GenomeSpace Tools and Data Sources

geWorkbench

Project Website: http://wiki.c2b2.columbia.edu/workbench/index.php/Home

geWorkbench (genomics Workbench) is an open source Java desktop application that provides access to an integrated suite of tools for the analysis and visualization of data from a wide range of genomics domains (gene expression, sequence, protein structure, and systems biology). More than 70 distinct plug-in modules are currently available, implementing both classical analyses (several variants of clustering, classification, homology detection, etc.) as well as state-of-the-art algorithms for the reverse engineering of regulatory networks and for protein structure prediction, among many others. geWorkbench leverages standards-based middleware technologies to provide seamless access to remote data, annotation, and computational servers, thus enabling researchers with limited local resources to benefit from available public infrastructure.

Example use cases include:

• loading data from local or remote data sources
• visualizing gene expression, molecular interaction networks, pathway, protein sequence, and protein structure data in a variety of ways
• providing access to client- and server-side computational analysis tools such as differential expression analysis, hierarchical clustering, self-organizing maps, support vector machines, regulatory network reconstruction, BLAST searches, pattern/motif discovery, protein structure prediction, GenePattern modules, etc.
• validating computational hypothesis through the integration of gene and pathway annotation information from curated sources as well as through Gene Ontology enrichment analysis

Help Links

geWorkbench Wiki

geWorkbench Website

GenomeSpace functionality in geWorkbench

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