Cytoscape_2.4

(Under construction...)

Use Cases Addressed

• Phase 2 for drawing pathways / metabolic networks.
• Organizing and navigating large networks.
• (please add other use cases)

Overall timeline

• Feature freeze: Mid-October 2006
  • Create source control branch for 2.4 release
  • Testing and bug fixing begins
• Application Testing: Mid-November 2006
  • Comprehensive application testing and bug fixing begins
• Projected 2.4 release date: December 2006

Release Coordinator/BugMaster

• Mike ????

Potential New Features

The new features for Cytoscape 2.4 are grouped according to development themes.

1. Publication quality image generation.

   1. Automatic node label position adjustment (place labels outside of the node). UCSD high

   2. [:VisualLegendGenerator:Automatic Visual Legend generator] (code is already available. Needs generic GUI). Kei high

   3. Use Arrow keys to move nodes. UCSD high

   4. Custom edge graphics. UCSD low

2. Organization/Retrieval/Search.

   1. [:QuickFindRFC:Quick Find]. Ethan medium

   2. Linkout for edges. Doron or Allan medium

   3. Linkout from node browser (i.e. right click in a cell and get the linkout data for that attribute). Kei low

3. Expressiveness and enrichment of the network model.

   1. Official release of Metanode plugin Scooter/Iliana++ medium

      • Editor support for metanodes/hyperedges Allan/Aditya medium

   2. GenMAPP annotations. Alex medium

   3. Attribute based layout. Agilent/MSKCC medium

   4. Ability to add "sticky notes" to a network - this basically just means adding a way to annotate a network. The current network attributes are a bit hard to use for this sort of thing. It would be hard to enter/read a paragraph of text describing a network with the current interface. Kei low

4. Data Integration and Handling

   1. ID Mapping Service. MSKCC medium

   2. BioPAX Editing / Support for Pathway Commons. MSKCC high (Will be released as a plugin, separate from 2.4).

   3. BioGRID import. UCSD medium

   4. Consolidated network import capabilities (i.e. gather all import plugins into one place). UCSD medium

   5. Immutable/Invisible CyAttributes (mainly for Metanodes). Ethan medium

   6. Expression Matrix import. UCSD medium

      • Make sure JActiveModules uses NodeAttributes rather than the Expression Matrix data structure.

      • Generalize expression matrix import so that it can import any type attribute.

      • Consider new CSV based import format (e.g. GeneSpring genome definition file).

   7. Ability to delete attributes. Kei/Ethan medium

   8. New BioDataServer to import everything in [http://www.geneontology.org/GO.downloads.shtml#ont OBO] and [http://www.geneontology.org/GO.current.annotations.shtml Gene Association] files directly to CyAttributes. Kei high

   9. GO Term viewer (display GO terms as DAG, just like [http://www.psb.ugent.be/cbd/papers/BiNGO/images/tutorial6.png BiNGO plugin]). medium Kei

      • Check out some DAG/tree viewer work like [http://www.dgp.toronto.edu/~ravin/videos/infovis2005_geneology.avi this] or [http://www.cs.umd.edu/hcil/spacetree/ this]

5. General Refactoring / Other

   1. Resize VizMapper windows. UCSD high

   2. Resize filter windows. UCSD high

   3. Fix node topology filter so that it doesn't depend on other filters. Ryan medium

   4. Develop scheme for plugins to save state, e.g. the filters plugin should save filter.props in the session file. Kei high

   5. Create a slider bar for the VizMapper that will slide through each mapping defined for a given attribute. Imagine that you have node color mappings defined for 10 different expression values. The slider dialog would present the list (drop down menu) of visual attributes (e.g. node color, node border, node size, etc.) and a slider. Once an attribute is selected, the slider would slide through each mapping, meaning that as the slider position changed, the mapping would change and the network view would update dynamically. Agilent low

   6. A HeatStrips visualization, which graphically displays multiple attribute values, such as expression values, as a set of color-coded bars attached to a node. Agilent medium

   7. Add unit tests galore. UCSD undergrads high

6. Future Directions

   1. GINY MetaNode refactoring. Everyone medium

   2. VizMapper design document. Allan/Melissa/Everyone medium

Refactoring Plan

1. Migration to Java Version 5
   • Test core plugins in v5 environments
   • Replace old library files

   • Optional: use [http://java.sun.com/j2se/1.5.0/docs/relnotes/features.html v5 new features] (such as generics, annotation, extended for loops, etc.) for writing more readable & stable codes

2. Move from CVS to [http://subversion.tigris.org Subversion]

Release plan