JAMES II 0.9.7 BETA September 25, 2014
maintenance, context concept, moved CA project to bitbucket
- 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
maintenance, moved DEVS project to bitbucket
- 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
new component-based ML-Rules simulator, tau-leaping for ML-Rules, GUISE, Steady-State, SASF to public
- 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]
- ML-DEVS: Fix for Thread-Leaking bug
JAMES II 0.9.4 BETA November 29, 2013
Maintenance release, new ML-DEVS simulator.
- ML-DEVS: added improved and enhanced version of the ML-DEVS simulator
- Core: improved interface for simulation start and end hooks [JAMESII-427]
- Result reporting: moved module 'resultreporting' to public
JAMES II 0.9.3 BETA September 20, 2013
Adaptive generic simulator, SBML support for SR and ML-Rules, public repository.
- 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]
JAMES II 0.9.2 BETA May 31, 2013
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
Plug-in declaration via annotations.
- 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
- NullPointerException when stopping an experiment immediately after starting it
- ExperimentVariables work properly even if modifier is set to
- 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
Java 7, instrumentation framework, streaming data management, workflow-based experiment execution.
JAMES II 0.8.8 ALPHA September 20, 2012
Support for ML-DEVS, new package structure.
- 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)
- Many critical issues in the code base have been fixed/refactored
ParameterBlock utility methods have been moved to
- 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
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
Support for attributed Pi Calculus and ML-Rules.
- Support for Attributed Pi Calculus (see M. John, "Reaction Constraints for the Pi-Calculus - A Language for the Stochastic and Spatial Modeling of Cell-Biological Processes," Ph.D. dissertation, University of Rostock, August 2010).
- Support for ML-Rules (see
C. Maus, S. Rybacki, and A. Uhrmacher, "Rule-based multi-level modeling of cell biological systems," BMC Systems Biology, vol. 5, no. 1, pp. 166+, 2011).
- Reduce warnings form starting the
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
- Improved SonarQube rule compliance.
- Various bug fixes.
JAMES II 0.8.5 ALPHA January 2, 2012
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
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
- 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
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
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
First release (preview).