Diff for "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, Allan as consultant) Also includes Layout algorithms for large networks
• Meta-Nodes; Phase I
  • (Iliana, Allan, Melissa, Aditya, Alex Pico, Scooter)
• Saving Project State (["Save current session as XML file"]) (Kei, Iliana); Depends on Meta-Nodes

  • TIMELINE Basic session reader and writer are done. Need to change them to accept Metanodes.

• Undo Manager (Allan w/ help from friends)
• Attribute browser
  • link attribute browser to network view (Kei)
  • Meta-node compatible browser window (Show/hide member nodes) (Kei)
• New, improved Cytoscape Tutorials (Melissa)

  • There will be eight new tutorials: 1. Getting started, 2. Filters & editor, 3. Fetching external data, 4. Expression analysis, 5. Literature searching, 6. GO analysis, 7. Modules and complexes, 8. Domain networks and other topology topics. Other topics may be added if the demand is sufficient. Estimated timeline: 3-4 weeks.

• Graph Merge, moved to core (already a plugin) (Ryan, UCSD)
• [6. Clean-up Viz Mapper and Filter UIs (["VizMapUI"]); make friendlier; move to cytopanels] [Mike S, Allan, (possibly Alex?)]

  • TIMELINE

• [7. 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 (Brad K at UCSD)
  • Brad is adding code to allow networks to be renamed. They are currently named based on the input file. This change will change that name throughout the system.

  • TIMELINE Nearly complete. All of the underlying code is in place, we just need to figure out how refresh the name in the network panel.

• Script to update source license
  • Some of the Cytoscape source is missing copyright and license information. This needs to be fixed.

  • TIMELINE We have a script that needs to be updated with the proper information and tweaked so that it doesn't stomp on existing copyrights.

• Generic Linkout Pop-up Menu (Doron B, MSKCC)
  • This is a plugin that will read URL patterns from a user-defined configuration file to populate the links in the context menu activated by right clicking on a node or edge. Configuration files for popular sites will be provided e.g. a yeast URL config file.

  • TIMELINE Estimated completion May 2006 (last estimated Jan.13.2006)

• Re-organize save/load/import/export menu items (["New File Menu"]) (Kei)