Use Cases Addressed

• Drawing and editing pathways / metabolic networks.
  • Expressiveness and enrichment of the network model
  • Editing pathways
  • Publication quality image generation
  • Organizing and navigating large networks.

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 Coordination

• (To be determined - Mike may be coordinator)
• What remains to do for the release:
  • Dec.21.2006
    • Documentation - (Mike)
      • Update the manual screenshots
        • Gary: 1-4
        • Mike: 5-8
        • Alex: 9,10
        • Sarah: 11
        • Allan: 12
        • Ben: 13
        • Kei: 15, 18
        • Peng: 16,17
    • Plugin testing (Mike to coordinate)
    • Website (Alex)
    • Release announcement
• We are at feature freeze (no code added that is unrelated to TODO list)
• Code freeze on November 27 (code is branched, no new code, just bug fixes)
• Testing is underway
• Tentative release on January 15

Release Notes

To be added to website upon official release. Feel free to add to the list.

Cytoscape 2.4
New Features include:

• New Quick Find Tool
  • Find nodes by name or other attribute
  • Highlights and centers view on results
• Create Publication-Quality Images
  • Adjusted label positions
  • Automatic legend generator

• New Data Import Features using BioDataServer

  • For importing ontologies and attributes
• Customizable Linkout Menus (a.k.a. Context Menus)
  • Link to web resources directly from nodes and edges

• Updated Wiki-Based Users Manual - here!

• New Toolbar Icons

2.4 New Features

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

1. Publication quality image generation - UCSD

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

   2. Automatic Visual Legend generator (code and GUI now available). UCSD - complete

   3. Use Arrow keys to move nodes. UCSD - complete

   4. Layout algorithm that reflects classes (GO, others implied by selectable attributes). Pasteur - Tero - 2.4 not dependent on this (it is a plugin)

2. Organization/Retrieval/Search - MSKCC/Agilent

   1. Quick Find. MSKCC - Ethan (Need to add support for edge attributes, optimize range selector, and tweak node selectio events, ETA: November 17)

   2. New Cytoscape icon set. MSKCC - Ethan (DONE)

   3. Context sensitive menus for edges (application: Linkout). MSKCC/Agilent - Doron or Allan. Status: Context sensitive menus work for edges. The main issue is the use cases for Linkout on edges. Allan and Doron are corresponding about this. TODO: Mike, Doron correspond on overlap between attribute linkout and node linkout.

3. Expressiveness and enrichment of the network model - UCSF/Agilent

   1. Editor support for hyperedges Agilent - Allan/Aditya (will only be hyperedges, not metanodes, because group/metanode API is not yet ready)

   2. Design of GenMAPP annotations. UCSF - Alex - on track as of Oct.13

   3. Clarification of directed edges in GINY and use throughout Cytoscape complete - all edges are directed

   4. Design of attribute based layout. Agilent/MSKCC/UCSF - Alex - on track as of Oct.13

4. Data Integration and Handling - UCSD

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

      • This includes function to load network files over the network (through http/ftp/etc.).

      • Integrate BioPAX PlugIn into Import Handler Framework (Ethan, DONE)

      • Integrate PSI-MI PlugIn into Import Handler Framework (Ethan, IN PROGRESS, ETA: November 3)

   2. New BioDataServer to import everything in OBO and Gene Association files directly to CyAttributes. UCSD - Kei (10/26 Status: Backend is done. Needd to integrate GUI to the text/Excel table import framework)

   3. General attribute/network text table reader and GUI. See text table import framework RFC.Kei (10/26/2006 Status: GUI is done. Remaining work is Excel import backend and Network table import.)

   4. Direct support for Excel (.xsl) files using POI Kei (Status 10/26/06: Currently working on the new reader for ExcelAttributeTableReader and ExcelNetworkTableReader)

   5. BioGRID import. UCSD - complete

   6. Immutable/Invisible CyAttributes (mainly for Metanode, Quick Find use cases). MSKCC/UCSD - complete.)

5. General Refactoring/Other - UCSD

   1. Fix resize VizMapper windows. UCSD - complete

   2. Fix resize filter windows. UCSD - complete

   3. Fix node topology filter so that it doesn't depend on other filters. UCSD - complete

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

   5. Add unit tests galore (including Swing tests). UCSD - ongoing

6. Usability

   1. Updates/Extensions to existing online tutorials to reflect current functionality Pasteur - Melissa

   2. Assessment and conclusions from user-based Cytoscape usability studies Pasteur - Melissa/Everyone

7. Future Directions - Everyone

   1. GINY refactoring. Everyone

      • Consider removing metanode concepts - yes, will be done later, during GINY refactoring
      • Add support for label placement "complete"
      • General cleanup/simplification now planned (retreat).

   2. VizMapper design document. Allan/Melissa/Everyone

      • Designed at retreat. Allan/Melissa/Everyone

      • For example, 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 (Unilever request).

8. Plugins

   1. BioPAX Editing / Support for Pathway Commons. MSKCC/Agilent (Allan for editor support) (Will be released as a plugin, separate from 2.4)

   2. Make sure JActiveModules uses NodeAttributes rather than the Expression Matrix data structure. UCSD - complete

   3. TreeView integration plugin Pasteur - Melissa - 2.4 not dependent on this

   4. Module finding by experiment-specific scoring of groups of nodes within an underlying interaction network. Pasteur - Tero - will not be ready for 2.4

2.4 Refactoring

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

   • Optional: use v5 new features (such as generics, annotation, extended for loops, etc.) for writing more readable & stable codes

2. Move from CVS to Subversion complete

3. Refactor the project files - Mike - mostly complete as of Oct.13

   • Move the unit tests into a separate directory tree so that the tests aren't included in the distribution jar. This also allows unit tests to share the same package as the classes they are testing without cluttering up the source directory.
   • Clean up documentation

     • Consider purchasing RenderX or Prince to generate pdfs. complete

     • Consolidate help and manual generation into one directory.

     • Remove all of the redundant manuals. Have only one manual and one pdf file in the docs directory. Use the versioning system for what it was intended! complete

   • Automate the release process using InstallAnywhere such that release creation is a one command process. complete - now using Install4j

   • Reduce the clutter! complete

/2.4 Features Organized by Development Group

Features for 2.5 and beyond

1. Publication quality image generation

   1. Custom edge graphics. UCSD

2. Organization/Retrieval/Search.

   1. Linkout from node attribute browser (i.e. right click in a cell and get the linkout data for that attribute) (Unilever request). UCSD - Kei

      1. Vision: attribute browser so that it mirrors all features of the network view (basically becomes a type of matrix view of the data)

3. Expressiveness and enrichment of the network model.

   1. Official release of Metanode plugin Scooter/Iliana++ TODO: ask Scooter if this is definitely/maybe for 2.4

   2. Attribute based layout. Agilent/MSKCC/UCSF - Alex

   3. 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 (Unilever request). UCSD - Kei TODO: clarify this task '

4. Data Integration and Handling

   1. ID Mapping Service. MSKCC

   2. Expression Matrix import. UCSD '

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

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

   3. GO Term viewer (display GO terms as DAG, just like BiNGO plugin). UCSD - Kei '

      • Check out some DAG/tree viewer work like this or this '

5. General Refactoring / Other

   1. Move vizmapper and filters to CytoPanels.

6. Plugins

   1. A HeatStrips visualization, which graphically displays multiple attribute values, such as expression values, as a set of color-coded bars attached to a node as a non-core plugin Agilent (possible for 2.4)