Next release date: tba.

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  • JAMES II 0.9.7 BETA September 25, 2014

    Full (71 MB) | Binaries only (71 MB) | Javadocs

    maintenance, context concept, moved CA project to bitbucket

    Changes
    • Core: Added a context concept to the plugin system to be able to observe the plugin hierarchy
    • CA: Moved the CA project to bitbucket
    • Adaptive Simulator: Added dynamic state space representation algorithms
    • ML-Rules: Added a parameter to dynamically set the initial solution
    • ML-Rules: Fixed a bug in tau-leaping with the error approximation
  • JAMES II 0.9.6 BETA June 6, 2014

    Full (60.4 MB) | Binaries only (53 MB) | Javadocs

    maintenance, moved DEVS project to bitbucket

    Changes
    • DEVS: Moved DEVS to bitbucket
    • DEVS: Added simple examples (models) for basic DEVS
    • DEVS: Fixed some bugs in two basic DEVS simulators (flatsequential and abstractsequential)
    • CA: Fixed an NPE within the CA simulator
    • ML-Rules: Improved the parser to support negative attribute values
  • JAMES II 0.9.5 BETA March 7, 2014

    Full (60.4 MB) | Binaries only (53 MB) | Javadocs

    new component-based ML-Rules simulator, tau-leaping for ML-Rules, GUISE, Steady-State, SASF to public

    Major changes
    • ML-Rules: Added revised component-based version of the ML-Rules simulator
    • ML-Rules: Added a new simulator based on tau-leaping (see here)
    • GUISE: Added project for guiding simulation experiments
    • Steady-State: Added project containing steady state estimators
    • Simulation Algorithm Selection Framework (SASF): Has been moved to the public repository [JAMESII-415]
    Fixes
    • ML-DEVS: Fix for Thread-Leaking bug
  • JAMES II 0.9.4 BETA November 29, 2013

    Full (60.4 MB) | Binaries only (53 MB) | Javadocs

    Maintenance release, new ML-DEVS simulator.

    Major changes
    • ML-DEVS: added improved and enhanced version of the ML-DEVS simulator
    Minor changes
    • Core: improved interface for simulation start and end hooks [JAMESII-427]
    • Result reporting: moved module 'resultreporting' to public repository [JAMESII-400]
    Fixes
  • JAMES II 0.9.3 BETA September 20, 2013

    Full (62.1 MB) | Binaries only (54.5 MB) | Javadocs

    Adaptive generic simulator, SBML support for SR and ML-Rules, public repository.

    Major changes Fixes
    • ML-Rules: Parser should prevent same name for species and attribute binding [JAMESII-377]
    • Result Report Generation: fails with R 3.x [JAMESII-380]
    • System-dependent test for post-serialization behavior of SecureRandom [JAMESII-393]
    Improvements
  • JAMES II 0.9.2 BETA May 31, 2013

    Full (54.9 MB) | Binaries only (47.8 MB) | Javadocs

    Maintenance release, some minor fixes and enhancements for the core and ML-Rules.

    • Core: Handle package naming convention less restrictively [JAMESII-335]
    • ML-Rules: NPE when editing constants in editor (which breaks subsequent parsing) [JAMESII-342]
  • JAMES II 0.9.1 BETA February 28, 2013

    Full (46.5 MB) | Binaries only (39.3 MB) | Javadocs

    Plug-in declaration via annotations.

    Major changes
    • Plug-in declaration can now be done via annotations (see Cellular Automata simulators for usage, e.g. org.jamesii.simulator.carules.CADiscreteEventMultiAdaptProcessorFactory in sub-project ca)
    Minor changes Fixes
    • NullPointerException when stopping an experiment immediately after starting it
    • ExperimentVariables work properly even if modifier is set to null
    • Invalid parameterization of text-based species-reactions models (depending on context) [JAMESII-302]
    • GUI Buttons that won't work with the given plug-ins are now disabled
    • 'Automatic selection' of observer listeners in the GUI does only refer to the given experiment, not others
  • JAMES II 0.9.0 BETA November 29, 2012

    Full (46.0 MB) | Binaries only (38.9 MB) | Javadocs

    Java 7, instrumentation framework, streaming data management, workflow-based experiment execution.

    Major changes Minor changes
  • JAMES II 0.8.8 ALPHA September 20, 2012

    Full (42.5 MB) | Binaries only (35.6 MB) | Javadocs

    Support for ML-DEVS, new package structure.

    Major changes
    • Added ML-DEVS models and simulator
    • Moved package structure to org.jamesii (this is work in progress, eventually this will be the super package of all JAMES II sources)
    Minor changes
    • Many critical issues in the code base have been fixed/refactored
    • Static ParameterBlock utility methods have been moved to org.jamesii.core.parameters.ParameterBlocks
    • Experiment IDs are now available before experiment execution started
    • Extended logging of important data for reproducibility and debugging (RNG seeds etc.)
    • Replication criteria are now handled via Factory/ParameterBlock tuples, as all other parts of an experiment
    • Fixes in the parse tree
    • Various fixes in the user interface (particularly for Mac OS X)
    • Refactoring of algorithm selectors and performance predictors in SASF
  • JAMES II 0.8.7 ALPHA June 21, 2012

    Full (42.6 MB) | Binaries only (35.9 MB) | Javadocs

    Support for attributed Pi Calculus and ML-Rules.

    Major Changes Fixes
    • Reduce warnings form starting the james2-core.jar in the release (by avoiding plug-in conflicts) [JAMESII-96]
    • Racing condition on modifying the list of jobs [JAMESII-146]
    • ImplementedModelReader not working with inner classes [JAMESII-149]
    • Various minor improvements and fixes (many of those inspired by SonarQube).
  • JAMES II 0.8.6 ALPHA March 16, 2012

    Full (31.3 MB) | Binaries only (25.3 MB) | Javadocs

    Maintenance release.

    • Improved SonarQube rule compliance.
    • Various bug fixes.
  • JAMES II 0.8.5 ALPHA January 2, 2012

    Full (31.0 MB) | Binaries only (25.1 MB) | Javadocs

    Added SRS, SASF, simple experiment editor.

    • Added Species-Reactions simulation methods for discretized Space (SRS, see M. Jeschke, "Efficient non-spatial and spatial simulation of biochemical reaction networks," Ph.D. dissertation, University of Rostock, October 2010).
    • Added Simulation Algorithm Selection Framework (SASF, see R. Ewald "Automatic Algorithm Selection for Complex Simulation Problems," Ph.D. dissertation, University of Rostock, October 2010).
    • Prototypical 3D visualization for the simulation output (see Unger et al.: "VioNeS-visual support for the analysis of the next sub-volume method," IV 2009).
    • Added draft of a simple (graphical) experiment editor.
    • Extended support for experimental algorithmics and algorithm selection (e.g. algorithmic change evaluator (ACE)).
    • New stopping criterion (based on confidence).
    • Sample experiments.
    • GMP simulation algorithm.
    • Next Subvolume Method simulation algorithm.
    • Spatial Tau-Leaping simulation algorithm.
    • Added basic library to generate simulation result reports.
    • Refactored: updated project structures.
    • Refactored: improved run time performance of species reaction implementation.
    • Refactored: experimentation layer now mostly works on computation tasks (instead of simulation runs).
    • Refactored: improved parallelism on multi-core machines (experimentation layer).
    • Refactored: many updates and fixes in experimentation layer.
  • JAMES II 0.8.3 ALPHA November 25, 2009

    Full (6.8 MB)

    Support for classic DEVS, stochastic Pi Calculus, SpacePi; additional event queues.

    • Additional languages/formalisms: SpacePi, StoPi, DEVS, a simple agent testbed (model + simulator) for teaching purposes (WumpusWorld) a simple (CPU, arithmetics) benchmark.
    • Improved syntax editor support (problems, quick fixes).
    • Fixed remote observation (and optimization, validation using remote runs).
    • Bundled with a data sink.
    • Fixed deadlock bug in simulation runner classes.
    • Fixed problem in filtered tree model (search is now cancelled on next char input).
    • Added more unit tests.
    • Added several additional (simple) event queue implementations.
    • Refactored: event queue interface; basic interface now allows arbitrary comparable data types as "time" values.
    • Refactored: moved simulation run specific classes from subpackage simulation to simulationrun.
    • Refactored: moved ParameterBlock class (and package) as it is used throughout the software (does not depend on a "simulation").
  • JAMES II 0.8.2 ALPHA July 24, 2009

    Full (5.5 MB)

    Improved flexibility of simulation stopping, maintenance.

    • Several (bug-)fixes.
    • Fixed infinite loop on drag and drop of a window (2D Chart)
    • Simple legend added (2D Chart)
    • Fixed 'flickering problem' on some machines (2D Chart)
    • Started unification of factory interfaces (instance creating method should always have the same name - ease of use)
    • Started better handling of factories and their parameters in the GUI
    • Added special "random number generators" which "filter" random numbers from any RNG somehow
    • Added new plug-in type for model structure browsing
    • Added new GUI control for displaying hierarchical structures in a table, adapted log view
    • Improved simulation run creation / handling
    • Improved data storage interface
    • Modified model reading / writing and symbolic model interplay: more flexibility, ease of model conversion, better support of multiple concurrent views on models
    • Increased flexibility of "simulation run stop handling"
    • Refactored: model, model parameter, experiment, experiment suite reader / writer plug-in integration
  • JAMES II 0.8.1 ALPHA March 23, 2009

    Full (4.0 MB)

    Support for PDEVS and SR, new CA formalism.

    • New version of CA formalism, added new simulation algorithms.
    • Added SR formalism and simulation algorithms to this release.
    • Added PDEVS formalism and a simulation algorithm to this release.
    • Added Icon library to this release
    • Improved simulation control in the GUI
    • Several bug-fixes
  • JAMES II 0.8.0 ALPHA February 16, 2009

    Full (3.4 MB)

    First release (preview).

    This release contains: