• Cytoscape 2.4
• 2.4 Features Organized by Development Group

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. 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 OBO and 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 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

0.75 FTE = 15 weeks (Ben & Ethan)

1. Organization/Retrieval/Search - MSKCC

   1. Quick Find. MSKCC - Ethan

   2. 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 - Ben, 1 week

   2. Design of attribute based layout. MSKCC

   3. VizMapper design document. Everyone

   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 15 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

1.4 FTE = 28 weeks (Melissa, Tero @ 0.7 FTE, possibly others)

1. Publication quality image generation (total: 4 weeks)

   1. Layout algorithm and implementation that reflects classes (GO, others implied by selectable attributes). Tero

2. Online tutorials (total: 1 week)

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

3. General Refactoring/Other (total: 13 weeks)

   1. TreeView integration plugin - Melissa: 8 weeks

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

   3. VizMapper design document. Melissa/Everyone: 2 weeks

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

4. Plugins (total: 10 weeks)

   1. Module finding by experiment-specific scoring of groups of nodes within an underlying interaction network. Tero

Our effort sums to 28 weeks.