SDP Model Builder

Cytoscape 3.0+ plugin to interface with an instance of the Selventa Development Platform (SDP) to explore and analyze biological networks (SDP models).

Functionality

• View, edit, and save models.
• Import paths found between two sets of nodes in an SDP knowledge network.
• Overlay RCR (Reverse Causal Reasoning) datasets on Cytoscape networks.
• Overlay Comparisons on Cytoscape networks.
• View, edit, and delete Sets.

Build process

This app is built using Maven and produces a single JAR (OSGi-enabled).

Requirements:

• Java 8
• Maven 3+

Installation steps:

• git clone https://github.com/Selventa/model-builder.git
• cd model-builder
• mvn clean package -DskipTests

Install process

Install from the AppStore.

• Open Cytoscape then Apps → App Manager and search for BEL Navigator.
• Install BEL Navigator App.

Install from source.

• Follow "Build process" section above.
• Open Cytoscape then Apps → App Manager → Install from File...
• Locate target/modelbuilder-VERSION.jar and click Open.

Development branches

experimental branch

• New/Unstable development

master branch

• Stable development for release.
• Releases are tagged here.

Unstable work:

• rcr_custom_painting branch

  • Contains work to build a custom painting interface for RCR scores. It is a work-in-progress, but about 90% complete.

Releases

To create a release of SDP Model Builder follow these steps:

1. Build a single OSGi bundle jar.

mvn clean package -DskipTests

2. Got to the Cytoscape App Store and submit a 3.0 application.

3. Locate target/modelbuilder-VERSION.jar and upload the file.

4. Receive confirmation from Cytoscape.

5. Update details on the App Store's project page.