{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T00:23:02Z","timestamp":1772151782729,"version":"3.50.1"},"reference-count":27,"publisher":"Oxford University Press (OUP)","issue":"19","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1154,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: The research area metabolomics achieved tremendous popularity and development in the last couple of years. Owing to its unique interdisciplinarity, it requires to combine knowledge from various scientific disciplines. Advances in the high-throughput technology and the consequently growing quality and quantity of data put new demands on applied analytical and computational methods. Exploration of finally generated and analyzed datasets furthermore relies on powerful tools for data mining and visualization.<\/jats:p><jats:p>Results: To cover and keep up with these requirements, we have created MeltDB 2.0, a next-generation web application addressing storage, sharing, standardization, integration and analysis of metabolomics experiments. New features improve both efficiency and effectivity of the entire processing pipeline of chromatographic raw data from pre-processing to the derivation of new biological knowledge. First, the generation of high-quality metabolic datasets has been vastly simplified. Second, the new statistics tool box allows to investigate these datasets according to a wide spectrum of scientific and explorative questions.<\/jats:p><jats:p>Availability: The system is publicly available at https:\/\/meltdb.cebitec.uni-bielefeld.de. A login is required but freely available.<\/jats:p><jats:p>Contact: \u00a0nkessler@cebitec.uni-bielefeld.de<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt414","type":"journal-article","created":{"date-parts":[[2013,8,6]],"date-time":"2013-08-06T05:30:10Z","timestamp":1375767010000},"page":"2452-2459","source":"Crossref","is-referenced-by-count":83,"title":["MeltDB 2.0\u2013advances of the metabolomics software system"],"prefix":"10.1093","volume":"29","author":[{"given":"Nikolas","family":"Kessler","sequence":"first","affiliation":[{"name":"1 Biodata Mining Group, CeBiTec, Bielefeld University, Bielefeld, Germany, 2Computational Genomics, CeBiTec, Bielefeld University, Bielefeld, Germany, 3Bruker Daltonik GmbH, Bremen, Germany, 4Proteome and Metabolome Research, Bielefeld University, Bielefeld, Germany and 5Max Rubner-Institute, Detmold, Germany"},{"name":"1 Biodata Mining Group, CeBiTec, Bielefeld University, Bielefeld, Germany, 2Computational Genomics, CeBiTec, Bielefeld University, Bielefeld, Germany, 3Bruker Daltonik GmbH, Bremen, Germany, 4Proteome and Metabolome Research, Bielefeld University, Bielefeld, Germany and 5Max Rubner-Institute, Detmold, Germany"}]},{"given":"Heiko","family":"Neuweger","sequence":"additional","affiliation":[{"name":"1 Biodata Mining Group, CeBiTec, Bielefeld University, Bielefeld, Germany, 2Computational Genomics, CeBiTec, Bielefeld University, Bielefeld, Germany, 3Bruker Daltonik GmbH, Bremen, Germany, 4Proteome and Metabolome Research, Bielefeld University, Bielefeld, Germany and 5Max Rubner-Institute, Detmold, Germany"}]},{"given":"Anja","family":"Bonte","sequence":"additional","affiliation":[{"name":"1 Biodata Mining Group, CeBiTec, Bielefeld University, Bielefeld, Germany, 2Computational Genomics, CeBiTec, Bielefeld University, Bielefeld, Germany, 3Bruker Daltonik GmbH, Bremen, Germany, 4Proteome and Metabolome Research, Bielefeld University, Bielefeld, Germany and 5Max Rubner-Institute, Detmold, Germany"},{"name":"1 Biodata Mining Group, CeBiTec, Bielefeld University, Bielefeld, Germany, 2Computational Genomics, CeBiTec, Bielefeld University, Bielefeld, Germany, 3Bruker Daltonik GmbH, Bremen, Germany, 4Proteome and Metabolome Research, Bielefeld University, Bielefeld, Germany and 5Max Rubner-Institute, Detmold, Germany"}]},{"given":"Georg","family":"Langenk\u00e4mper","sequence":"additional","affiliation":[{"name":"1 Biodata Mining Group, CeBiTec, Bielefeld University, Bielefeld, Germany, 2Computational Genomics, CeBiTec, Bielefeld University, Bielefeld, Germany, 3Bruker Daltonik GmbH, Bremen, Germany, 4Proteome and Metabolome Research, Bielefeld University, Bielefeld, Germany and 5Max Rubner-Institute, Detmold, Germany"}]},{"given":"Karsten","family":"Niehaus","sequence":"additional","affiliation":[{"name":"1 Biodata Mining Group, CeBiTec, Bielefeld University, Bielefeld, Germany, 2Computational Genomics, CeBiTec, Bielefeld University, Bielefeld, Germany, 3Bruker Daltonik GmbH, Bremen, Germany, 4Proteome and Metabolome Research, Bielefeld University, Bielefeld, Germany and 5Max Rubner-Institute, Detmold, Germany"}]},{"given":"Tim W.","family":"Nattkemper","sequence":"additional","affiliation":[{"name":"1 Biodata Mining Group, CeBiTec, Bielefeld University, Bielefeld, Germany, 2Computational Genomics, CeBiTec, Bielefeld University, Bielefeld, Germany, 3Bruker Daltonik GmbH, Bremen, Germany, 4Proteome and Metabolome Research, Bielefeld University, Bielefeld, Germany and 5Max Rubner-Institute, Detmold, Germany"}]},{"given":"Alexander","family":"Goesmann","sequence":"additional","affiliation":[{"name":"1 Biodata Mining Group, CeBiTec, Bielefeld University, Bielefeld, Germany, 2Computational Genomics, CeBiTec, Bielefeld University, Bielefeld, Germany, 3Bruker Daltonik GmbH, Bremen, Germany, 4Proteome and Metabolome Research, Bielefeld University, Bielefeld, Germany and 5Max Rubner-Institute, Detmold, Germany"}]}],"member":"286","published-online":{"date-parts":[[2013,8,5]]},"reference":[{"key":"2023012810462603300_btt414-B1","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate: a practical and powerful approach to multiple testing","volume":"57","author":"Benjamini","year":"1995","journal-title":"J. R. Stat. Soc. 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