toolkit for the manipulation and analysis of Logical Qualitative Models of biological regulatory networks
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README.md

BioLQM: Logical Qualitative Models of biological networks

BioLQM is a toolkit for the manipulation and analysis of Logical (Qualitative) Models of biological networks. A model is composed of a list of components, associated to Boolean or multi-valued activity levels and to dynamical rules driving changes in their activity levels.

BioLQM provides a collection of import/export formats, enabling the exchange of models between complementary tools (motivated by the CoLoMoTo discussion group) and the design of complex analysis workflows. It also allows to define model modifications, to represent biological modifications (mutations) or to facilitate further analysis (model reduction, Boolean mapping of multi-valued models). Finally, it provides some analysis tools, focussing on the identification of attractors and on building-blocks for model simulation.

How to use it?

It can be used either as a standalone command-line tool, or as a programming interface: the Java API can be integrated in other software or used through scripts. Documentation and further information are available on http://colomoto.org/biolqm/.

Licence and authors

This code is available under LGPL v3+/CeCILL-C.

The code started as a refactoring of GINsim to cleanup its core and enable more code sharing. Discussions among CoLoMoTo participants showed a growing interest for improved interoperability. This motivated the qualitative extension for SBML and this toolkit.

Aurelien Naldi designed and maintains the project, with feedback and contributions from:

Claudine Chaouiya
Denis Thieffry
Duncan Berenguier
Francisco Plana
Gautier Stoll
Julien Dorier
Loïc Pauleve
Pedro Monteiro
Rui Henriques