In version 2.3, a function to save entire Cytoscape session will be added. The file will be called "<filename>.cys" (cys = CYtoscape Session). Basically, this is a zip file containing the following:

  1. CySession.xml

  2. vizmap.prop
  3. cytoscape.prop
  4. Arbitrary number of network files written in XGMML.

A timestamped directory will be created and files above will be stored in the dir. This function is implemented using JAXB.

How to use CytoscapeSessionReader class

Session file will be read through a class called CytoscapeSessionReader. This class has two types of constructor:

The first one is for local files and the second is mainly for remote files. The parametersource should be the location of the.cys file. For example, if plugin writer want to load a session file in a web server, the code to call the reader will be:

CytoscapeSessionReader csr = new CytoscapeSessionReader(new URL(

On-demand Loader for Gene Ontology Server (tentative, 2.3 or 2.4)

It is not realistic to save entire biodataserver object to the session file. Also, loading entire Gene Ontology data into memory is not space-efficient. To avoid this problem, some sort of mechanism to load GO data only for loaded network files. This can be done with the following:

  1. Prepare GO file in RDF-XML format (available here).

  2. Save the GO server's location in CySession.xml or cytoscape.prop

  3. Create a checkbox "Load GO data for the network" in the "load network" dialog.
  4. Generate query to select annotation only for nodes to be loaded.
  5. Execute query and store them drectry into CyAttributes or add it to BDS object

We need to refactor biodataserver class and add XQuery/SPARQL libraly to the Cytoscape. This method is universal to all data sources written in XML. I.e., if the database is available in XML format, we can query/load the data as a part of attributes in Cytoscape.

Save_current_session_as_XML_file (last edited 2009-02-12 01:03:18 by localhost)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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