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

JABLONSKI, Michal, Jana STARČUKOVÁ and Zenon STARČUK. Processing tracking in jMRUI software for magnetic resonance spectra quantitation reproducibility assurance. BMC Bioinformatics. London: BMC, 2017, vol. 18, No 1, p. 1-11. ISSN 1471-2105. Available from: https://dx.doi.org/10.1186/s12859-017-1459-5.

Basic information

• Original name: Processing tracking in jMRUI software for magnetic resonance spectra quantitation reproducibility assurance
• Authors: JABLONSKI, Michal (616 Poland, guarantor, belonging to the institution), Jana STARČUKOVÁ (203 Czech Republic) and Zenon STARČUK (203 Czech Republic).
• Edition: BMC Bioinformatics, London, BMC, 2017, 1471-2105.

Other information

• Original language: English
• Type of outcome: Article in a journal
• Field of Study: 10201 Computer sciences, information science, bioinformatics
• Country of publisher: United Kingdom of Great Britain and Northern Ireland
• Confidentiality degree: is not subject to a state or trade secret
• WWW: Full Text
• Impact factor: Impact factor: 2.213
• RIV identification code: RIV/00216224:14310/17:00108758
• Organization unit: Faculty of Science
• Doi: http://dx.doi.org/10.1186/s12859-017-1459-5
• UT WoS: 000397487400003
• Keywords in English: Magnetic Resonance Spectroscopy; Signal Processing; SQL database; jMRUI
• Tags: rivok
• Tags: International impact, Reviewed

Abstract

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.