Cytoscape Wiki|
← Revision 1 as of 2005-12-02 01:11:28 →
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Size: 1798
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| Deletions are marked like this. | Additions are marked like this. |
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| =Cytoscape 2.3= | = Cytoscape 2.3 = |
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| ==Use cases addressed:== | == Use cases addressed: == |
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* Save State, Undo * VizMapper / Filters Specific Issues |
* Save State, Undo * Viz Mapper / Filters Specific Issues |
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| ==New Features:== | == New Features: == |
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* Attribute browser; link attribute browser to network view (Kei) |
* Attribute browser; link attribute browser to network view (Kei) |
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==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) |
== 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) |
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| =Cytoscape 2.4 and Beyond= | = Cytoscape 2.4 and Beyond = |
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| ==Refactoring / Design Issues== | == Refactoring / Design Issues == |
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)
- [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)
Cytoscape 2.4 and Beyond
Features
MetaNodes; working as core
- 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