bioLQM: Logical Qualitative Modelling toolkit

bioLQM is a Java toolkit for the conversion, transformation, and analysis of Logical Qualitative Models of biological regulatory networks.

Overview

The bioLQM toolkit supports the SBML-qual exchange format, as well as specialised formats used by existing tools, facilitating the design of workflows combining these tools.

Model transformations enable the definition of perturbations, model reduction, as well as model Booleanization for the study of multivalued models with tools limited to the Boolean case.

Finally, bioLQM provides reference implementation of common analysis tools, in particular the common updating modes for model simulation, as well as some static analysis tools for the identification of attractors.

This toolkit can be integrated into analysis workflows through command line and scripting interfaces. It also provides core data structures underlying the GINsim and EpiLog interactive tools.

Documentation

User documentation and API documentation are available.

Download

Source code and releases are available on github.

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]