Metscape: a Cytoscape plug-in for visualizing and interpreting metabolomic data in the context of human metabolic networks.

SUMMARY: Metscape is a plug-in for Cytoscape, used to visualize and interpret metabolomic data in the context of human metabolic networks. We have developed a metabolite database by extracting and integrating information from several public sources. By querying this database, Metscape allows users to trace the connections between metabolites and genes, visualize compound networks and display compound structures as well as information for reactions, enzymes, genes and pathways. Applying the pathway filter, users can create subnetworks that consist of compounds and reactions from a given pathway. Metscape allows users to upload experimental data, and visualize and explore compound networks over time, or experimental conditions. Color and size of the nodes are used to visualize these dynamic changes. Metscape can display the entire metabolic network or any of the pathway-specific networks that exist in the database. AVAILABILITY: Metscape can be installed from within Cytoscape 2.6.x under 'Network and Attribute I/O' category. For more information, please visit http://metscape.ncibi.org/tryplugin.html.

Integrating and annotating the interactome using the MiMI plugin for cytoscape.

UNLABELLED: The MiMI molecular interaction repository integrates data from multiple sources, resolves interactions to standard gene names and symbols, links to annotation data from GO, MeSH and PubMed and normalizes the descriptions of interaction type. Here, we describe a Cytoscape plugin that retrieves interaction and annotation data from MiMI and links out to multiple data sources and tools. Community annotation of the interactome is supported. AVAILABILITY: MiMI plugin v3.0.1 can be installed from within Cytoscape 2.6 using the Cytoscape plugin manager in 'Network and Attribute I/0' category. The plugin is also preloaded when Cytoscape is launched using Java WebStart at http://mimi.ncibi.org by querying a gene and clicking 'View in MiMI Plugin for Cytoscape' link.

User requirements for exploring a resource inventory for clinical research.

The CTSA Inventory of Resources Explorer facilitates searching and finding relevant biomedical resources in this rich, federated inventory. We used efficient and non-traditional formal usability methods to define requirements and to design the Explorer, which may be extended to similar web-based tools.