Changes in version 2.4 alpha (since 2.3): This preview release includes features used in our most recent (or submitted) publications New Features: * logical functions: logical parameters can now be generated by writing logical functions. These functions support parenthesis and logical operators ("!", "&" and "|" as "NOT", "AND" and "OR", respectvely). These logical functions automatically generate the corresponding parameters, which are then listed (and grayed out as they cannot be edited) in the "parameter" panel. The interface for function definition is still expected to change. * input nodes: the values of these components are determined by their initial values (implicit self-regulation). Any defined parameters will be ignored. * the basal value is now defined as a regular logical parameter (deselecting all incoming interactions). * model reduction: this new feature enables the definition of a "reduced" version of a model by "hidding" a user-selected list of components. See http://gin.univ-mrs.fr/GINsim/publications/naldi2009.html * documentation export: export the list of components along with their annotation and logical parameters, into a documentation file (HTML or OpenDocument format). * GINsim can now be used in script mode, using Jython. This experimental feature relies on the internal structure of GINsim, which is subject to change. Contact us for example scripts and instructions. Improvements: * "open and launch" option to launch any action on a saved file without displaying it first. * better annotation links supporting common databases (pubmed, HUGO) and references (using a BibTeX file) * the SVG export matches more closely the layout Update: * fix a course condition at startup randomly blocking the graphical interface ------------------------------------------------------------------------- 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.