Version 2.9.4. Changes since version 2.9.3: Analysis of the regulatory graph: * Model Booleanizer * Model reverter Exports: * NuSMV format detects stable states through the Var_std condition instead of explicitly computing all stable states * Added a SAT export that writes a CNF file of the model: stability conditions or stable states Other: * small bug fixes --------------------------------------------------------------------------------------------------------------------- Version 2.9.3. Changes since version 2.9.2: Other: * small bug fixes * added GPL v3 license file --------------------------------------------------------------------------------------------------------------------- Version 2.9.2. Changes since version 2.4: General Changes: * large refactoring, now require java6 * due to size of external libs: versions with/without libraries included * styles for graphical settings * some features were moved to the LogicalModel lib * semi-official script-mode (using jython) * Welcome screen * Local Graph * PNG export resolution is now proportional to Zoom Definition of the regulatory graph: * new (simpler) definition of perturbations Simulation module: * strip outputs option Exports: * SBML qual (using LogicalModel) * Truth Table (using LogicalModel) * New NuSMV format using a single module, with support for: . Updating modes: Sync, async, priorities . Output nodes reduced as macros . Input nodes can be: projected on the transitions, be fixed or be varying. * Avatar/Firefront for stochastic quantification of attractors * PRISM model checker * MaBoSS Imports: * SBML qual * Truth table (using LogicalModel) --------------------------------------------------------------------------------------------------------------------- Version 2.4. Changes since version 2.3: Definition of the regulatory graph: * logical functions * change in the definition of interactions: now it uses only one threshold (instead of a range with min and max). * removal of the "basal value": it is now a regular logical parameter * Model "Simplification" Select a set of nodes for removal, a new model will be created with the remaining nodes * Improve model documentation: links can now be opened and shortcuts have been introduced: pubmed, hugo, ref (relying on a bibtex file, allows to open pdf/doi of refs within GINsim) Simulation module: * remove radio buttons for (a)synchronous/priorities: (a)synchronous and priority definitions are all available in a single combo-box * refactor the simulation module to share more code As a result of these two changes, breadth first is now available for simulations by priority. Exports: * GNA export * Cytoscape export * Documentation export: build a document with the description of the model and stable states for every mutants. Two backends are available: "xhtml" and "open document" --------------------------------------------------------------------------------------------------------------------- Version 2.3. Changes since version 2.2: Analysis of the regulatory graph: * functionnality of circuits * export the regulatory graph to petri net (INA, PNML and APNN)! using the tree representation of logical parameters each node is represented by two places * export in smv format, for model-checking by NuSMV * a "model checker" plugin has been started, to run several NuSMV tests automatically 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 * the XML save has been cleaned up, more code is now reused and the encoding is well set * error and info messages have been added (within a bar, on the bottom of the graph, allowing to run action when appropriate) --------------------------------------------------------------------------------------------------------------------- Version 2.2. Changes since version 2.0: Definition of the regulatory graph: * warn about wrong logical parameters: if an invalid logical parameter is created (for exemple one using two mutually-exclusive interactions), it will be marked in red * allow reordering of logical parameters Simulation module: * faster simulation, using a tree representation of logical parameters * new simulation mode using priority classes: - Genes are grouped into priority classes - Each priority class has a rank (defined automatically as they are reordered): only transitions belonging to the highest ranked priority class will be triggered - Concurrent transitions inside each class can happen either synchronously or asynchronously - Transitions corresponding to increases and decreases can be separated - Several classes can be grouped to have the same ranking grouping classes that are already part of groups leads to merging these groups concurrent transitions between classes of the same group happen asynchronously Working on state transition graphs: * The property-panel of edge and vertices of the state transition-graphs now allows to select the next state. Other: * use latest jgraph version, should fix some graph visualization bugs and slowdown * path-search starts with an existing state: one of the initial states of the simulation * updated default DTD to the new website address * additionnal new distribution format in a single .jar: + lighter, one-click-to-run - can't add additional plugin - without documentation * put the local DTD inside the jar file, some code changes to deal with this, jar dist also have a fallback DTD now * add saving/restoring of "options" (in {HOME}/.ginsimrc) - visual settings - grid status - recent files * new version of the documentation (in progress) --------------------------------------------------------------------------------------------------------------------- Version 2.0. Changes (bug fixes only) since version 2-beta: In the simulation module: * the transition blocking was too strict (restricted to the blocking of a single value in the specified range). * initial states: * when using ranges of values for initial states, some states were not created and some were created twice. * when building a "full" state transition graph, one state was not created. --------------------------------------------------------------------------------------------------------------------- Version 2.0 beta. Changes since the primary version v1.0: Definition of the regulatory graph: * the user interface has been redesigned and simplified mainly for the definition of the parameters * it is now possible to add some graph level annotations (the GINML DTD has been changed to take into account the new element "annotation") * a new copy/paste implementation (still only internal to GINsim) only available for regulatory graphs available between different GINsim windows with a cleaner implementation graphical attributes are also restored, and pasted items are automatically selected Simulation module: * after a simulation has been launched, a more detailed "what to do" window allows to choose an action to be performed on the state transition graph * new options have been added in the specification of the options for the simulation, transition blockings are now possible (facilitating the simulation of mutants) simple priority mode defining a strict priority order between the nodes of the regulatory graph Working on state transition graphs: * graph of the Strongly Connected Components (SCCs) of a state transition graph its calculation can now be stopped (may take a while) new support for the extraction of the subgraph of the state transition graph corresponding to a set of nodes of the SCC graph * paths determination/discovery in a state transition graph interactive construction, the regulatory graph is colored to match the selected state interactive shortest path search (going through a set of states), for this option, there is no need to display the state transtion graph a path can be exported to a gnuplot script Management of regulatory graphs and state transition graphs: * graphviz and biolayout export * graphical attributes now support line width and can apply to all elements or to the selected elements * graph association performed automatically when possible: association between a regulatory graph and a state transition graph (used for animation) association between a state transition graph and the graph of its stronlgy connected components (SCCs) (used to extract a subgraph of the state transition graph corresponding to selected SCCs) * new SVG export using markers and bezier tools from jgraph * automatic fallback to local DTD when the specified one is not available * improvement of the default options when saving a graph (deduced from the previously saved data) * new option to put all vertices foreground or background in such a way that selection is easier in large graphs New runtime options: --lang [C/FR] to set the language (C for english, FR for french) [file] to open the specified file