CytoscapeRPC new

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CytoscapeRPC is a Cytoscape plugin which allows users to communicate with Cytoscape over XML-RPC. This means that you can create, query and modify Cytoscape networks from virtually any programming language.

Installation

Install CytoscapeRPC through the Cytoscape plugin manager or manually by copying the jar to the <cytoscape_root>/plugins folder.

Usage

CytoscapeRPC was created to provide easy, interactive access to Cytoscape through diffent programming languages. We've listed a number of uses of the plugin that we think are useful.

  • Use CytoscapeRPC for data loading: doing this using the GUI takes a lot of time, opening diffent noa, eda and sif files and then applying layouts and vizmaps is cumbersome. The plugin can be used to script all these events, looping over all the files in a directory to add all the information to a Cytoscape network. Example script here.
  • Packages such as RCytoscape make using CytoscapeRPC from a programming environment (in this case R) a lot easier. These types of packages abstract away from the underlying XML-RPC code to make calling remote functions even easier.
  • Interactive use of CytoscapeRPC is possible using e.g. IPython or the IRB.
  • Create movies by scripting events in Cytoscape and saving the network as image files. The 'convert' command can be used to link these images together into a movie. Example script here.

Examples

External links