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 Coordinator/BugMaster

• (To be determined - maybe Mike)

2.4 New Feature Summary

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

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

   3. Use Arrow keys to move nodes. UCSD

2. Organization/Retrieval/Search - MSKCC/Agilent

   1. [:QuickFindRFC:Quick Find]. MSKCC - Ethan

   2. [:CytoscapeIcons:New Cytoscape icon set]. MSKCC - Ethan

   3. Context sensitive menus for edges (application: Linkout). MSKCC/Agilent - Doron or Allan

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

   1. Editor support for metanodes/hyperedges Agilent - Allan/Aditya

   2. Design of GenMAPP annotations. UCSF - Alex

   3. Clarification of directed edges in GINY and use throughout Cytoscape Everyone

   4. Design of attribute based layout. Agilent/MSKCC/UCSF - Alex

4. Data Integration and Handling - UCSD

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

   2. 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. UCSD - Kei

   3. BioGRID import. UCSD

   4. Ability to delete attributes somehow (Unilever request). UCSD - Kei ( TODO: needs clarification by Mike)

   5. Immutable/Invisible CyAttributes (mainly for Metanodes). MSKCC/UCSD - Ethan (CyAttributes)/Kei (AttributeBrowser)

5. General Refactoring/Other - UCSD

   1. Fix resize VizMapper windows. UCSD

   2. Fix resize filter windows. UCSD

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

   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 - undergrads

6. Future Directions - Everyone

   1. GINY MetaNode refactoring. Everyone TODO: Consult with Scooter to decide high/low

   2. VizMapper design document. Allan/Melissa/Everyone

      • Make this a session at the retreat, with appropriate preparation. 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).

7. Plugins

   1. BioPAX Editing / Support for Pathway Commons. MSKCC/Agilent (Allan for editor support) (Will be released as a plugin, separate from 2.4). Not a core plugin.

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

2.4 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]

3. Refactor the project files
   • 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.
     • 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!

   • Automate the release process using InstallAnywhere such that release creation is a one command process.

   • Reduce the clutter!

2.4 Features Organized by Development Group

This section restates the features described in the previous section, but organized by development group. All features should be represented here and no features should be missing. Some features that multiple groups will work on are represented under all groups working on the feature.

We have approximately 5 months until release which translates to 20 weeks. Therefore, 1 FTE would have 20 weeks of development and testing time.

UCSD

2 FTE = 40 weeks (Mike @ 1/2 FTE, Kei @ 3/4 FTE, Others[undergrads, new programmer, Ryan] @ 3/4 FTE)

1. Publication quality image generation (total: 10 weeks)

   1. Automatic node label position adjustment (place labels outside of the node). - 4 weeks

   2. [:VisualLegendGenerator:Automatic Visual Legend generator] (code is already available. Needs generic GUI). - 4 weeks

   3. Use Arrow keys to move nodes. - 2 weeks

2. Data Integration and Handling (total: 7 weeks)

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

   2. 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. - 4 weeks

   3. BioGRID import. - 1 week

   4. Immutable/Invisible CyAttributes (mainly for Metanodes). - 1 week

3. General Refactoring/Other (total: 29 weeks)

   1. Fix resize VizMapper windows. - 1 week

   2. Fix resize filter windows. - 1 week

   3. Fix node topology filter so that it doesn't depend on other filters. - 1 week

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

   5. Add unit tests galore (including Swing tests). - 4 weeks

   6. Make sure JActiveModules uses NodeAttributes rather than the Expression Matrix data structure. - 2 weeks

   7. VizMapper design document. - 2 weeks

   8. Clarification of directed edges in GINY and use throughout Cytoscape - 1 week

   9. GINY MetaNode refactoring. Everyone TODO: Consult with Scooter to decide high/low - 2 weeks

   10. Migration to Java Version 5

       • Test core plugins in v5 environments - 2 weeks

       • Replace old library files - 1 week

   11. Move from CVS to [http://subversion.tigris.org Subversion] - 1 week

   12. Refactor the project files - 1 week

   13. General project management - 6 weeks

Our effort sums to 46 weeks... which is close and probably OK given the ROUGH nature of the estimates.

MSKCC

? FTE = ? weeks (Ben @ 1/2 FTE, Ethan @ ?)

1. Organization/Retrieval/Search - MSKCC

   1. [:QuickFindRFC:Quick Find]. MSKCC - Ethan

   2. [:CytoscapeIcons:New Cytoscape icon set]. MSKCC - Ethan

2. Data Integration and Handling

   1. Immutable/Invisible CyAttributes (mainly for Metanodes). MSKCC - Ethan (CyAttributes)

3. Plugins (total: 8 weeks)

   1. BioPAX Editing Plugin / Support for Pathway Commons. MSKCC - Ben, 8 weeks

4. General Refactoring/Other

   1. Context sensitive menus for edges (application: Linkout). MSKCC - Doron

   2. VizMapper design document. Everyone

   3. Design of attribute based layout. MSKCC

   4. Clarification of directed edges in GINY and use throughout Cytoscape Everyone

   5. GINY MetaNode refactoring. Everyone TODO: Consult with Scooter to decide high/low

Our effort sums to ? weeks

Agilent

1 FTE = 20 weeks (Allan @ 1/2 FTE, Aditya @ 1/4 FTE, Mike Creech @ 1/4 FTE)

1. Organization/Retrieval/Search - Agilent (total: 15-1/2 weeks)

   1. Context sensitive menus for edges (application: Linkout). Agilent - Allan - 1/2 week

2. Expressiveness and enrichment of the network model - Agilent

   1. Editor support for metanodes/hyperedges Agilent - Allan/Aditya/Mike Creech - 12 weeks

   2. Design of attribute based layout. Agilent - 3 weeks

3. Plugins (total: 2 weeks)

   1. BioPAX Editing / Support for Pathway Commons. Agilent (Allan for editor support) (Will be released as a plugin, separate from 2.4). Not a core plugin. - 2 weeks

4. General Refactoring/Other (total: 5 weeks)

   1. VizMapper design document. Allan/Everyone - 3 weeks

   2. Clarification of directed edges in GINY and use throughout Cytoscape Everyone - 1 week

   3. GINY MetaNode refactoring. Everyone TODO: Consult with Scooter to decide high/low - 1 week

Our effort sums to 22-1/2 weeks... which seems in line with other groups' estimates.

UCSF

3/4 FTE = 15 weeks (Alex [plus others in Conklin Lab])

1. Expressiveness and enrichment of the network model (total: 10 weeks)

   1. Design of GenMAPP annotations. UCSF - Alex: 5 weeks

   2. Design of attribute based layout. UCSF - Alex: 5 weeks

2. General Refactoring/Other (total: 5 weeks)

   1. VizMapper design document. Everyone (Alex: 2.5 weeks)

   2. Clarification of directed edges in GINY and use throughout Cytoscape Everyone

   3. GINY MetaNode refactoring. Everyone (Alex: 2.5 weeks) TODO: Consult with Scooter to decide high/low

Our effort sums to 15 weeks.

Pasteur

? FTE = ? weeks (? @ ? FTE)

1. General Refactoring/Other

   1. VizMapper design document. Melissa/Everyone

   2. GINY MetaNode refactoring. Everyone TODO: Consult with Scooter to decide high/low

Our effort sums to ? weeks

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 [http://www.psb.ugent.be/cbd/papers/BiNGO/images/tutorial6.png BiNGO plugin]). UCSD - 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. 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)