Changes in version 2.3.1 (since 2.3):

This version changes the behaviour of perturbations.
In version 2.3 perturbations prevented a component from leaving the specified range,
they are now more strict and pushes them within this range unconditionnaly.
This behaviour is consistent with that of version 2.4.

-------------------------------------------------------------------------

Changes in version 2.3 (since 2.3 beta):

New Feature:
* cytoscape export

Bug fixes:
* breadth first simulation
* "merge graph" and "save subgraph" actions

Improvements:
* SCC search is now faster
* update of jgraph removes some useless redraws
* many parts of the GUI have been refined
* the documentation (tutorial and manual) has been updated


Changes in version 2.3-beta1 (since 2.2):

Analysis of the regulatory graph:
* compute the functionnality context of feedback circuits 
* find all stable states without simulation 
* export the regulatory graph to petri net (INA, PNML and APNN)
   using the tree representation of logical parameters
   each node will be represented by two places

Simulation module:
* the interface to set simulation parameters has been completely redone
* mutants are now separate objects
* mutants and simulation parameters are now saved with the graph (in extended mode)

General
* add "extended" save: save into a ZIP file, allows to save additional files along with the graph
* error and info messages have been added (within a bar, on the bottom of the graph)

-------------------------------------------------------------------------

Changes in version 2.2-rc (since beta3):

* New documentation
* Updated text in the GUI

-------------------------------------------------------------------------

Changes in version 2.2-beta3 (since beta2):

Simulation module:
* fix a problem where changes to transition blocking where not used during the simulation.

Definition of the regulatory graph:
* do not allow to set a value for the last logical parameter, please use the "basal value"

-------------------------------------------------------------------------

Changes in version 2.2-beta2 (since first beta):

Interface:
* Console messages have been removed.
* Some error dialogs have been added (for uncommon errors).
* The interface for building priority classes has been improved (phrasing and layout).

-------------------------------------------------------------------------

Changes in version 2.2-beta1 (since version 2.0):

General interface options:
* The interface has been polished and should be easier to use;
* Saving/restoring options are now stored in a file and then restored
when opening GINsim (in {HOME}/.ginsimrc). These options are:
  - visual settings;
  - grid status;
  - recent files (in the File menu).


Definition of the regulatory graph:
* New warning signalling wrong logical parameters: if an invalid
logical parameter is created, it is marked  in red (e.g. a parameter
referring to two mutually-exclusive interactions);
* Possibility of a reordering of the logical parameters.


Simulation module:
* New simulation mode using priority classes:
  - genes are grouped into priority classes;
  - each priority class has a rank (defined automatically by its
position within the classes); at each state, only transitions on
genes of the class  with the highest rank are triggered;
  - concurrent transitions inside each class are triggered either
synchronously or asynchronously (attribute of the class);
  - transitions on a gene  can be distinguished upon their signs
(increase or decrease of the level);
  - several classes can be grouped and then have the same rank:
concurrent transitions on genes of two different classes of the same
group are triggered asynchronously (note that grouping classes that
are already part of groups leads to a merging of these groups);
* Logical parameters are now represented as Decision Diagrams during
the simulation to improve performances;

Working on state transition graphs:
* On the secondary window, the "Selection attribute" tab  now allows
the selection of a next state (when a state or an arc is selected);
* On the secondary window, the "Graph attributes" tab now show the
choices made for the simulation (initial state(s), priorities, ...);
* The search for a path (menu Action) now proposes a first state to
start (it is by default the first  initial state specified for the
simulation, or the zero state if no initial state has been specified).


Other implementation improvements:
* Implementation of a custom jgrapht model to improve memory usage and
thus build larger state transtion graphs;
* Use of the newer jgraph version (5.7.4.7) which should fix some bugs
and slowdown of the graph visualisation;
* Updating of the default DTD address to the new website address
(gin.univ-mrs.fr/GINsim/GINML_2_1.dtd);
* Additionnal new distribution format in a single .jar which is
lighter, is one-click-to-run but do not allow the addition of new
plugins and comes without documentation.