= Cytoscape 2.3 =

== Use cases addressed: ==

  * First steps towards drawing pathways / metabolic networks.
  * Support for large networks
  * Key Usability Issues
      * Save State, Undo
      * Viz Mapper / Filters Specific Issues

== New Features: ==
  * New rendering engine;  lots of plugin dependencies
	(Nerius, Ethan, Allan as consultant; possibly Ben)
	Also includes Layout algorithms for large networks
  * Meta-Nodes;  Phase I
	(Iliana, Allan, Melissa, Aditya, Alex Pico, Scooter)
  * Saving Project State (Kei, Iliana);  Depends on Meta-Nodes
  * Undo Manager (Allan w/ help from friends)
  * Attribute browser;  link attribute browser to network view (Kei)
  * New, improved Cytoscape Tutorials (Melissa)
  * Graph Merge, moved to core (already a plugin) (Ryan, UCSD)
  * [6.  Clean-up Viz Mapper UI;  make friendlier;  move to cytopanels] [Mike S; currently understaffed]
  * [7.  Clean-up Filter UI][Mike S;  currently understaffed]
  * [8. ID Mapping Services, Phase I] [Optional?] (Gary)	

== Refactoring / Design Issues: ==
  * Node id issue – creation of a default “label” CyAttribute (Ben)
  * New documentation options;  docbook, wiki, etc. (Gary, Mike)
  * Take care of delete/hide/remove situation (Allan, in conjunction with Cytoscape Editor)
  * Flagging/selection of nodes/edges (Iliana)

== Misc. Small Items ==
  * Ability to rename networks
  * Script to update source license
  * Generic Linkout Pop-up Menu (Doron B, MSKCC)
  
= Cytoscape 2.4 and Beyond =

== Features ==
  * MetaNodes, Phase 2
  * Attribute Based Layout
  * Multi-colored nodes
  * Better hide/show for edges/ nodes
  * Real-time vizmapper update
  * KEGG Reader / Reaction node + editor
  * Interactive Slider Widget
  * Visual Legend
  * Standardize context menus for nodes/edges
  * Network specific node and edge attributes

== Refactoring / Design Issues ==
  * New GraphObject class; for nodes/edges
  * Formalize what goes in the core
  * Improving / Refactoring Event Model