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OCSANA

This software is a CytoScape plugin to compute optimal combinations of interventions in biological signaling networks. The original version of OCSANA was a plugin for Cytoscape 2, published in 2013 in "OCSANA: optimal combinations of interventions from network analysis". It has been rewritten for Cytoscape 3 with new algorithms for improved performance.

Running the software

Load your network in Cytoscape. From the "Apps" menu, select the "OCSANA" option.

Building the software

To build the software, you must first clone this repository on your computer. You must also install the Maven build management system. From the root directory of the project, you can then run mvn package to build the plugin JAR file and run the test suite. Once the build is completed, you must copy the file target/OCSANA-1.0-SNAPSHOT.jar to your CytoscapeConfiguration/3/apps/installed directory.

Database files

Parser scripts are included to build OCSANA's internal databases from files which can be downloaded from the Internet. These files are very large, so they are not included in the repository.

  • The drug targets database can be downloaded from DrugBank (select the "XML" option for "All drugs").
  • The human proteins database can be downloaded from UniProt (select "Download", then "XML").