SysMet is a web-based application consisting of a suite of tools to help users uncover the relationships between diseases and metabolites and enhance the role of metabolomics in systems biology research. Differential Analysis Tool applies statistical analysis of metabolites using a univariate binomial logistic regression model. This is followed by differential network analysis to calculate a network activity score for each metabolite. Multi-Omic Integration Tool integrates metabolomic data with another omic dataset acquired from the same set of samples to find disease-associated metabolites. First, a differential network is constructed using metabolomic data, and network activity scores are calculated. Then, new nodes and edges are added to the differential network based on correlation between the metabolites and other biomolecules from the second omic dataset. Finally, the network activity scores are updated due to the integrated network.