SBML support for BoolNet

BoolNet 1.60 includes support for SBML-qual:

• toSBML() exports network models to SBML-qual.
• loadSBML() loads SBML documents with the qual package. It should support all models that can be represented as Boolean models, i.e. all logical models with not more than 2 values for each species.

The package is now available at CRAN and can be installed in R using

install.packages("BoolNet")

The functions are described in the manual (type ?toSBML or ?loadSBML in R when BoolNet is loaded) and in Section 4.2 of the package vignette.

Example models exported by BoolNet:

• Mammalian cell cycle [1]: Original Boolean functions | DNF
• Yeast cell cycle [2]: Original Boolean functions | DNF

We appreciate any test cases, comments, bug reports or feature requests regarding the SBML import/export functions! Please contact Hans A. Kestler or Christoph Müssel.
 

[1] Fauré, A., Naldi, A., Chaouiya, C., and Thieffry, D. (2006). Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle. Bioinformatics,22(14), e124–e131.
[2] Orlando, D. A., Lin, C. Y., Bernard, A., Wang, J. Y., Socolar, J. E. S., Iversen, E. S., Hartemink, A. J., Haase, S. B. (2008). Global control of cell-cycle transcription by coupled CDK and network oscillators. Nature, 453, 944-947.