BEL Navigator

Explore OpenBEL knowledge networks within Cytoscape 3.

Capabilities

• Configure multiple connections to OpenBEL Web API.

• Search for nodes within a knowledge network.

• Expand knowledge neighborhood of selected nodes.

  • Expand all edges
  • Expand edges using faceted search

• Show supporting evidence for the selected network edge.

• Link an entire Cytoscape network to a knowledge network.

• Validate BEL syntax for network nodes and edges.

• Knowledge network visual styles.

Requirements

• Cytoscape 3.x

Installation

Note: The BEL Navigator plugin must be installed manually (see enhancement issue #34).

1. Download current release from OpenBEL/bel-nav.
2. Start Cytoscape.
3. Go to Apps ➡ App Manager ➡ Install from File...
4. Select the downloaded JAR and click Install.

Development

The BEL Navigator plugin is built with Groovy and uses a maven build system.

Additionally it includes the gosh shell tool to drive development functions. This shell tool is based on bash so it works within Mac, Linux, and Windows w/ Cygwin.

An isolated version of Cytoscape 3 is included in the repository to ease development. This enables plugins to automatically reload within Cytoscape after a build or test cycle succeeds.

To get started follow these steps:

1. Clone repository: git clone [email protected]:OpenBEL/bel-nav.git
2. Install maven.
3. Execute the go.sh shell script.

[tony@starship bel-nav]$ ./go.sh 

Entering go shell, [CTRL-C] to exit.
                                                                                                                                                                                
1) clean		2) build			3) test	
4) deploy		5) undeploy			6) loop (compile)	
7) loop (compile/test)	8) loop (compile/deploy)	9) loop (compile/test/deploy)	
10) start		11) debug			12) stop	
13) cytoscape log	14) groovy shell

dev / lifecycle / tools

go: 

3. For example to clean build artifacts, build modules, deploy to cytoscape, and start cytoscape execute:

./go.sh 1 2 4 10

Releases

To create a release of BEL Navigator 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/belnav-VERSION.jar and upload the file.

4. Receive confirmation from Cytoscape.

5. Update details on the project page.