Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace.

Complex biomedical analyses require the use of multiple software tools in concert and remain challenging for much of the biomedical research community. We introduce GenomeSpace (http://www.genomespace.org), a cloud-based, cooperative community resource that currently supports the streamlined interaction of 20 bioinformatics tools and data resources. To facilitate integrative analysis by non-programmers, it offers a growing set of 'recipes', short workflows to guide investigators through high-utility analysis tasks.

MetDisease--connecting metabolites to diseases via literature.

MOTIVATION: In recent years, metabolomics has emerged as an approach to perform large-scale characterization of small molecules in biological systems. Metabolomics posed a number of bioinformatics challenges associated in data analysis and interpretation. Genome-based metabolic reconstructions have established a powerful framework for connecting metabolites to genes through metabolic reactions and enzymes that catalyze them. Pathway databases and bioinformatics tools that use this framework have proven to be useful for annotating experimental metabolomics data. This framework can be used to infer connections between metabolites and diseases through annotated disease genes. However, only about half of experimentally detected metabolites can be mapped to canonical metabolic pathways. We present a new Cytoscape 3 plug-in, MetDisease, which uses an alternative approach to link metabolites to disease information. MetDisease uses Medical Subject Headings (MeSH) disease terms mapped to PubChem compounds through literature to annotate compound networks. AVAILABILITY AND IMPLEMENTATION: MetDisease can be downloaded from http://apps.cytoscape.org/apps/metdisease or installed via the Cytoscape app manager. Further information about MetDisease can be found at http://metdisease.ncibi.org CONTACT: akarnovs@med.umich.edu SUPPLEMENTARY INFORMATION: Supplementary Data are available at Bioinformatics online.

Metscape 2 bioinformatics tool for the analysis and visualization of metabolomics and gene expression data.

MOTIVATION: Metabolomics is a rapidly evolving field that holds promise to provide insights into genotype-phenotype relationships in cancers, diabetes and other complex diseases. One of the major informatics challenges is providing tools that link metabolite data with other types of high-throughput molecular data (e.g. transcriptomics, proteomics), and incorporate prior knowledge of pathways and molecular interactions. RESULTS: We describe a new, substantially redesigned version of our tool Metscape that allows users to enter experimental data for metabolites, genes and pathways and display them in the context of relevant metabolic networks. Metscape 2 uses an internal relational database that integrates data from KEGG and EHMN databases. The new version of the tool allows users to identify enriched pathways from expression profiling data, build and analyze the networks of genes and metabolites, and visualize changes in the gene/metabolite data. We demonstrate the applications of Metscape to annotate molecular pathways for human and mouse metabolites implicated in the pathogenesis of sepsis-induced acute lung injury, for the analysis of gene expression and metabolite data from pancreatic ductal adenocarcinoma, and for identification of the candidate metabolites involved in cancer and inflammation. AVAILABILITY: Metscape is part of the National Institutes of Health-supported National Center for Integrative Biomedical Informatics (NCIBI) suite of tools, freely available at http://metscape.ncibi.org. It can be downloaded from http://cytoscape.org or installed via Cytoscape plugin manager. CONTACT: metscape-help@umich.edu; akarnovs@umich.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Cytoscape: the network visualization tool for GenomeSpace workflows.

Modern genomic analysis often requires workflows incorporating multiple best-of-breed tools. GenomeSpace is a web-based visual workbench that combines a selection of these tools with mechanisms that create data flows between them. One such tool is Cytoscape 3, a popular application that enables analysis and visualization of graph-oriented genomic networks. As Cytoscape runs on the desktop, and not in a web browser, integrating it into GenomeSpace required special care in creating a seamless user experience and enabling appropriate data flows. In this paper, we present the design and operation of the Cytoscape GenomeSpace app, which accomplishes this integration, thereby providing critical analysis and visualization functionality for GenomeSpace users. It has been downloaded over 850 times since the release of its first version in September, 2013.