Cytoscape_2.3

Use cases addressed:

• First steps towards drawing pathways / metabolic networks.
• Support for large networks
• Key Usability Issues
  • Save State, Undo
  • Viz Mapper / Filters Specific Issues

Overall timeline

• Phase I feature freeze: Mid-April 2006
  • This includes everything but the editor
  • Testing and bug fixing begins
• Phase II feature freeze: End of April 2006 (includes the editor)
  • Comprehensive application testing and bug fixing begins
• Projected 2.3 release date: End of May 2006

Release plan

• Cytoscape is currently under internal testing (testing by Cytoscape developers). Please report bugs in the bug tracker. Public testing will begin April 25th, coinciding with the Cytoscape user group meeting in Seattle.
• Roles:
  • Bug Master: Mike Smoot
• Documentation:

  • Cytoscape 2.3 User Manual

  • Assignments:
• Cytoscape 2.3 User Manual
• Introduction
• Launching Cytoscape
• Quick Tour of Cytoscape
• Command Line Arguments and Properties
• Building and Storing Interaction Networks
• Loading Gene Expression Data
• Node and Edge Attributes
• Navigation and Layout
• Visual Styles
• Editing Networks

• CytoPanels

• Annotation
• Filters
• Acknowledgements
• Appendix A: Old Annotation Server Format
• Appendix B: GNU Lesser General Public License

New Features:

• New rendering engine; lots of plugin dependencies
  • (Nerius, Allan as consultant) A new rendering engine is being written that does not depend on external code; the engine uses Java2D directly. The motivation for the new rendering engine is to gain tremendous performance improvements and to clean up a massive load of bugs that have proven near impossible to fix. The new rendering engine is capable of smoothly displaying user-interactable networks 1000 times larger than what Cytoscape is currently capable of. We hope to also implement layout algorithms for large networks; without such algorithms viewing large networks is near pointless.

  • TIMELINE merged with the core: 3/23/06, code freeze 4/1/06

  • see RFC_TooltipsAndContextMenusForRender for a discussion of approaches for adding tooltips and context menu functionality to the renderer.

• Meta-Nodes; Phase I (Iliana, Allan, Melissa, Aditya, Alex Pico, Scooter) See MetaNodes_RFC and for the latest see: API/NewApiApproachForMetaNodes

  • TIMELINE ready for review: 4/6/06 look here for a web-start and final JavaDoc: http://db.systemsbiology.net/cytoscape/metanodes/

• Saving Project State (Save_current_session_as_XML_file) (Kei, Iliana); Depends on Meta-Nodes

  • TIMELINE Added URL support on 4/4/2006. Please read Save_current_session_as_XML_file for more detail. CVS version has no support for Metanode.

• Undo Manager (Allan w/ help from friends)

  • Define and build an undo manager that handles both "global" edits and edits that are "local" to a specific network. Maintain one edit stack per network. Distribute "global" edits to all network stacks. See UndoManager_RFC

  • TIMELINE ready for testing: 4/13/06

• Attribute browser
  • link attribute browser to network view (Kei) *Complete. Ready for testing
  • Improved support for List and Map objects (Kei)
  • Network Attribute Editor (Edit network meta info from GUI) *Complete. Ready for testing

  • TIMELINE ready for testing: 4/6/06

• New, improved Cytoscape Tutorials (Melissa)

  • There will be eight new tutorials: 1. Getting started, 2. Filters & editor, 3. Fetching external data, 4. Expression analysis, 5. Literature searching, 6. GO analysis, 7. Modules and complexes, 8. Domain networks and other topology topics. Other topics may be added if the demand is sufficient.

  • TIMELINE complete: 4/6/06

• Graph Merge, moved to core (already a plugin) (Ryan, UCSD)

  • TIMELINE complete.

  • The class GraphSetUtils was added to the Cytoscape core (src/cytoscape/util). This class provides methods for basic set operations.

  • The GraphMerge dialog has been added to pre-coreplugins as a core plugin. GraphMerge.jar has been added to the cytoscape CVS project.

• [6. Clean-up Viz Mapper and Filter UIs (VizMapUI); make friendlier; move to cytopanels] [Mike S, Allan, (possibly Alex?)]

  • TIMELINE on hold until Mike has more time. At this point this won't be included in 2.3.

• 7. ID Mapping Services, Phase I (Gary)
  • To integrate e.g. gene/protein networks, we need to create a Cytoscape API to handle database identifier (ID) mapping. For example, if a gene network is defined by Affymetrix identifiers and a loaded PSI-MI file is defined by Entrez Gene identifiers, Cytoscape must be able to map Affymetrix IDs to Entrez Gene IDs. Note: cPath already maintains identifier mapping information and sends this information to Cytoscape in BioPAX or PSI-MI, however Cytoscape does not have an ability to automatically link the identifiers and currently represents the differently identified genes as two different nodes. A simple Cytoscape identifier mapping API that could handle linking these genes would solve this problem. This work will not create an extensive collection of identifier mappings because this task is difficult, outside of project scope and is being worked on by multiple different bioinformatics groups. Instead, this API will simply resolve identical biological objects using whatever existing mapping information is given to it. The API will support four use cases: 1. unification of network nodes, such as proteins, during dataset merging, 2. link out to related information, such as protein function annotation, 3. identifier translation from one type of identifier to another and 4. searching a network using a preferred gene name or alias.

  • TIMELINE Currently this task is on hold. The MSKCC group has a design and can create an RFC, but are not yet sure if they can prioritize implementation by 2.3 release.

• 8. Greater flexibility in expression data loading (Melissa)
  • This provides a short-term solution to part of the ID mapping problem of #7, above. Specifically, this gives the user the ability to load expression data according to some node attribute instead of the node ID. This supports the use case that the user has a large expression dataset labeled by a commercial probe set ID. If the user first specifies the probe set ID as a node attribute, the expression data can then be mapped to nodes according to this attribute.

  • TIMELINE Finished.

Refactoring / Design Issues:

• (CyNode_Identification) – creation of a default “label” CyAttribute (Ben)

  • TIMELINE awaiting MSKCC

  • Canonical/Common/Aliases are removed from core. Now the idea is local to GO Server.

• New documentation options; docbook, wiki, etc. (Gary, Mike, Allan) - See RFC_3

  • TIMELINE some sort of prototype: 4/6/06

• Take care of delete/hide/remove situation (Allan, in conjunction with Cytoscape Editor)
  • Clarify the difference between removing a node/edge from a particular network and removing it globally from Cytoscape. Clarify which attributes should be deleted when a node/edge is removed from a network or globally from Cytoscape. (Status: Allan will write an RFC)

  • TIMELINE ready for testing: 4/20/06

• Flagging/selection of nodes/edges (Iliana)

  • TIMELINE COMPLETE

Misc. Small Items

• Ability to rename networks (Brad K at UCSD - complete)
  • Brad is adding code to allow networks to be renamed. They are currently named based on the input file. This change will change that name throughout the system.

  • TIMELINE Complete and checked in. Right click on the the network name in the network panel to try it out.

• Script to update source license
  • Some of the Cytoscape source is missing copyright and license information. This needs to be fixed.

  • TIMELINE Complete and checked in. See License_clean-up_RFC for details.

• Generic_Linkout Pop-up Menu (Doron B, MSKCC)

  • This is a plugin that will read URL patterns from a user-defined configuration file to populate the links in the context menu activated by right clicking on a node or edge. Configuration files for popular sites will be provided e.g. a yeast URL config file.

  • TIMELINE Complete and checked in.

• Re-organize save/load/import/export menu items (New_File_Menu) (Kei: Finished, although I need to do some minor modification. Now everything under actions package related to save/load is called import/export.)

  • TIMELINE: Complete.

• Refactor entire menu items - this includes rename/delete menu items and make them more intuitive. (Refactored_Menu)

  • TIMELINE: Complete. Need to fix minor problems caused by some plugins.

User Feedback

See information on UserInterviews page.