Version 0.9.9 (Released Feb. 22, 2010)

New features

  • Parallel paths between objects (e.g. a gap junction and a synapse between the same pair of neurons) are now visibly separated.
  • A pre-routed version of the Van Essen diagram was added to the sample scripts.
  • Scripts that were saved as "display only" can now be run on networks that are missing some of the original objects. The "orphaned" objects are then permanently highlighted in red.
  • Added a dialog box to the "Adjacency Matrix" script that allows the user to indicate whether the connections are pathways, chemical synapses or gap junctions.
  • Added a bug reporter/feature requester that submits issues to the new bug tracking system at <>.

Resolved issues

  • The glow effect used to show selected and "orphaned" objects now handles varying sizes better.
  • Fixed a bug that caused the 2D display to be blank in some situations.
  • Fixed a bug where some progress messages were not shown.
  • Fixed a regression saving "dummy" neurites (used to support simple connections) to scripts.
  • Fixed a bug in "Add Arrowheads" script that caused arrowheads to be created that pointed to invisible (transparent) objects.

Version 0.9.8 (Released Jan. 7, 2010)


  • The progress of long running tasks (scripts, layouts, etc.) is now displayed and allows canceling in some cases.
  • Navigation:
    • Added new zooming options to the view menu, toolbar and scripting interface.
    • The display automatically re-centers when zooming out so that the network is not left partially off-screen.
    • You can now click and drag to scroll the display, à la Google maps. (In 3D you can choose between scrolling and rotating.)
  • There is a new option to control highlighting of connected objects when multiple objects are selected. Either all connected objects can be selected (the default) or only those that connect objects within the selection.
  • Pathways now have an activation attribute (excitatory, inhibitory or unknown) for each terminus.
  • Networks can now specify a custom weighting function that is used when calculating shortest paths, centrality, etc.
  • New sample script for creating a region-level network from an adjacency matrix.
  • New sample script for detecting network communities.
  • The C. elegans network is now also being loaded from adjacency matrices rather than using generated code.
  • Console:
    • The history of commands is now saved with each network.
    • Cutting, copying, pasting, undoing and redoing now work.
  • The spectral layout now auto-scales to a unit-cube by default.
  • Packaging
    • Updated to the latest version of NetworkX.
    • Graphviz has been removed from the package due to licensing restrictions and must now be installed separately if desired.
    • The installer now creates a shortcut to the sample scripts on the Windows desktop.
  • Lots of modest performance improvements.
  • Fixed a bug that caused the help window not to appear in some cases.