Workflow4Metabolomics: a collaborative research infrastructure for computational metabolomics

By F. Giacomoni, Gildas Le Corguillé, Misharl Monsoor, M. Landi, Pierre Pericard, M. Pétéra, C. Duperier, Marie Tremblay-Franco, Jean-François Martin, D. Jacob and 3 more. Bioinform., 2014

400 citations recorded by the source corpus.

Summary: The complex, rapidly evolving field of computational metabolomics calls for collaborative infrastructures where the large volume of new algorithms for data pre-processing, statistical analysis and annotation can be readily integrated whatever the language, evaluated on reference datasets and chained to build ad hoc workflows for users. We have developed Workflow4Metabolomics (W4M), the first fully open-source and collaborative online platform for computational metabolomics. W4M is a virtual research environment built upon the Galaxy web-based platform technology. It enables ergonomic integration, exchange and running of individual modules and workflows. Alternatively, the whole W4M framework and computational tools can be downloaded as a virtual machine for local installation. Availability and implementation: http://workflow4metabolomics.org homepage enables users to open a private account and access the infrastructure. W4M is developed and maintained by the French Bioinformatics Institute (IFB) and the French Metabolomics and Fluxomics Infrastructure (MetaboHUB). Contact: contact@workflow4metabolomics.org

Subfields: Biophysics, Health, Toxicology and Mutagenesis, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/292fd78024fe3e8dc31deac2fa76f327429fc13c

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In Biophysics

1. Jianguo Xia
2. David S. Wishart
3. Jasmine Chong
4. Weijun Luo
5. Cory R. Brouwer

In Health, Toxicology and Mutagenesis

1. David S. Wishart

In Molecular Biology

1. David S. Wishart
2. Jianguo Xia
3. Jasmine Chong
4. Guangyan Zhou
5. Shuzhao Li
6. Zhiqiang Pang
7. Mark R. Viant
8. Othman Soufan

Citations in the corpus

• MetaboAnalyst 5.0: narrowing the gap between raw spectra and functional insights (2021, methodology): “Among the remaining tools, Workflow4Metabolomics (W4M) (62) is a Galaxy-based workflow which uses the XCMS package for raw LC–MS data processing.”
• MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis (2018, methodology): “Several web-based as well as several web-enabled tools for metabolomic data analysis have been developed over recent years, including XCMS Online, Workflow4Metabolomics (46), Galaxy-M (47), and Metabox (48).”
• MetaboAnalyst 6.0: towards a unified platform for metabolomics data processing, analysis and interpretation (2024, methodology): “Table 1 compares the main features of MetaboAnalyst 6.0 with other popular tools including the previous version, XCMS online ( 23 ), GNPS ( 45 ), Workflow4Metabolomics (W4M) ( 67 ) and MetExplore ( 68 ).”
• metaX: a flexible and comprehensive software for processing metabolomics data (2017, methodology): “Open-source software, such as XCMS [4], CAMERA [5], MAIT [6], MetaboAnalyst [7] and Workflow4Metabolomics [8], usually cover limited processing steps.”
• Non-targeted UHPLC-MS metabolomic data processing methods: a comparative investigation of normalisation, missing value imputation, transformation and scaling (2016, methodology): “2016) and Workflow4Metabolomics (Giacomoni et al. 2015)] and R packages [e.”