• Cytoscape 2.3 and Beyond

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