Versions

– July 30 2010 –

Version 0.403 files and source have been uploaded.  The Initializer now includesundo/redo history that can be controlled by CTRL-Z and CTRL-Y.  Minor fixes have been made to Cds and are listed in the revision history file.

– May 24 2010 –

Version 0.401 files and source have been uploaded.  Source files now include the Initializer and Visualizer.  A test suite of abstract simulationshave also been included which are used to test various features of the simulator.  These simulations will also give new users ideas on how to implement features.

– April 8 2010 –

Version 0.400 files and source have been uploaded.  The structure of the code has been altered to allow for multiple algorithms to be added.  Minor changes have been made to the input file which makes it incompatible with previous versions (mainly just the world names).  CdsInit has been modified accordingly.

– March 5 2010 –

Version 0.343 and source has been uploaded.  Modified SingleTracking to work better with interval tracking.  Updated Reaction Output to handle association reactions when the reactant is absorbed.

– October 6 2009 –

Bug Fix: CdsInit now looks for the appropriate script when running in Linux and OS X. The convention for Windows is to lookup the “Cds.bat” script and for all Linux based systems “Cds”.  UserGuide has been updated.  Hotkeys added to CdsInit. Menus have issues when using Cygwin’s X-Windows emulator to remotely use CdsInit on a Linux box, so hotkeys are added to supplement menu commands.

– September 14 2009 –

Version 0.342 has been uploaded.  Updated some additional support to TraceOutput.  Added the ability for actions added to reactions to contain wildcards. So if there is a group reaction, the arguments on the group will be passed to the actions.  Element/Compartment and Element/MovingCompartment reactions are now calculated during collision detection in the same manner as Element/Element collisions.  Modules added with an active/inactive switch that can be triggered by actions. All modules have been modified to check this flag when retrieving information.

– July 27 2009 –

Version 0.341 has been uploaded.  Fixed a bug where actions weren’t being applied to the parent in an unbinding event.  Fixed bug where counters cycling through faces on element on element collision detection weren’t thread safe. The counter used was an element’s implicit counter rather than an external counter reference which is thread safe.  Added ability to have wildcards in the actions of group reactions. Where the group reaction is copied with the wildcard GRP.  Added a separate lateralDiffusionCE and lateralStepFunction that automatically becomes effective when a molecule becomes surface bound.

– June 24 2009 –

The CDS website is now up.  Several example simulation files used in our first manuscript (in preparation) are available for download as well as the simulator package.  More simulations from publications in preparation will soon be included as well as the source code for CDS.