Help:Tools using WikiPathways

From WikiPathways

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Revision as of 04:54, 15 January 2011

List of bioinformatics software tools using WikiPathways

PathVisio

PathVisio is a tool for displaying and editing biological pathways. In a sense PathVisio lets you draw pathways as you would in any drawing program, like PowerPoint or Photoshop. But the difference is that PathVisio can understand the biological context of a pathway, because you can link biological entities (genes or proteins) in your pathways to biological data using database identifiers. This will let you map experimental data (e.g. microarray data) and visualize it on top of the pathway drawing.

GenMAPP

GenMAPP is a free computer application designed to visualize gene expression and other genomic data on maps representing biological pathways and groupings of genes. WikiPathways is the official repository for GenMAPP pathways.

Cytoscape

Cytoscape is an open source software platform for visualizing complex-networks and integrating these with any type of attribute data. A lot of plugins are available for various kinds of problem domains, including bioinformatics, social network analysis, and semantic web. With the GPML plugin, pathways from WikiPathways can be imported via web services.

EuGene

Eu.Gene Analyzer is an easy-to-use, stand-alone application that allows rapid and powerful microarray data analysis in the context of biological pathways. Its intuitive graphical user interface makes it an easy and flexible tool, even for the first-time user. Pathways can be downloaded from WikiPathways in EuGene's .pwf format.

GO-Elite

GO-Elite is a software tool designed to identify a minimal non-redundant set of Gene Ontology (GO) biological terms or pathways to describe a particular set of genes. GO-Elite uses WikiPathways as its official pathway source. GO-Elite is also available as a Cytoscape plugin.

WebGestalt

WebGestalt is a "WEB-based GEne SeT AnaLysis Toolkit". It is designed for functional genomic, proteomic and large-scale genetic studies from which large number of gene lists (e.g. differentially expressed gene sets, co-expressed gene sets etc) are continuously generated. WebGestalt incorporates information from different public resources and provides an easy way for biologists to make sense out of gene lists.