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SBMLsqueezer version 2.0
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@draeger draeger released this 03 Mar 23:19
· 163 commits to master since this release
v2.0
caaf930

New Features

Many concepts that have been introduced with version 1.3 have been revised and updated. The entire handling of user settings has been massively changed and now uses the concept of user preferences instead of configuration files. The source code has been cleaned and re-factored in many positions and lots of development time has been invested into with the library JSBML.

SBMLsqueezer can now be used in several different ways:

  • As fully-featured stand-alone program without the need to install any further software, based on the official JSBML version 1.0β1
  • As a stand-alone program based on a libSBML back-end, which means that real off-line SBML validation is possible.
  • Irrespective of whether JSBML or libSBML is used as SBML library, the stand-alone version provides both, a graphical user interface as well as a fully-featured command-line version. For large-scale rate law generation, this command-line interface has already proven to be useful (as part of the path2models project).
  • SBMLsqueezer can be launched directly from the project's website as a Java™ Web Start program without the need of any local installation.
  • As a plug-in for CellDesigner 4.3
  • As a Garuda gadget, as which it can communicate with further Garuda gadgets

Hence, the usage of the program has been greatly simplified. Further new program features comprise:

  • SBMLsqueezer fully supports all Levels and Versions of SBML up to the most recent specification Level 3 Version 1.
  • A direct query wizard for SABIO-RK has been implemented and allows users to extract experimentally obtained rate laws from this database together with parameters, values, and units. The search engine provides several settings for experimental conditions.
  • SBMLsqueezer includes now several JUnit test cases to check if the generated kinetic equations are correct.
  • It includes now a full version of SBML2LaTeX and can directly open PDF files that are generated to document the content of the model.
  • The renderer for equations and formula has been changed and provides more capabilities. SBMLsqueezer windows and context menus are now zoom-able and re-sizable.
  • Improved user preferences menu and management for each major operating system (tested under Microsoft Windows, Linux, and Mac OS X).
  • The user interface (graphical user interface and command-line) is fully bilingual (German and English), and partially also translated to Chinese, but models and their labels are only created in English for the sake of a better international re-usability.
  • A new search function allows users to query the model data structure in the graphical user interface.
  • Lots of effort has been put to better adapt SBMLsqueezer to individual platforms. The support for Mac OS X has been greatly improved; the program now provides many features of native applications for Mac OS X.
  • The documentation of the application programming interface has been improved.

Bug Fixes

The communication between SBMLsqueezer and CellDesigner was very inefficient. The new plug-in interface in JSBML provides much better performance. Errors in kinetic equations and units of parameters have been detected and solved:

  • Sometimes SBMLsqueezer created invalid identifiers for newly introduced units.
  • The units of the association and dissociation constant in generalized mass action kinetics could not be derived correctly if a catalyst interfered with the reaction because the units of the catalyst were not taken into account.
  • The units of the half-saturation constant in the (generalized) Hill equation were not correctly derived. The derivation of units of kinetic parameters has been improved.

Several minor issues with the graphical user interface have been solved.

Known Issues

In SBML models, it should be possible to evaluate all kinetic equations to the extent 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.

References

See the new Users' Guide that covers various aspects of working with SBMLsqueezer 2.

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