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:
- quickfind (Ethan) ETA: Nov 17
- TODO: search on edge attributes, performance profiling of range finder, tweak node selection event handling
- context sensitive menus for edges - ETA: ?
- (coding in progress, waiting for use-cases)
- Need update from Doron - Gary will email to find ETA, let him know about conference
hyperedge plugin (& editor support) - ETA: mid-November release (Aditya, Mike C, Allan (testing))
- importing framework - ETA:
- File export: Finish export to PSI-MI (Ethan, DONE)
- Importing a network via URL - (Peng ETA: Nov.7)
- cPath plugin update - move menu into the file menu (from plugins) (Mike S)
- biodata server/network and attribute import (Kei)
- Beta version checked in (Ontology core classes, Network/Attribute/Ontology import).
- Excel reader for attribute table and ontology import - first version checkedin
- Excel reader for network import - first version checkedin
- Need to fix some minor GUI issue.
- tutorials
- TODO: Writing Cytoscape tutorial paper first
- quickfind (Ethan) ETA: Nov 17
- We are at feature freeze (no code added that is unrelated to TODO list)
- Tentative code freeze on November 17 (code is branched, no new code, just bug fixes)
- Tentative release on December 15 (may slip to early 2007 depending on holiday schedules)
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 - complete.
[:VisualLegendGenerator:Automatic Visual Legend generator] (code and GUI now available). UCSD - complete
Use Arrow keys to move nodes. UCSD - complete
Layout algorithm that reflects classes (GO, others implied by selectable attributes). Pasteur - Tero - 2.4 not dependent on this (it is a plugin)
Organization/Retrieval/Search - MSKCC/Agilent
[:QuickFindRFC:Quick Find]. MSKCC - Ethan (Need to add support for edge attributes, optimize range selector, and tweak node selectio events, ETA: November 17)
[:CytoscapeIcons:New Cytoscape icon set]. MSKCC - Ethan (DONE)
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.
Expressiveness and enrichment of the network model - UCSF/Agilent
Editor support for hyperedges Agilent - Allan/Aditya (will only be hyperedges, not metanodes, because group/metanode API is not yet ready)
Design of GenMAPP annotations. UCSF - Alex - on track as of Oct.13
Clarification of directed edges in GINY and use throughout Cytoscape complete - all edges are directed
Design of attribute based layout. Agilent/MSKCC/UCSF - Alex - on track as of Oct.13
Data Integration and Handling - UCSD
Consolidated network import capabilities (i.e. gather all import plugins into one place). UCSD
[: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 (10/26 Status: Backend is done. Needd to integrate GUI to the [:TextFileImport:text/Excel table import framework])
General attribute/network text table reader and GUI. See [:TextFileImport:text table import framework RFC.]Kei (10/26/2006 Status: GUI is done. Remaining work is Excel import backend and Network table import.)
Direct support for Excel (.xsl) files using [http://jakarta.apache.org/poi/ POI] Kei (Status 10/26/06: Currently working on the new reader for ExcelAttributeTableReader and ExcelNetworkTableReader)
BioGRID import. UCSD - complete
Immutable/Invisible CyAttributes (mainly for Metanode, Quick Find use cases). MSKCC/UCSD - complete.)
General Refactoring/Other - UCSD
Fix resize VizMapper windows. UCSD - 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 - yes, will be done later, during GINY refactoring
- Add support for label placement "complete"
- General cleanup/simplification now planned (retreat).
VizMapper design document. Allan/Melissa/Everyone
Designed at retreat.
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 - complete
TreeView integration plugin Pasteur - Melissa - 2.4 not dependent on this
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
- Migration to Java Version 5 - complete
- 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 - 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.
- 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
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)