. In the admin panel users can upload their files, assign them their correct file types and edit some additional fields that that file type has. This solution allows users to easily keep their files organized by file type and to have functionalities like sorting and searching while looking for a specific file in a bunch of files of that type. Additionally, this solution offers checking the directories that contain the uploaded files for files that are not in the system. Those files are then moved to the unassigned files and user has to process them, he has to assign them their file type and additional fields if it's necessary. This solution doesn't have the best user experience, it would've been better if it had a separate frontend because Djangos admin panel has some limitations. Even though, this solution should give a good starting point for the development of a more complex solution for organizing data in bioinformatics.

• Keywords: bioinformatika; bioinformatička analiza podataka; organizacija podataka
• Keywords (english): bionformatics; bioinformatics analysis pipeline; data organisation
• Language: croatian
• URN:NBN: urn:nbn:hr:168:431271
• 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: Closed access
• Created on: 2023-01-13 09:41:39