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.