Explore OpenBEL knowledge networks within Cytoscape 3.
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Configure multiple connections to OpenBEL Web API.
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Search for nodes within a knowledge network.
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Expand knowledge neighborhood of selected nodes.
- Expand all edges
- Expand edges using faceted search
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Show supporting evidence for the selected network edge.
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Link an entire Cytoscape network to a knowledge network.
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Validate BEL syntax for network nodes and edges.
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Knowledge network visual styles.
- Cytoscape 3.x
Note: The BEL Navigator plugin must be installed manually (see enhancement issue #34).
- Download current release from OpenBEL/bel-nav.
- Start Cytoscape.
- Go to Apps ➡ App Manager ➡ Install from File...
- Select the downloaded JAR and click Install.
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:
- Clone repository:
git clone git@github.com:OpenBEL/bel-nav.git
- Install maven.
- 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:
- For example to clean build artifacts, build modules, deploy to cytoscape, and start cytoscape execute:
./go.sh 1 2 4 10
To create a release of BEL Navigator follow these steps:
- Build a single OSGi bundle jar.
mvn clean package -DskipTests
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Got to the Cytoscape App Store and submit a 3.0 application.
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Locate target/belnav-VERSION.jar and upload the file.
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Receive confirmation from Cytoscape.
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Update details on the project page.