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

Heiko Neuweger, Stefan P. Albaum, Michael Dondrup, Marcus Persicke, Tony Watt, Karsten Niehaus, Jens Stoye, Alexander Goesmann
2008 Computer applications in the biosciences : CABIOS  
MeltDB is a web-based software platform for the analysis and annotation of datasets from metabolomics experiments.  ...  and integrated storage and analysis of data obtained from metabolomics experiments.  ...  MeltDB was designed as a platform-independent software for the analysis and integration of metabolomics experiments.  ... 
doi:10.1093/bioinformatics/btn452 pmid:18765459 fatcat:6kraieexyvaq7hcx4fikyqg5gq

Learning to Classify Organic and Conventional Wheat – A Machine Learning Driven Approach Using the MeltDB 2.0 Metabolomics Analysis Platform

Nikolas Kessler, Anja Bonte, Stefan P. Albaum, Paul Mäder, Monika Messmer, Alexander Goesmann, Karsten Niehaus, Georg Langenkämper, Tim W. Nattkemper
2015 Frontiers in Bioengineering and Biotechnology  
More than 300 GC-MS measurements were recorded and subsequently processed and analyzed in the MeltDB 2.0 metabolomics analysis platform, being briefly outlined in this paper.  ...  Our results clearly show that years have most and wheat cultivars have second-most influence on the metabolic composition of a sample.  ...  Funding: The authors acknowledge the financial support provided by the German Federal Ministry of Food and Agriculture under the Federal Scheme for Organic Farming and other forms of sustainable agriculture  ... 
doi:10.3389/fbioe.2015.00035 pmid:25853128 pmcid:PMC4371749 fatcat:2zoeadoqbbesff7m5mn35t4som

Omics Fusion – A Platform for Integrative Analysis of Omics Data

Benedikt G. Brink, Annica Seidel, Nils Kleinbölting, Tim W. Nattkemper, Stefan P. Albaum
2016 Journal of Integrative Bioinformatics  
We present Omics Fusion, a new web-based platform for integrative analysis of omics data.  ...  Omics Fusion provides a collection of new and established tools and visualization methods to support researchers in exploring omics data, validating results or understanding how to adjust experiments in  ...  Acknowledgements This work is partially funded by the German-Canadian DFG International Research Training Group GRK 1906 and received financial support from the BMBF in the frame of the de.NBI initiative  ... 
doi:10.1515/jib-2016-296 fatcat:geiaxflfcrhdrmig2s64eyzkbm

COMPUTATIONAL TOOLS FOR THE SECONDARY ANALYSIS OF METABOLOMICS EXPERIMENTS

Sean C. Booth, Aalim M. Weljie, Raymond J. Turner
2013 Computational and Structural Biotechnology Journal  
to each other and the perturbed condition of the experiment.  ...  While many databases, tools and projects such as the human metabolome database [1] have focused on creating tools specifically for interpreting human metabolomics experiments, the options for more diverse  ...  MeltDB [30] is another comprehensive suite for metabolomics data analysis designed explicitly as a free and platform independent integrated project management and analytical pipeline that takes raw GC  ... 
doi:10.5936/csbj.201301003 pmid:24688685 pmcid:PMC3962093 fatcat:4zfhlfrvjnhzhbdzgx6dh63cpe

Visualizing post genomics data-sets on customized pathway maps by ProMeTra – aeration-dependent gene expression and metabolism of Corynebacterium glutamicum as an example

Heiko Neuweger, Marcus Persicke, Stefan P Albaum, Thomas Bekel, Michael Dondrup, Andrea T Hüser, Jörn Winnebald, Jessica Schneider, Jörn Kalinowski, Alexander Goesmann
2009 BMC Systems Biology  
To demonstrate the functionality of ProMeTra, we use quantitative data obtained during a fermentation experiment of the L-lysine producing strain Corynebacterium glutamicum DM1730.  ...  It has become obvious that the application of web-based and user driven software tools has great potential and benefits from the use of open and standardized formats for the description of pathways.  ...  Acknowledgements HN would like to thank the International Graduate School in Bioinformatics and Genome Research for providing financial support.  ... 
doi:10.1186/1752-0509-3-82 pmid:19698148 pmcid:PMC2744654 fatcat:mmit5eaw4jcbbfs6yvqus7xdii

The MetabolomeExpress Project: enabling web-based processing, analysis and transparent dissemination of GC/MS metabolomics datasets

Adam J Carroll, Murray R Badger, A Harvey Millar
2010 BMC Bioinformatics  
data repositories suitable for data mining and meta-analysis.  ...  While a number of web-tools offer access to datasets and/or tools for raw data processing and statistical analysis, none of these systems are currently set up to act as a public repository by easily accepting  ...  The research was funded by the Australian Research Council through the ARC Centre of Excellence in Plant Energy Biology (CEO561495) to AHM and MB.  ... 
doi:10.1186/1471-2105-11-376 pmid:20626915 pmcid:PMC2912306 fatcat:6nnkx77ezfgrxnn6t4uihzdru4

MetaboAnalyst: a web server for metabolomic data analysis and interpretation

J. Xia, N. Psychogios, N. Young, D. S. Wishart
2009 Nucleic Acids Research  
The data processing challenges in metabolomics are quite unique and often require specialized (or expensive) data analysis software and a detailed knowledge of cheminformatics, bioinformatics and statistics  ...  In an effort to simplify metabolomic data analysis while at the same time improving user accessibility, we have developed a freely accessible, easy-to-use web server for metabolomic data analysis called  ...  With the rapid growth of this field, there is an increasing demand for dedicated software tools that support the processing and analysis of metabolomic data from a variety of analytical platforms.  ... 
doi:10.1093/nar/gkp356 pmid:19429898 pmcid:PMC2703878 fatcat:y2s3onankbdgbagkj2mqhfjnoi

An interactive online software platform for the analysis of small molecules using hyphenated mass spectrometry: MeltDB and ALLocator

Nikolas Kessler
2018
MeltDB, 'a software platform for the analysis and integration of data from metabolomics experiments', has been published by Neuweger et al. (2008) .  ...  Current progress in metabolomics data analysis Due to the diversity of instrumental set ups and experimental approaches that are applied for metabolome analysis, the metabolomics software landscape consists  ...  MeltDB 2.0: Handling hundreds of chromatograms efficiently The MeltDB web platform can deal with large experiments containing hundreds of chromatograms, and it offers a vast toolbox of statistics that  ... 
doi:10.4119/unibi/2932648 fatcat:z54kr2wsxndf5m2wjqqiwgtwjy

MeRy-B: a web knowledgebase for the storage, visualization, analysis and annotation of plant NMR metabolomic profiles

Hélène Ferry-Dumazet, Laurent Gil, Catherine Deborde, Annick Moing, Stéphane Bernillon, Dominique Rolin, Macha Nikolski, Antoine de Daruvar, Daniel Jacob
2011 BMC Plant Biology  
Platforms are required for profile management, as a function of experimental design, and for metabolite identification, to facilitate the mining of the corresponding data.  ...  experimental and analytical metadata, (ii) for queries and visualization of the data, (iii) to discriminate between profiles with spectrum visualization tools and statistical analysis, (iv) to facilitate  ...  MeltDB [36] and SetupX [37] , two web-based software platforms for the systematic storage, analysis and annotation of datasets from mass spectrometry (MS)-based metabolomics experiments, have recently  ... 
doi:10.1186/1471-2229-11-104 pmid:21668943 pmcid:PMC3141636 fatcat:q7ltjove5fcy7fw644pu272fpi

Tools for the functional interpretation of metabolomic experiments

M. Chagoyen, F. Pazos
2012 Briefings in Bioinformatics  
These, together with generic tools for metabolic analysis and visualization not specifically designed for metabolomics will for sure be in the toolbox of the researches doing metabolomic experiments in  ...  Metabolomics is one of the last additions to the 'omics' family and it deals with the characterization of the set of metabolites in a given biological system.  ...  Her research interests include functional bioinformatics, integrated data analysis and biological data management.  ... 
doi:10.1093/bib/bbs055 pmid:23063930 fatcat:zpbjkyiy75gsrojfhcln4y26pm

An R package for the integrated analysis of metabolomics and spectral data

Christopher Costa, Marcelo Maraschin, Miguel Rocha
2016 Computer Methods and Programs in Biomedicine  
Importantly, the implemented methods provide adequate support for the analysis of data from diverse experimental techniques, integrating a large set of functions from several R packages in a powerful,  ...  Indeed, from the available software tools, none addresses the multiplicity of existing techniques and data analysis tasks.  ...  Acknowledgments The work is partially funded by Project 23060, PEM -Technological Support Platform for Metabolic Engineering, co-funded by FEDER through Portuguese QREN under the scope of the Technological  ... 
doi:10.1016/j.cmpb.2016.01.008 pmid:26853041 fatcat:b3t66jstrbcdtnpwxivowiv2w4

Plants Metabolome Study: Emerging Tools and Techniques

Manish Kumar Patel, Sonika Pandey, Manoj Kumar, Md Intesaful Haque, Sikander Pal, Narendra Singh Yadav
2021 Plants  
Metabolomics is now considered a wide-ranging, sensitive and practical approach to acquire useful information on the composition of a metabolite pool present in any organism, including plants.  ...  Moreover, metabolomics can be easily applied for the phenotyping of plants; and thus, it has great potential to be used in genome editing programs to develop superior next-generation crops.  ...  Data Availability Statement: All data included in the main text. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/plants10112409 pmid:34834772 pmcid:PMC8621461 fatcat:kd4y3zlz3fg6zlwcqbyjwpjc5m

EasyLCMS: an asynchronous web application for the automated quantification of LC-MS data

Sergio Fructuoso, Ángel Sevilla, Cristina Bernal, Ana Lozano, José Iborra, Manuel Cánovas
2012 BMC Research Notes  
Although numerous applications have been previously developed for metabolomics data handling, automated calibration and calculation of the concentrations in terms of μmol have not been carried out.  ...  Moreover, most of the metabolomics applications are designed for GC-MS, and would not be suitable for LC-MS, since in LC, the deviation in the retention time is not linear, which is not taken into account  ...  Acknowledgements We thank Inbionova Biotech S.L. for hosting EasyLCMS.  ... 
doi:10.1186/1756-0500-5-428 pmid:22884039 pmcid:PMC3494514 fatcat:6hu3krfyuvhqhngixcgknoun5y

ChromA: signal-based retention time alignment for chromatography–mass spectrometry data

Nils Hoffmann, Jens Stoye
2009 Computer applications in the biosciences : CABIOS  
We describe ChromA, a web-based alignment tool for chromatography-mass spectrometry data from the metabolomics and proteomics domains.  ...  ChromA offers different visualizations of the alignment for easier qualitative interpretation and comparison of the data.  ...  ACKNOWLEDGEMENTS The authors would like to thank Tony Watt for providing the example GC-MS data available for evaluation on the web site. Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btp343 pmid:19505941 pmcid:PMC2722998 fatcat:cikw7hvfe5f5jkwnd6zbo636ai

Navigating freely-available software tools for metabolomics analysis

Rachel Spicer, Reza M. Salek, Pablo Moreno, Daniel Cañueto, Christoph Steinbeck
2017 Metabolomics  
Conclusion This review presents the most widely used tools for metabolomics analysis, categorised based on their main functionality.  ...  As future work, we suggest a direct comparison of tools' abilities to perform specific data analysis tasks e.g. peak picking.  ...  Galaxy (Afgan et al. 2016 ) provides a biological workflow platform, allowing for integration of multiple software tools into complete analytical workflows.  ... 
doi:10.1007/s11306-017-1242-7 pmid:28890673 pmcid:PMC5550549 fatcat:tydxcin3krafnpke4z3ptyfel4
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