MeltDB: a software platform for the analysis and integration of metabolomics experiment data

Neuweger H, Albaum S, Dondrup M, Persicke M, Watt T, Niehaus K, Stoye J, Goesmann A (2008)
Bioinformatics 24(23): 2726-2732.

Journal Article | Published | English

No fulltext has been uploaded

Abstract
Motivation: The recent advances in metabolomics have created the potential to measure the levels of hundreds of metabolites which are the end products of cellular regulatory processes. The automation of the sample acquisition and subsequent analysis in high-throughput instruments that are capable of measuring metabolites is posing a challenge on the necessary systematic storage and computational processing of the experimental datasets. Whereas a multitude of specialized software systems for individual instruments and preprocessing methods exists, there is clearly a need for a free and platform-independent system that allows the standardized and integrated storage and analysis of data obtained from metabolomics experiments. Currently there exists no such system that on the one hand supports preprocessing of raw datasets but also allows to visualize and integrate the results of higher level statistical analyses within a functional genomics context. Results: To facilitate the systematic storage, analysis and integration of metabolomics experiments, we have implemented MeltDB, a web-based software platform for the analysis and annotation of datasets from metabolomics experiments. MeltDB supports open file formats (netCDF, mzXML, mzDATA) and facilitates the integration and evaluation of existing preprocessing methods. The system provides researchers with means to consistently describe and store their experimental datasets. Comprehensive analysis and visualization features of metabolomics datasets are offered to the community through a web-based user interface. The system covers the process from raw data to the visualization of results in a knowledge-based background and is integrated into the context of existing software platforms of genomics and transcriptomics at Bielefeld University. We demonstrate the potential of MeltDB by means of a sample experiment where we dissect the influence of three different carbon sources on the gram-negative bacterium Xanthomonas campestris pv. campestris on the level of measured metabolites. Experimental data are stored, analyzed and annotated within MeltDB and accessible via the public MeltDB web server. Availability: The system is publicly available at http://meltdb.cebitec.uni-bielefeld.de.
Publishing Year
ISSN
eISSN
PUB-ID

Cite this

Neuweger H, Albaum S, Dondrup M, et al. MeltDB: a software platform for the analysis and integration of metabolomics experiment data. Bioinformatics. 2008;24(23):2726-2732.
Neuweger, H., Albaum, S., Dondrup, M., Persicke, M., Watt, T., Niehaus, K., Stoye, J., et al. (2008). MeltDB: a software platform for the analysis and integration of metabolomics experiment data. Bioinformatics, 24(23), 2726-2732.
Neuweger, H., Albaum, S., Dondrup, M., Persicke, M., Watt, T., Niehaus, K., Stoye, J., and Goesmann, A. (2008). MeltDB: a software platform for the analysis and integration of metabolomics experiment data. Bioinformatics 24, 2726-2732.
Neuweger, H., et al., 2008. MeltDB: a software platform for the analysis and integration of metabolomics experiment data. Bioinformatics, 24(23), p 2726-2732.
H. Neuweger, et al., “MeltDB: a software platform for the analysis and integration of metabolomics experiment data”, Bioinformatics, vol. 24, 2008, pp. 2726-2732.
Neuweger, H., Albaum, S., Dondrup, M., Persicke, M., Watt, T., Niehaus, K., Stoye, J., Goesmann, A.: MeltDB: a software platform for the analysis and integration of metabolomics experiment data. Bioinformatics. 24, 2726-2732 (2008).
Neuweger, Heiko, Albaum, Stefan, Dondrup, Michael, Persicke, Marcus, Watt, Tony, Niehaus, Karsten, Stoye, Jens, and Goesmann, Alexander. “MeltDB: a software platform for the analysis and integration of metabolomics experiment data”. Bioinformatics 24.23 (2008): 2726-2732.
This data publication is cited in the following publications:
This publication cites the following data publications:

36 Citations in Europe PMC

Data provided by Europe PubMed Central.

Metabolic Adaptations of White Lupin Roots and Shoots under Phosphorus Deficiency.
Muller J, Godde V, Niehaus K, Zorb C., Front Plant Sci 6(), 2015
PMID: 26635840
Metabolite profiling of somatic embryos of Cyclamen persicum in comparison to zygotic embryos, endosperm, and testa.
Winkelmann T, Ratjens S, Bartsch M, Rode C, Niehaus K, Bednarz H., Front Plant Sci 6(), 2015
PMID: 26300898
Learning to Classify Organic and Conventional Wheat - A Machine Learning Driven Approach Using the MeltDB 2.0 Metabolomics Analysis Platform.
Kessler N, Bonte A, Albaum SP, Mader P, Messmer M, Goesmann A, Niehaus K, Langenkamper G, Nattkemper TW., Front Bioeng Biotechnol 3(), 2015
PMID: 25853128
Metabolite profiling on wheat grain to enable a distinction of samples from organic and conventional farming systems
Bonte A, Neuweger H, Goesmann A, Thonar C, Mader P, Langenkamper G, Niehaus K., J. Sci. Food Agric. 94(13), 2014
PMID: IND600814173
Metabolite profiling on wheat grain to enable a distinction of samples from organic and conventional farming systems.
Bonte A, Neuweger H, Goesmann A, Thonar C, Mader P, Langenkamper G, Niehaus K., J. Sci. Food Agric. 94(13), 2014
PMID: 24425170
Computational tools for the secondary analysis of metabolomics experiments.
Booth SC, Weljie AM, Turner RJ., Comput Struct Biotechnol J 4(), 2013
PMID: 24688685
Metabolomic fingerprinting: challenges and opportunities.
Kosmides AK, Kamisoglu K, Calvano SE, Corbett SA, Androulakis IP., Crit Rev Biomed Eng 41(3), 2013
PMID: 24579644

Export

0 Marked Publications

Open Data PUB

Web of Science

View record in Web of Science®

Sources

PMID: 18765459
PubMed | Europe PMC

Search this title in

Google Scholar