Release notes - version 1.0 beta 2 - December 4, 2006

These release notes cover:

  • Biopathways Workbench toolkit, version 1.0 beta 2
  • Pathway Editor application, version 1.0 beta 2

This is an beta release. It includes most principal functionality that is supposed to work.

Overview

This release includes two components:

  • The Biopathways Workbench is a Java programming toolkit for managing pathway data.
    • The toolkit provides core classes for describing pathways, nodes, processes, compounds, and time course data sets.
    • Support classes describe database access, file formats, plugins, publications, author lists, change logs, vocabularies, ontologies, chemical formulas, organisms, cell compartments, and so on.
    • The toolkit also provides user interface components for presenting and editing this data.
    • Please see the API documentation for more details.

     

  • The Pathway Editor is a Java application built using the Biopathways Workbench.
    • It presents a pathway drawing area, menu bar, toolbar, and operations to open, edit, and save pathways, and search databases of pathways, compounds, and time course data.

Features

Key features in this release include:

  • Read pathways, compounds, and time course data sets from the LipidMAPS databases.
  • Read and write pathway files in KEGG's KGML format and the Workbench's PATH format.
  • Edit pathways in a drawing program style. Click-and-drag pathway components.
  • Edit node, process, and compound attributes.
  • Pan, zoom, and tilt the pathway.

Changes since the 0.4 alpha release

Key changes include:

  • Updated data model to support the latest database schema.
  • Updated PATH file format to support the latest database schema.
  • Splash window during startup and showing startup progress.
  • Streamlined startup.
  • Automatic database updates at startup.
  • Updated look and feel.
  • Multiple simultaneous document windows.
  • Updated information windows for all compound types, nodes, processes, and pathways.
  • New management windows for listing nodes and processes.
  • New plugin and file format windows for listing application features.
  • Updated database search windows.
  • Updated window icons, toolbar icons, and color schemes.
  • Updated 3D node and process icons and color schemes.
  • Updated 3D line drawing for cleaner edges.
  • Updated 3D labels for cleaner text.
  • Line arrows/bars based upon node role in a process and process type.
  • Line and icon colors based upon node and process types.
  • Line arrows slide along edges of nodes without jumping.
  • Line arrows are double-ended for reversible processes.
  • Better file format recognition for opening files.
  • Better tracking of changes and notification of need to save.
  • Printing.
  • Cut, copy, paste, delete, and undo.
  • Drag-and-drop between windows.
  • Better cross-platform support.
  • Uses latest Java OpenGL release.
  • Universal binary support for Intel Macs.
  • Application and window menus on MacOSX.
  • Better drawing performance.
  • Better database query performance.
  • Much lower CPU load.
  • Processes can be marked as reversible.
  • Node roles can be set (in the process information window).

Known bugs

Problems we know about:

  • User interface:
    • Can't undo delete of individual connections in a process.
    • "About Pathway Editor..." choice on MacOSX gets two windows, instead of one.
    • Search windows sometimes get hidden behind the pathway window, making it impossible to close them and continue use of the application.
  • Hasn't been tested on Linux yet.

Known missing features

Features intended, but not there yet:

  • User interface:
    • Preferences window for selecting colors.

Feature wish list

Possible features for the future:

  • Import/export:
    • Time course file import/export.
    • SBML file import/export.
    • BioPAX file import/export.
  • Drawing:
    • Snap to grid.
    • Align to grid.
    • Align nodes.
    • Unique icon shape for nucleic acid nodes.
  • User interface:
    • Animation panel to highlight experimental data values at selected and moving times.
    • Preferences to set up rules for coloring and icon choices.
    • Preferences for selecting fonts.
  • Data:
    • Organism, tissue, cell, and compartment identification.
    • Publications.
    • Author/history of pathway.
    • Pathway grouping (generic vs. specific organism pathways).
    • Sub-pathway support (e.g. KEGG maplink).
    • Compound groups (generic vs. specific compounds).