PPiMapBuilder

PPiMapBuilder is a Cytoscape 3 app for protein-protein interaction network generation and protein-protein interaction prediction via the Phylogenetic profiling method as described by:

Echeverría PC, Bernthaler A, Dupuis P, Mayer B, Picard D (2011) An interaction network predicted from public data as a discovery tool: application to the Hsp90 molecular chaperone machine. PLoS One 6: e26044.doi:10.1371/journal.pone.0026044.

PPiMapBuilder uses PSICQUIC services to retrieve interaction data, InParanoid 8 for protein orthology and UniProt for protein data.

This project was initiated by Pablo Echeverría from as a bio-informatic master project.

Installation

From release

1. Download the lastest PPiMapBuilder release
2. Install PPiMapBuilder-X.X.jar

• In Cytoscape go to Apps>App Manager then Install from file and select the PPiMapBuilder jar

OR

• Move the PPiMapBuilder jar to USER_DIRECTORY/CytoscapeConfiguration/3/apps/installed/

From source code

1. Clone this git repository or download source

2. Run maven install

3. Install target/PPiMapBuilder-X.X.jar

• In Cytoscape go to Apps>App Manager then Install from file and select the PPiMapBuilder jar

OR

• Move the PPiMapBuilder jar to USER_DIRECTORY/CytoscapeConfiguration/3/apps/installed/

Reference webservices used

PSICQUIC