Processing tracking in jMRUI software for magnetic resonance
spectra quantitation reproducibility assurance

J 2017

Processing tracking in jMRUI software for magnetic resonance spectra quantitation reproducibility assurance

JABLONSKI, Michal, Jana STARČUKOVÁ a Zenon STARČUK

Základní údaje

Originální název

Processing tracking in jMRUI software for magnetic resonance spectra quantitation reproducibility assurance

Autoři

JABLONSKI, Michal (616 Polsko, garant, domácí), Jana STARČUKOVÁ (203 Česká republika) a Zenon STARČUK (203 Česká republika)

Vydání

BMC Bioinformatics, London, BMC, 2017, 1471-2105

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10201 Computer sciences, information science, bioinformatics

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

Full Text

Impakt faktor

Impact factor: 2.213

Kód RIV

RIV/00216224:14310/17:00108758

Organizační jednotka

Přírodovědecká fakulta

DOI

http://dx.doi.org/10.1186/s12859-017-1459-5

UT WoS

000397487400003

Klíčová slova anglicky

Magnetic Resonance Spectroscopy; Signal Processing; SQL database; jMRUI

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 11. 5. 2020 09:38, Mgr. Marie Šípková, DiS.

Anotace

V originále

Background: Proton magnetic resonance spectroscopy is a non-invasive measurement technique which provides information about concentrations of up to 20 metabolites participating in intracellular biochemical processes. In order to obtain any metabolic information from measured spectra a processing should be done in specialized software, like jMRUI. The processing is interactive and complex and often requires many trials before obtaining a correct result. This paper proposes a jMRUI enhancement for efficient and unambiguous history tracking and file identification. Results: A database storing all processing steps, parameters and files used in processing was developed for jMRUI. The solution was developed in Java, authors used a SQL database for robust storage of parameters and SHA-256 hash code for unambiguous file identification. The developed system was integrated directly in jMRUI and it will be publically available. A graphical user interface was implemented in order to make the user experience more comfortable. The database operation is invisible from the point of view of the common user, all tracking operations are performed in the background. Conclusions: The implemented jMRUI database is a tool that can significantly help the user to track the processing history performed on data in jMRUI. The created tool is oriented to be user-friendly, robust and easy to use. The database GUI allows the user to browse the whole processing history of a selected file and learn e. g. what processing lead to the results, where the original data are stored, to obtain the list of all processing actions performed on spectra.

Citovat

JABLONSKI, Michal, Jana STARČUKOVÁ a Zenon STARČUK. Processing tracking in jMRUI software for magnetic resonance spectra quantitation reproducibility assurance. BMC Bioinformatics. London: BMC, 2017, roč. 18, č. 1, s. 1-11. ISSN 1471-2105. Dostupné z: https://dx.doi.org/10.1186/s12859-017-1459-5.

@article{1393123,
   author = {Jablonski, Michal and Starčuková, Jana and Starčuk, Zenon},
   article_location = {London},
   article_number = {1},
   doi = {http://dx.doi.org/10.1186/s12859-017-1459-5},
   keywords = {Magnetic Resonance Spectroscopy; Signal Processing; SQL database; jMRUI},
   language = {eng},
   issn = {1471-2105},
   journal = {BMC Bioinformatics},
   title = {Processing tracking in jMRUI software for magnetic resonance spectra quantitation reproducibility assurance},
   url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5260066/},
   volume = {18},
   year = {2017}
}

TY  - JOUR
ID  - 1393123
AU  - Jablonski, Michal - Starčuková, Jana - Starčuk, Zenon
PY  - 2017
TI  - Processing tracking in jMRUI software for magnetic resonance spectra quantitation reproducibility assurance
JF  - BMC Bioinformatics
VL  - 18
IS  - 1
SP  - 1-11
EP  - 1-11
PB  - BMC
SN  - 14712105
KW  - Magnetic Resonance Spectroscopy
KW  - Signal Processing
KW  - SQL database
KW  - jMRUI
UR  - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5260066/
L2  - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5260066/
N2  - Background: Proton magnetic resonance spectroscopy is a non-invasive measurement technique which provides information about concentrations of up to 20 metabolites participating in intracellular biochemical processes. In order to obtain any metabolic information from measured spectra a processing should be done in specialized software, like jMRUI. The processing is interactive and complex and often requires many trials before obtaining a correct result. This paper proposes a jMRUI enhancement for efficient and unambiguous history tracking and file identification. Results: A database storing all processing steps, parameters and files used in processing was developed for jMRUI. The solution was developed in Java, authors used a SQL database for robust storage of parameters and SHA-256 hash code for unambiguous file identification. The developed system was integrated directly in jMRUI and it will be publically available. A graphical user interface was implemented in order to make the user experience more comfortable. The database operation is invisible from the point of view of the common user, all tracking operations are performed in the background. Conclusions: The implemented jMRUI database is a tool that can significantly help the user to track the processing history performed on data in jMRUI. The created tool is oriented to be user-friendly, robust and easy to use. The database GUI allows the user to browse the whole processing history of a selected file and learn e. g. what processing lead to the results, where the original data are stored, to obtain the list of all processing actions performed on spectra.
ER  -

JABLONSKI, Michal, Jana STARČUKOVÁ a Zenon STARČUK. Processing tracking in jMRUI software for magnetic resonance spectra quantitation reproducibility assurance. \textit{BMC Bioinformatics}. London: BMC, 2017, roč.~18, č.~1, s.~1-11. ISSN~1471-2105. Dostupné z: https://dx.doi.org/10.1186/s12859-017-1459-5.

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