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Metabolomics is a key approach in modern functional genomics and systemsbiology. Due to the complexity of metabolomics data, the variety ofexperimental designs, and the variety of existing bioinformatics tools,providing experimenters with a simple and efficient resource to conductcomprehensive and rigorous analysis of their data is of utmost importance. In2014, we launched the Workflow4Metabolomics (W4M,http://workflow4metabolomics.org) online infrastructure for metabolomics builton the Galaxy environment, which offers user-friendly features to build and rundata analysis workflows including preprocessing, statistical analysis, andannotation steps. Here we present the new W4M 3.0 release, which contains twiceas many tools as the first version, and provides two features which are, to ourknowledge, unique among online resources. First, data from the four majormetabolomics technologies (i.e., LC-MS, FIA-MS, GC-MS, and NMR) can be analyzedon a single platform. By using three studies in human physiology, algaevolution, and animal toxicology, we demonstrate how the 40 available tools canbe easily combined to address biological issues. Second, the full analysis(including the workflow, the parameter values, the input data and outputresults) can be referenced with a permanent digital object identifier (DOI).Publication of data analyses is of major importance for robust and reproduciblescience. Furthermore, the publicly shared workflows are of high-value fore-learning and training. The Workflow4Metabolomics 3.0 e-infrastructure thusnot only offers a unique online environment for analysis of data from the mainmetabolomics technologies, but it is also the first reference repository formetabolomics workflows.

the international journal of biochemistry and cell biology

Create, run, share, publish, and reference your LC-MS, FIA-MS, GC-MS,  and NMR data analysis workflows with the Workflow4Metabolomics 3.0 Galaxy  online infrastructure for metabolomics