MetaboAnalyst is a comprehensive, web-based tool designed for processing, analyzing, and interpreting metabolomic data. It handles most of the common metabolomic data types including compound concentration lists, spectral bin lists, peak lists, and raw mass spectrometry (MS) spectra.

PubMed: 25897128, 27603023, 22553367, 21637195, 21633943, 19429898, 30909447, 29955821, 29762782

• MetATT is an easy-to-use, web-based tool designed for time-series and two-factor metabolomics data analysis. MetATT offers a number of complementary approaches including 3D interactive principal component analysis, two-way heatmap visualization, two-way ANOVA, ANOVA-simultaneous component analysis, and multivariate empirical Bayes time-series analysis.
  PubMed: 21712247
• MetPA (Metabolomics Pathway Analysis) is a free and easy-to-use web application designed to perform pathway analysis and visualization of quantitative metabolomic data.
  PubMed: 2062807
• MSEA is a web-based tool to help identify and interpret patterns of metabolite concentration changes in a biologically-meaningful context for human and mammalian metabolomic studies.
  PubMed: 20457745
• ROCCET is a freely-available, web-based tool designed to assist clinicians and bench biologists in performing common ROC-based analyses on their metabolomic data using both classical univariate and more recently developed multivariate approaches. Receiver operating characteristic (ROC) curves are generally considered the method of choice for evaluating the performance of potential biomarkers.
  PubMed: 23543913

BioTransformer 3.0 is a freely-available software package for accurate, rapid, and comprehensive in silico metabolism prediction and compound identification. BioTransformer combines a machine learning-based approach with a knowledge-based approach to predict small molecule metabolism in human tissues (e.g. liver tissue), the human gut, as well as the environment (soil and water microbiota).

PubMed: 3553652, 30612223

ClassyFire is a web-based application for automated structural classification of chemical entities. This application uses a rule-based approach that relies on a comprehensible, comprehensive, and computable chemical taxonomy. ClassyFire provides a hierarchical chemical classification of chemical entities (mostly small molecules and short peptide sequences), as well as a structure-based textual description, based on a chemical taxonomy named ChemOnt, which covers 4825 chemical classes of organic and inorganic compounds. It can be accessed via the web interface or via the ClassyFire API. ClassyFire is offered to the public as a freely-accessible web server. Use and redistribution of the data, in whole or in part, for commercial purposes requires explicit permission of the authors and explicit acknowledgement of the source material (ClassyFire) and the original publication (see below). We ask that users who download portions of the database or use the service (via the server or the API) cite the ClassyFire paper in any resulting publications.

Pubmed: 27867422

MAGMET is a web-based system that automatically identifies and quantifies metabolites using 1D 1H NMR spectra of serum. MAGMET first performs all spectral processing steps, including Fourier transformation, phasing, solvent filtering, chemical shift referencing, baseline correction, and reference line shape convolution automatically. It then deconvolutes the resulting NMR spectrum using a reference spectral library, which here contains the signatures of more than 60 metabolites. This deconvolution process determines both the identity and quantity of the compounds in the biofluid mixture. Extensive testing shows that MAGMET meets or exceeds the performance of highly-trained human experts.

PubMed: 21360156

PolySearch 2.0 is an online search engine and text-mining system for identifying relationships between human diseases, genes, proteins, drugs, metabolites, toxins, metabolic pathways, organs, tissues, subcellular organelles, positive health effects, negative health effects, drug actions, Gene Ontology terms, MeSH terms, ICD-10 medical codes, biological taxonomies, and chemical taxonomies. PolySearch 2.0 supports a generalized ‘given X, find all associated Ys’ query, where X and Y can be selected from the aforementioned biomedical entities.

PubMed: 25925572, 18487273