Release notes of SBMLsqueezer version 1.1

New features

SBMLsqueezer now allows you to specify whether new parameters should be stored locally (only vailid within the respective kinetic law) or globally (valid for the whole model). Both, the main window and the context menu contain switches to make this decision. Please note that the k_G parameters of the thermodynamically independent convenience kinetics are always stored globally because these do not belong to a specific reaction but to a specific reacting species.

The context menu of SBMLsqueezer now also shows already existing kinetic equations and renders their formula. The name of the kinetic equation created by SBMLsqueezer is now written to the notes element of the newly created kinetic law.

The LaTeX export function was improved:

  1. Several choices allow for a customization of the output.
  2. The context menu also allows you to export a LaTeX file for a specific kinetic equation.
  3. It now includes HTML2LaTeX that converts notes elements from XHTML to LaTeX. Therfore, SBMLsqueezer also includes your notes in its model report.
Please note that SBMLsqueezer's LaTeX export function is, however, still not comprehensive. For a fully-featured model report generator, we strongly recoment to have a look on our latest project: SBML2LaTeX on http://webservices.cs.uni-tuebingen.de and http://www.ra.cs.uni-tuebingen.de/software/SBML2LaTeX.

SBMLsqueezer version 1.1 is distributed under the terms of the GNU General Public License (GPL).

Bugs that were fixed

In some cases SBMLsqueezer's context menu did not offer the full list of available and applicable kinetic equations for certain reactions.

If the number of products was higher than the number of reactants a null pointer exception was thrown in the thermodynamically independent form of the convenience kinetics due to an incorrect access to the list of products of a reaction.

In the thermodynamically independent convenience kinetics the root function was called with only one argument. This is actually not incorrect but earlier versions of libSBML are unable to interpret such an implicit square root and require a 2 as the second argument.

In the thermodynamically independent convenience kinetics the exponent of the anabol term and the catabol term were incorrect if the stoichiometry was not equal to one. In this case, a division of the exponent by 2 was missing.

In the mass action kinetics a copy and paste error in the source code lead to incorrect pre-factors for activation and inhibition if both effects were assigned to the same reaction. Instead of receiving one activation function and one inhibition function there was the same activation twice.

For several reasons null pointer exceptions could occur when trying to create LaTeX code from a model.