Software

MetScape 3 for Cytoscape provides a bioinformatics framework for the visualization and interpretation of metabolomic and expression profiling data in the context of human metabolism.

MetScape allows users to build and analyze networks of genes and compounds, identify enriched pathways from expression profiling data, and visualize changes in metabolite data.

Correlation Calculator is a standalone Java application providing various methods of calculating pairwise correlations among repeatedly measured entities. It is designed for use with quantitative metabolite measurements such as MS data on a set of samples. The workflow allows inspection and/or saving of results at various stages, and the final correlation results can be dynamically imported into MetScape (version 3.1 or higher) as a correlation network.

Binner is a Java application that takes a numerical feature table obtained from any preprocessing software (e.g. XCMS, MZmine) as input and outputs a file with clusters of closely eluting, highly correlated metabolite features that are most related, along with their pairwise correlations, mass differences, and putative annotations.

MetDisease is an app for Cytoscape, the bioinformatics network visualization tool. The app is used to annotate a metabolic network with MeSH disease terms, explore related diseases within a network, and link to PubMed references corresponding to any network node and selection of MeSH terms. MeSH terms are controlled vocabulary terms used by the National Library of Medicine to describe the content of the articles indexed in PubMed.

Metab2MeSH uses a statistical approach to reliably and automatically annotate compounds with concepts defined in Medical Subject Headings, and the National Library of Medicine's controlled vocabulary for biomedical concepts. These annotations provide links from compounds to biomedical literature and complement existing resources such as PubChem and the Human Metabolome Database.