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Logical Qualitative Modelling toolkit


This library provides a datastructure for the representation of logical models, and a collection of filters to load or save these models in various formats, facilitating the interoperability between tools which do not directly support SBML qual. It relies on JSBML for SBML qual support.

It can be used on the command line for model conversion or stable state identification. It can also provide the "boring core" for other tools (such as GINsim and Epilog) which can benefit from additional API for the representation of perturbations or simulation engines.

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools
C. Chaouiya, D. Bérenguier, S.M. Keating, A. Naldi, M.P. van Iersel, N. Rodriguez, A. Dräger, F. Büchel, T. Cokelaer, B. Kowal, B. Wicks, E. Gonçalves, J. Dorier, M. Page, P.T. Monteiro, A. von Kamp, I. Xenarios, H. de Jong, M. Hucka, S. Klamt, D. Thieffry, N. Le Novère, J. Saez-Rodriguez, T. Helikar (2013)
BMC Syst Biol 7:135 [doi:10.1186/1752-0509-7-135] [pubmed:24321545]

Supported formats

list of functions used by the boolsim tool
SBML qual
Exchange format for logical models based on SBML
Represents the synchronouns dynamics formated as a two-column text file.