Release Notes of SBMLsqueezer version 2.1

Download of SBMLsquezeezer

You can always download the latest version of SBMLsqueezer at http://www.cogsys.cs.uni-tuebingen.de/software/SBMLsqueezer/downloads.

New Features

  • SBMLsqueezer fully supports all Levels and Versions of SBML up to the most recent specifications Level 2 Version 5 and Level 3 Version 1.
  • The CellDesigner plug-in version has been adapted to work with version 4.4.
  • The Garuda backend has been updated.
  • The report generator SBML2LaTeX has been updated and the new version is now part of this release of SBMLsqueezer.
  • SBMLsqueezer comes with the most recent version of JSBML (revision 2354), which can read all current extension packages.
  • Slightly improved API documentation and updated Users' Guide.
  • Correctly indented SBML output files.

Bug Fixes

  • Under Windows, it was sometimes not possible to correctly display user messages. This has been fixed.
  • Several minor issues have been solved.

Known Issues

In SBML models, it should be possible to evaluate all kinetic equations to extend of reaction units per time units. Usually, the extend of a reaction would be a variant of a substance unit. However, it has been recognized that some kinetic equations cannot under all conditions be evaluated to extend per time units. The reasons are often the structure of the definition of the rate law. Some equations that have been defined for gene-regulatory networks, for instance, give a purely phenomenological description of the system (e.g., S- or H-systems). In other equations, it is assumed that the equilibrium constant is always dimensionless. If this is not the case, it cannot be guaranteed that SBMLsqueezer will create correct units for these equations (e.g., modular rate laws and convenience kinetics). It is therefore recommended to check the units of generated rate laws, even if in the vast majority of cases these will be correct. Please note that in this version the general unit handling has been extensively revised and improved and is in the vast majority of cases very reliable. SBMLsqueezer displays the derived units of equations, so that problematic equations can be easily identified.