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.
Publication quality image generation - UCSD
Automatic node label position adjustment (place labels outside of the node). UCSD
[:VisualLegendGenerator:Automatic Visual Legend generator] (code is already available. Needs generic GUI). UCSD - Kei
Use Arrow keys to move nodes. UCSD
Tentative: Layout algorithm that reflects classes (GO, others implied by selectable attributes). Pasteur - Tero
Organization/Retrieval/Search - MSKCC/Agilent
[:QuickFindRFC:Quick Find]. MSKCC - Ethan
[:CytoscapeIcons:New Cytoscape icon set]. MSKCC - Ethan
Context sensitive menus for edges (application: Linkout). MSKCC/Agilent - Doron or Allan
Expressiveness and enrichment of the network model - UCSF/Agilent
Editor support for metanodes/hyperedges Agilent - Allan/Aditya
Design of GenMAPP annotations. UCSF - Alex
Clarification of directed edges in GINY and use throughout Cytoscape Everyone
Design of attribute based layout. Agilent/MSKCC/UCSF - Alex
Data Integration and Handling - UCSD
Consolidated network import capabilities (i.e. gather all import plugins into one place). UCSD
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
BioGRID import. UCSD
Ability to delete attributes somehow (Unilever request). UCSD - Kei ( TODO: needs clarification by Mike)
Immutable/Invisible CyAttributes (mainly for Metanodes). MSKCC/UCSD - Ethan (CyAttributes)/Kei (AttributeBrowser)
General Refactoring/Other - UCSD
Fix resize VizMapper windows. UCSD
Fix resize filter windows. UCSD
Fix node topology filter so that it doesn't depend on other filters. UCSD - Ryan
Develop scheme for plugins to save state, e.g. the filters plugin should save filter.props in the session file. UCSD - Kei
Add unit tests galore (including Swing tests). UCSD - undergrads
Future Directions - Everyone
GINY MetaNode refactoring. Everyone TODO: Consult with Scooter to decide high/low
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).
Plugins
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.
Make sure JActiveModules uses NodeAttributes rather than the Expression Matrix data structure. UCSD
2.4 Refactoring Plan
- 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
Move from CVS to [http://subversion.tigris.org Subversion]
- 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)
Publication quality image generation (total: 10 weeks)
Automatic node label position adjustment (place labels outside of the node). - 4 weeks
[:VisualLegendGenerator:Automatic Visual Legend generator] (code is already available. Needs generic GUI). - 4 weeks
Use Arrow keys to move nodes. - 2 weeks
Data Integration and Handling (total: 7 weeks)
Consolidated network import capabilities (i.e. gather all import plugins into one place). - 1 week
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
BioGRID import. - 1 week
Immutable/Invisible CyAttributes (mainly for Metanodes). - 1 week
General Refactoring/Other (total: 29 weeks)
Fix resize VizMapper windows. - 1 week
Fix resize filter windows. - 1 week
Fix node topology filter so that it doesn't depend on other filters. - 1 week
Develop scheme for plugins to save state, e.g. the filters plugin should save filter.props in the session file. - 4 weeks
Add unit tests galore (including Swing tests). - 4 weeks
Make sure JActiveModules uses NodeAttributes rather than the Expression Matrix data structure. - 2 weeks
VizMapper design document. - 2 weeks
Clarification of directed edges in GINY and use throughout Cytoscape - 1 week
GINY MetaNode refactoring. Everyone TODO: Consult with Scooter to decide high/low - 2 weeks
- Migration to Java Version 5
Test core plugins in v5 environments - 2 weeks
Replace old library files - 1 week
Move from CVS to [http://subversion.tigris.org Subversion] - 1 week
Refactor the project files - 1 week
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 @ ?)
Organization/Retrieval/Search - MSKCC
[:QuickFindRFC:Quick Find]. MSKCC - Ethan
[:CytoscapeIcons:New Cytoscape icon set]. MSKCC - Ethan
Data Integration and Handling
Immutable/Invisible CyAttributes (mainly for Metanodes). MSKCC - Ethan (CyAttributes)
Plugins (total: 8 weeks)
BioPAX Editing Plugin / Support for Pathway Commons. MSKCC - Ben, 8 weeks
General Refactoring/Other
Context sensitive menus for edges (application: Linkout). MSKCC - Doron, 2 weeks
VizMapper design document. Everyone
Design of attribute based layout. MSKCC
Clarification of directed edges in GINY and use throughout Cytoscape Everyone
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)
Organization/Retrieval/Search - Agilent (total: 15-1/2 weeks)
Context sensitive menus for edges (application: Linkout). Agilent - Allan - 1/2 week
Expressiveness and enrichment of the network model - Agilent
Editor support for metanodes/hyperedges Agilent - Allan/Aditya/Mike Creech - 12 weeks
Design of attribute based layout. Agilent - 3 weeks
Plugins (total: 2 weeks)
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
General Refactoring/Other (total: 5 weeks)
VizMapper design document. Allan/Everyone - 3 weeks
Clarification of directed edges in GINY and use throughout Cytoscape Everyone - 1 week
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])
Expressiveness and enrichment of the network model (total: 10 weeks)
Design of GenMAPP annotations. UCSF - Alex: 5 weeks
Design of attribute based layout. UCSF - Alex: 5 weeks
General Refactoring/Other (total: 5 weeks)
VizMapper design document. Everyone (Alex: 2.5 weeks)
Clarification of directed edges in GINY and use throughout Cytoscape Everyone
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)
Publication quality image generation
Tentative: Layout algorithm and implementation that reflects classes (GO, others implied by selectable attributes). Tero
Oneline tutorials (total: 4 weeks)
Updates/Extensions to existing online tutorials to reflect current functionality - Melissa: 4 weeks
General Refactoring/Other (total: 10 weeks)
Assessment and conclusions from user-based Cytoscape usability studies - Melissa/Everyone: 4 weeks
VizMapper design document. Melissa/Everyone: 6 weeks
GINY MetaNode refactoring. Everyone TODO: Consult with Scooter to decide high/low'
Our effort sums to 28 weeks.
Features for 2.5 and beyond
Publication quality image generation
Custom edge graphics. UCSD
Organization/Retrieval/Search.
Linkout from node attribute browser (i.e. right click in a cell and get the linkout data for that attribute) (Unilever request). UCSD - Kei
Vision: attribute browser so that it mirrors all features of the network view (basically becomes a type of matrix view of the data)
Expressiveness and enrichment of the network model.
Official release of Metanode plugin Scooter/Iliana++ TODO: ask Scooter if this is definitely/maybe for 2.4
Attribute based layout. Agilent/MSKCC/UCSF - Alex
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
Data Integration and Handling
ID Mapping Service. MSKCC
Expression Matrix import. UCSD
Consider new CSV based import format (e.g. GeneSpring genome definition file). UCSD
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
General Refactoring / Other
Move vizmapper and filters to CytoPanels.
Plugins
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)