Cytoscape 2.x Plugins Release Note

Plugin Name: AgilentLiteratureSearch

Version: 2.78

Release Note:

The following updates were made:
1. Fixed USPTO searching to work again.
2. Removed OMIM searching (due to licensing issues).
3. Added \'Source\' and \'Target\' attributes to ALS network edges where the Source attribute gives the name of the source node connected to that edge and the Target attribute gives the targe node name.
4. Fixed bug in incorrect removal of information when edges deleted.
Fixed bug in ALSUtils.removeGraphObjectAttributes() for CyEdges.
5. Fixed bug in incorrect setting of NUMBER_SOURCES in ALSUtils.setNumSentencesAndSources().
Changed to be tsi.getNumSources() vs tsi.size().
6. Fixed bug where saving and loading an ALS CyNetwork was not remembering search terms.
Changed code to save and restore search term attribute information.

7. Made resulting Cytoscape network naming smarter.
Changed Alfa2Cytoscape.computeNetworkName() generate names such as \'A & B\'; \'A, B, & C\'; etc.
8. Changed threshold for laying out networks as a grid vs hierarchical layout from 250 edges to 500 edges.
9. Fixed minor bug in Extend Network (and Discover Connection) where the nodes to use for the operation were the ones selected vs the ones selected and having a required property.
10. Updated license agreement.