Version 2.1

New Features

• SBSCL is now available from Maven Central!
• Consequently, the README file was improved to cover these new developments and the new preprint on SBSCL.
• Several efficiency improvements to the numerical solvers (the AbstractDESSolver and the Rosenbrock solver), e.g., avoiding unnecessary conversion of double values to BigDecimal objects and by reducing some nested loops in the Rosenbrock solver: Thanks to Leonhard Markert.
• Testing against constraint-based models from the BiGG Models Database has been improved. The new functionality enables saving simulation results in a CSV file. For testing purposes, simulation results were generated with COBRApy to benchmark SBSCL. These automated tests were incorporated into the continuous integration.
• Improvements to the Java™ documentation by using correct reaction arrows and italicizing variable names, improvement of source-code expressions, where needed.

Bug Fixes

• Bump dependencies on third-party software:
  • JUnit from version 4.11 to 4.13.1
  • JavaDoc from version 2.10.2 to 3.2.0
• Fix of several error-prone issues and minor source-code improvements, exploiting more recent Java™ language features (such as using the diamond operator or no longer needed conversions of basic data types to their corresponding objects): Thanks to Leonhard Markert.
• Fix of the SBML test suite download script (detected a wrong directory path and made the Bash less strict to improve the efficiency of automated testing): Thanks to Leonhard Markert.
• Code cleaning (e.g., removing unnecessary public declarations from interface methods): Thanks to Leonhard Markert.
• Cleaning up remainders of earlier libSBML dependency within the fern package, such as removing unnecessary casts to int, long, or SBML data types within iteration: Thanks to Leonhard Markert.
• Minor improvement to the output while testing (proper display of directory structures).
• Additions to the .gitignore file.
• Additions of missing @Override tags and removal of unnecessary import statements within the fern package

Version 2.0

New features

• Support for SBML Level 3 Version 2 is added in SBSCL
• Updated project to JSBML 1.5
• Support for stochastic simulation added (using FERN)
• Support for running results in SBML Test Runner using a wrapper
• Feature of getting simulation results at every update instead of waiting for the simulation to complete.
• New user guidelines and developer guides added
• Full support of SBML Test Suite v3.3.0
• Full support of Stochastic Test Suite
• Full support of BiGG models database
• Tests for all the features supported

Adaptation

• SBMLinterpreter breaked into two classes EquationSystem for initialization and SBMLinterpreter for processing
• Readme and project website updated
• Complete documentation updated
• Formats the library as per Google Style Guides
• Library structure updated
• CobraSolver is refactored and updated to FluxBalanceAnalysis
• Travis CI build fixed
• Several bug fixes, minor changes, and code improvements were performed

Version 1.5

New features

• A new configuration file MyLog4j.properties now defines how messages should be logged.
• The new class COBRAsolver has been created for performing flux balance analysis based on the FBA algorithm in COBRApy and comes with an example use case COBRAsolverExample. At the moment, these use CPLEX as a solver backend. This might change in the future.

Adaptation

• The project has been migrated from SVN (subversion) to Git, causing several subsequent changes and alterations.
• Several third-party libraries were updated and subsequent adjustments needed to be performed to deal with changes in their API.
• Minor changes and code improvements were performed.
• A new Markdown-based README.md file was created for the project.

Version 1.4

New features:

• The processing of rules has been improved in order to avoid too many re-computations.
• The new version of JSBML 1.0 has been incorporated and changes have been made accordingly.
• Updated project to Java 1.6.

Bug fixes:

• An error in the computation of amounts/concentrations of a species has been corrected.
• A potential source for IndexOutOfBoundsExceptions in MultiTable has been corrected.
• In some situations, the CVS file reader did not close the files.

Version 1.3

New features:

• The violation of SBML constraints can now be treated using specialized listeners. In this way it has become much easier to customize what should happen in case of unsatisfied constraints during the simulation.
• The csymbol delay can now be interpreted with arbitrary expressions.

Bug fixes:

• Models with fast reactions are now simulated more precisely.
• Some inefficiencies in the simulation routine have been removed.

Version 1.2

New features:

• A new pom.xml file has been added to the project in order to support Maven for this library.
• The new interface ParameterizedDESystem has been implemented in order to facilitate the change of values for some elements of a differential equation system.
• The user can now decide whether to determine the amount or the concentration of a species.
• A wrapper class for the SBML Test Suite has been added.
• Simulation Core Library now supports all models of the SBML test suite (release 23).
• Import of CSV files is now possible.
• Distance functions for comparison with experimental data are included in the library.
• KiSAO terms of integration routines are included.

Changes in this version:

• Renamed getNumAdditionalValues() in RichDESystem to getAdditionalValueCount() in order to be compliant with many other Java classes.
• The processing of the ASTNodes has been improved.
• The API documentation has been improved.

Bug fixes:

• There was an error in the calculation of the concentration of some species: Sometimes the amount was not divided by the associated compartment's size.

Version 1.1

New features:

• Support for SED-ML (Simulation Experiment Description Markup Language, Waltemath et al., 2011) to facilitate the re-use and reproduction of simulation experiments by reading and executing SED-ML files. See the new package org.simulator.sedml and the new test cases in the test folder.
• There is now a convenient ant file build.xml that provides several options, such as inclusion of SED-ML support or the automatic creation of UML graphs.
• The documentation in JavaDoc has been extensively improved.

Changes in this version:

• Renamed org.simulator.math.odes.EventInProcess to org.simulator.math.odes.EventInProgress
• Renamed org.simulator.sbml.SBMLEventInProcessWithDelay to org.simulator.sbml.SBMLEventInProgressWithDelay
• The separation between the interfaces for arbitrary differential equation systems and SBML-specific implementation has become very strict. The previous release contained some dependency in the event handling to SBML. This has now been resolved by introducing a modified type hierarchy of Event object handling.
• The treatment of intermediate results during the evaluation of ASTNodes had to be changed due to changes in the JSBML library.

Bug fixes:

• There was a redundant representation of interpreters for SBML-specific ASTNode data types. Now there is only one class for this purpose that works more efficient than the previous ones.
• An error in the evaluation of AlgebraicRules was corrected. In some cases the variable was not correctly identified.
• In some cases the species concentrations were now updated correctly after changes of the size of their surrounding compartments. This issue has been fixed now.

Version 1.0

New features:

• MathML expressions with delayed variables are now supported.
• Solvers can be canceled while computing.

Changes in this version:

• Default values are now used for parameters, species and compartments, if no values are set.
• The event processing of the Rosenbrock solver is more efficient.
• The processing of kinetic laws and rules is faster.

Bug fixes in this version:

• Steady state computations are not in conflict with events any more.
• Events with delays are processed correctly.

Version 0.9

First public release of this library.