Companion Tools

bioLQM

bioLQM is a tool for the manipulation of multi-valued logical models. It provides a set of core interfaces for the interoperability between different logical modelling tools (such as GINsim and EpiLog). You can get it at https://github.com/colomoto/biolqm.

EpiLog

EpiLog is a tool which makes use of LogicalModel to implement a cellular automata, defining a convenient framework for the qualitative modelling of epithelium pattern formation. You can obtain more information at http://epilog-tool.org.

MDDlib

MDDlib is a simple toolkit written in Java for the manipulation of Multi-valued Decision Diagrams (MDD). GINsim uses MDDlib at his core, since all logical functions are represented as MDDs. You can get it at https://github.com/colomoto/mddlib.

Basins of attraction

Using bioLQM in combination with BoolSim a set of Python scripts enable the computation of: attractors, basins of attraction and frontiers between attractors/basins of attraction. You can get more information and get the code at basins-attraction.

pyFunctionHood

pyFunctionHood is a Python library to locally compute the set of distance-k neighbouring of any monotone Boolean Function. It considers the set of rules described in to avoid generating all possible O(2^2^n) Boolean functions. You can read the associated publication at https://arxiv.org/abs/2407.01337 and get the code at https://github.com/ptgm/pyfunctionhood.