lgca

biolgca is a Python package for simulating different types of lattice-gas cellular automata (LGCA) in the biological context. It is under active development.

It is tightly coupled to the theoretical method presented by Deutsch et al. [1]. The get_lgca function returns an LGCA object of the requested type with the given initial conditions. It can simulate for a given number of timesteps and has different plotting functions for analysis, depending on the geometry. The interaction function can be chosen from built-in ones or defined by the user. Currently, classical LGCA and identity-based LGCA with and without volume exclusion, respectively, are supported on 1D, 2D square, 2D hexagonal, 3D cubic and 3D Moore lattices.

References

[1]

Deutsch A, Nava-Sedeño JM, Syga S, Hatzikirou H (2021) BIO-LGCA: A cellular automaton modelling class for analysing collective cell migration. PLoS Comput Biol 17(6): e1009066. https://doi.org/10.1371/journal.pcbi.1009066

Functions

get_lgca([geometry, ib, ve, n_species])

Build an LGCA with the specified geometry and initial conditions.

Modules

base	Abstract base classes.
base_extensions	Compatibility reexports for base classes moved to dedicated modules.
cubic_ext	Extended 3D cubic LGCA models.
ib_base	Extensions to the base LGCA classes.
ib_interactions	Interaction functions and helper functions for identity-based LGCA with volume exclusion.
interactions	Interaction functions and helper functions for classical LGCA with volume exclusion.
lgca_1d	Classes for one-dimensional LGCA.
lgca_3dmoore	3D Moore lattice LGCA implementations.
lgca_cubic	3D cubic lattice LGCA implementations.
lgca_hex	Classes for two-dimensional LGCA on a hexagonal arm-share lattice.
lgca_square	Classes for two-dimensional LGCA on a square lattice.
list_utils	Helpers for object arrays containing per-channel cell-label lists.
ms_1d	Multi-species 1D LGCA implementations.
ms_cubic	Multi-species cubic lattice LGCA implementations.
ms_hex	Multi-species hexagonal LGCA implementations.
ms_interactions	Interaction rules for classical multi-species LGCA.
ms_moore	Multi-species 3D Moore lattice LGCA implementations.
ms_square	Multi-species square lattice LGCA classes.
multispecies_base	Multi-species LGCA base classes.
nove_base	Extensions to the base LGCA classes.
nove_ib_base	Extensions to the base LGCA classes.
nove_ib_interactions	Interaction functions and helper functions for identity-based LGCA without volume exclusion.
nove_interactions	Interaction functions and helper functions for LGCA without volume exclusion.
plots	Utilities for plotting properties and outputs of all LGCA types.
square_ext	Extended 2D square LGCA models.
square_plotting	Plotting utilities for square lattice LGCA.