The application of omics (i.e., metabolomics, proteomics, transcriptomics, genomics) has become greatly popular in the life sciences. These technologies unlock the investigation of metabolism across thousands of genes, proteins, and metabolites, and provide a holistic perspective on the system of interest. However, to gather a systems-level understanding of biological functions in health and disease, omics data must be integrated in the relevant metabolic networks, in the context of allosteric, signaling and other regulatory layers. Metabolites can be regarded as a functional readout for the activity of a biological system. Therefore, their measured abundances can be leveraged to guide the interpretation of other omics layers of information. In this workshop, we provide an introduction and hands-on practical exercises on state-of-the art workflows and tools for the integration and interpretation of metabolomics data sets in the context of transcriptomics, proteomics, and genomics data. We will first introduce tools for processing metabolomics data at high throughput, such as the XCMS, MetaboAnalyst, METLIN, LIPID MAPS, The Human Metabolome Database, and the GNPS. We will further present tools for multi-omics integration and interpretation, including PathView, Reactome, MixOmics, PARADIGM, among others. The objective of this workshop is to i) provide a comprehensive overview on tools and resources for metabolomics data analysis and multi-omics interpretation, ii) provide hands-on training on open-source tools for systems biology of metabolism. This workshop is addressed to empirical biologists and computational biologists interested in metabolism.