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PathVisio 3

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posted on 2014-05-22, 19:53 authored by Anwesha BohlerAnwesha Bohler, Martina KutmonMartina Kutmon, Martijn P van Iersel, Thomas Kelder, Kristina Hanspers, Alexander R Pico, Chris T Evelo

In 2008, we presented the first version of our pathway visualization and analysis tool PathVisio. Since then, PathVisio has been used in a number of studies to create pathway maps, perform pathway statistics or visualize biological data on pathways. The core application of PathVisio has now been refactored using the OSGi framework (Open Service Gateway initiative) with the goal to achieve a better, modular system that can be easily extended with plugins.

We will focus on the newest features and extensions of PathVisio 3, namely
Plugin repository and manager: The new plugin manager helps users to search for available plugins in the repository and provides easy and fast installation.
Annotation of interactions: Biological interactions can now be annotated with identifiers from online databases, like Reactome or KEGG Reaction, to provide additional information.
Multi-omics data visualization: PathVisio 3 enables users to simultaneously visualize transcriptomics, proteomics, metabolomics and fluxomics data on biological pathways.
XMLRPC interface for PathVisio: PathVisio functionality can now be used from different programming languages directly.

PathVisio plugins are extensions of the core application that provide features relevant for a specific task. Plugins are accessible to users through the new plugin repository and they can be installed through the plugin manager from within the application. This is an important aspect of usability that will allow users to build an application with all the necessary modules relevant for their work. We will show some use cases to demonstrate the extended abilities of PathVisio 3.

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