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1. General attribute text table reader and GUI. (Kei) |
1. General attribute/network text table reader and GUI. Kei (10/11/2006 Status: Need to change GUI for more general purpose attribute/network import.) 1. Direct support for Excel (.xsl) files using [http://jakarta.apache.org/poi/ POI] ''Kei'' |
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)
2.4 New Features
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 - Beta is complete. The decision is whether to use all of the refactoring involved in release 2.4. If not, it would take ~3-4 days to port the new code back into the hideous, horrible, old way of doing things.
[:VisualLegendGenerator:Automatic Visual Legend generator] (code is already available. Needs generic GUI). UCSD - Kei
Use Arrow keys to move nodes. UCSD - complete
Layout algorithm that reflects classes (GO, others implied by selectable attributes). Pasteur - Tero
Organization/Retrieval/Search - MSKCC/Agilent
[:QuickFindRFC:Quick Find]. MSKCC - Ethan (Aug 17 Status: Beta version now checked into cytoscape/plugins/core)
[:CytoscapeIcons:New Cytoscape icon set]. MSKCC - Ethan (Aug 17 Status: Beta icons now checked into cytoscape)
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.
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 complete - all edges are directed
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
- This includes function to load network files over the network (through http/ftp/etc.).
[:BioDataServerRFC: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 (9/13 Status: Basic classes are checked in. Need to add GUI for importing annotation (Gene Association))
- General attribute/network text table reader and GUI. Kei (10/11/2006 Status: Need to change GUI for more general purpose attribute/network import.)
Direct support for Excel (.xsl) files using [http://jakarta.apache.org/poi/ POI] Kei
BioGRID import. UCSD (Their format is PSI-MI v1 and 2.5, so we already have the plugins.)
Immutable/Invisible CyAttributes (mainly for Metanode, Quick Find use cases). MSKCC/UCSD - Ethan (CyAttributes)/Kei (AttributeBrowser) (Aug 24 Status: Revised CyAttributes API now checked in.)
General Refactoring/Other - UCSD
Fix resize VizMapper windows. UCSD - almost complete
Fix resize filter windows. UCSD - complete
Fix node topology filter so that it doesn't depend on other filters. UCSD - complete
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 - ongoing
Usability
Updates/Extensions to existing online tutorials to reflect current functionality Pasteur - Melissa
Assessment and conclusions from user-based Cytoscape usability studies Pasteur - Melissa/Everyone
Future Directions - Everyone
GINY refactoring. Everyone
- Consider removing metanode concepts.
- General cleanup/simplification.
- To be discussed at the retreat.
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)
Make sure JActiveModules uses NodeAttributes rather than the Expression Matrix data structure. UCSD
TreeView integration plugin Pasteur - Melissa
Module finding by experiment-specific scoring of groups of nodes within an underlying interaction network. Pasteur - Tero
2.4 Refactoring
- 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] complete
- 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. 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
Anchor(time_estimates) [:Cytoscape 2.4/2.4 Features Organized by Development Group:/2.4 Features Organized by Development Group]
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
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
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]
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)