Development news

  • December 2006
    • Beta 2 public release! CANCELED
  • November 2006
    • Beta 1 public release!
    • API has 500 classes, 188,000 lines of Java code, and 319,130 lines of API documentation.
    • API upgrades complete for the database layer, cross-platform features, and locale-specific features. GUI classes upgraded to the latest features. Supported added for time course experiments, data sets, series, and plots. Further updates to the 3D drawing for better performance, anti-aliased content, and dynamically placed arrow heads.
    • Pathway Editor substantially upgraded to support windows and visual elements made possible by upgrades to the API. New colors, icons, menus, and window layout. Multiple window support, plus cut, copy, paste, delete, undo, and redo.
  • October 2006
    • API database layer upgrades continue with additions for changes in the time course data schema. Cross-platform support continues development. Substantial rewrite begun to support locale-specific text labels and user preferences to control colors and icons.
    • Pathway Editor restructuring in progress to support multiple pathway windows, a splash window during application loads, and multiple threads for background loading.
  • September 2006
    • Substantial rewrite begun of the API database layer to provide better performance and better support for planned changes to the database schema. Substantial rewrite begun on cross-platform features for dynamically adjusted GUI look and feel to match that of the local platform.
  • August 2006
    • Upgrades to the API to support the latest JOGL distribution for 3D drawing. Updates to database support for the latest schema.
  • June-July 2006
    • Hiatus.
  • May 2006
    • Alpha 0.4 public release!
    • API has 417 classes, 130,299 lines of Java code, and 330,333 lines of API documentation.
  • April 2006
    • Upgrades to the API to support time course data, time course experiments, time course plotting, preloading, startup configuration, and vocabulary file import/export. Updates also include database code for pathways, compounds, time courses, and types. Revamp of the GUI to support property sidebars. New GUIs for database search and results display. See the updated API documentation.
    • Substantial updates to the Pathway Editor application to add the sidebar at the left, support cut/copy/paste of pathway components, show time course data, integrate property summaries, automatically assign compounds and time course data, etc.
  • March 2006
    • Consolidation in the API to make the listener and authority mechanisms more generic and extensible. Updates to the I/O classes to support database import/export, registration of GUI components, etc. Updates to property handling and the core data structures to support the database data model. See the updated API documentation.
    • Updates to the Pathway Editor application and API to support the above changes.
  • February 2006
    • Restructuring in progress as the database schema evolves.
  • January 2006
    • Changes and consolidation in the API to bring the data model in sync with the forthcoming database schema. See the updated API documentation.
    • Updates to the Pathway Editor application and API to support cut, copy, paste, delete, import, and export operations on lists of synonyms, references, authors, properties, etc. Updates to color schemes, dialog layouts, and menus to prepare for the forthcoming database connectivity.
  • December 2005
    • Additions and consolidation of the API to support more file formats, including KEGG's KGML pathway format and a tab-delimited time series format. Extensions to better support cross-platform user interfaces that match the native style, including adjustments to window and widget appearance, widget layout, menu structure, shortcut keys, and other GUI features that vary from Mac to Windows to Linux. Additions for display and animation of time series. See the updated API documentation.
    • Temporary disabling of plugins for Cytoscape's SIF file format, the Workbench's UNITS file format, and NCBI's taxonomy file format pending completion of restructuring of dynamic plugin support.
    • Updates to the Pathway Editor application to present multiple file format support, import time series, animate time series, adapt the GUI to the native platform's conventions, and present more features of the underlying data model. Icons and menus have been redesigned.
    • Updates to the Web site's Workbench Overview to reflect the current view of the data model, file formats, etc. See the updated Overview.
    November 2005
    • Extensive additions to the API to support faster and more flexible 3D drawing, 3D text, and anti-aliasing. Additions to support the attachment of arbitrary attributes to participants, interactions, and pathways. Dynamic loading of plugins for file format handling, attribute definitions, and customized user interfaces. Updates to the Workbench PATH format to support arbitrary attributes. See the updated API documentation.
    • Updates to the Pathway Editor application for smoother pathway display and editing and to use the new API features.
  • October 2005
    • Extensive additions to the API for 3D pathway layout, drawing, and interaction. Additions for GUI dialogs to view and edit data. Support for reading and writing a new Workbench PATH format using XML. See the updated API documentation.
    • Created the Pathway Editor application to load, view, and edit pathways
  • September 2005
    • Additions to the API for 3D drawing using the Java bindings for OpenGL. 3D is used to accelerate the drawing of future large pathways and to support future visualizations that plot data "upwards" out of the plane of the pathway, or that layer pathways atop each other for comparison. API additions also include new GUI classes to view and edit data. See the updated API documentation.
  • August 2005
    • Extensive additions to the API for pathways, interactions, participants, lists of vocabularies, the SIF file format, and particularly for GUI classes to view and edit all data types. See the updated API documentation.
  • July 2005
    • Restructuring of the API to sort classes into topical packages. Internationalization for all text, including error messages, button labels, and menu items. Update to all vocabulary and term classes to support "authority" and "listener" lists. Authority classes restrict changes (such as for closed vocabularies), while listeners monitor changes (such as to keep GUIs uptodate). Additional GUI classes to present terms and their derivatives. See the updated API documentation.
  • June 2005
    • Updates to the API to include the principal classes dealing with pathways, participants, interactions, and chemical species. See the updated API documentation.
    • Applets created to illustrate (and test) file format and data model support for the Workbench's UNITS file format, and NCBI's taxonomy file format. See the Applet documentation.
  • May 2005
  • April 2005
    • Extensive additions to the API to handle the definition of terms and flat or hierarchical vocabularies of those terms. These are the base classes for most named objects in the Workbench, including those planned for participants, interactions, pathways, chemical compounds, organisms, compartments, file format definitions, attribute definitions, and so on. API additions also support standard definitions for units of measure (eg. grams) and user-defined units of measure. See the updated API documentation.
  • March 2005
  • February 2005