CytoscapeRPC plug-in available

10 Jun 2010

For visualisation of network data, Cytoscape is a commonly used tool. To increase user-friendliness and create additional possibilities for visualisation, Jan Bot, BioAssist scientific programmer within the group of Marcel Reinders at Delft University of Technology, has developed a CytoscapeRPC plug-in, which is now available through the NBIC gforge.

Easy does it
Getting data into Cytoscape, performing layouts and changing the visual parameters can be tedious when done by hand. The new CytoscapeRPC plug-in allows you to perform these functions through an XML-RPC interface, which enables access to Cytoscape from every programming language that supports XML-RPC (e.g. Perl, Python, R, Ruby, etc.). 
A function call allows for easy data loading instead of exporting data to a XGMML file and subsequently loading that into Cytoscape. Visual properties can be changed by using Visual Mappers or by setting the attributes manually. 

See the movie
The tool is also capable of exporting networks to a variety of picture formats, which allows you to depict changes as a movie. This can help to visualize, for example, network changes in pathways. The tool can also be used interactively through, amongst others, the Python interpreter. This way, networks can be queried, modified and extended from the (Python) command line.

Re-run the script
A real life example illustrates the benefits and ease of use of the CytoscapeRPC plug-in. To visualise data from the Integromics database, members of the group of Frank Holstege (UMC Utrecht) would create a script to extract the data from the database, convert it to XGMML, manually load the data into Cytoscape and perform some visualization and layout algorithms. Every change of information in the database would require repeating this cycle. But thanks to the CytoscapeRPC plug-in, it's just a matter of re-running the script. Visualisation made easy.

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