Skip to content
ncatlett edited this page Aug 15, 2012 · 42 revisions

KAM Navigator Cytoscape Plugin User Manual

KAM Navigator is a Cytoscape plugin that allows users of the OpenBEL Framework to query, visualize, and analyze Knowledge Assembly Models (KAMs).

The plugin uses the BEL Framework Web Services application to access KAMs and create native Cytoscape networks that can be analyzed and manipulated using the rich set of Cytoscape network analysis tools.

The KAM Navigator plugin was designed and developed by Selventa and released as open source under the LGPL v3 license.

Requirements

KAM Navigator is compatible with Cytoscape version 2.8 and the BEL Framework 2.0.0 or later.

Quick Start - Demo

A demo server with a pre-compiled KAM is available for investigating the functionality of KAM Navigator. All you need to get started is Cytoscape 2.8 and the KAM Navigator plug-in!

  1. Download and install Cytoscape.

  2. Start Cytoscape and select Plugins -> Manage Plugins from the main menu. The plugin manager window will be displayed.

  3. Install the plugin by using the following URL in the Cytoscape Plugin Manager:

    https://raw.github.com/OpenBEL/Cytoscape-Plugins/master/plugins.xml

  1. Navigate to Plugins -> KAM Navigator -> BELFramework Configuration and connect the plugin to the public demo server by setting the Webservice Location (WSDL URL) to:

    http://demo.openbel.org/openbel-ws/belframework.wsdl

  2. Navigate to File -> New -> Network -> Empty Network to create a new network window.

  3. Navigate to Plugins -> KAM Navigator -> Add KAM Nodes to select one of the available example KAMs, and add node(s) to the network window.

To use the KAM Navigator plugin with your own KAMs you must have the OpenBEL Framework Web Services application running. See the OpenBEL website for more information on compiling KAMs and starting the OpenBEL Framework Web Services application.

Latest Release

0.9

  • Updated to OpenBEL 2.0.0, the newly open sourced framework
  • Networks with KAM attached elements can now be saved and reloaded and will properly reattach to the KAM they were loaded from, assuming the KAM is still present
  • Remove separate step for KAM load, now KAMs are loaded as you search for nodes
  • Misc bugfixes and improvements

Refer to the full Changelog for the changes in previous releases.

Additional Information

You can’t perform that action at this time.