EpiLog: A software for the logical modelling of epithelial dynamics

Varela, Pedro L.; Ramos, Camila V.; Monteiro, Pedro T.; Chaouiya, Claudine

http://hdl.handle.net/10400.7/938

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Abstract(s)

Cellular responses are governed by regulatory networks subject to external signals from surrounding cells and to other micro-environmental cues. The logical (Boolean or multi-valued) framework proved well suited to study such processes at the cellular level, by specifying qualitative models of involved signalling pathways and gene regulatory networks. Here, we describe and illustrate the main features of EpiLog, a computational tool that implements an extension of the logical framework to the tissue level. EpiLog defines a collection of hexagonal cells over a 2D grid, which embodies a mono-layer epithelium. Basically, it defines a cellular automaton in which cell behaviours are driven by associated logical models subject to external signals. EpiLog is freely available on the web at http://epilog-tool.org. It is implemented in Java (version ≥1.7 required) and the source code is provided at https://github.com/epilog-tool/epilog under a GNU General Public License v3.0.

Keywords

Logical modelling, Multicellular regulatory networks, Cellular automaton, Hexagonal grid

URI

http://hdl.handle.net/10400.7/938

Citation

Varela PL, Ramos CV, Monteiro PT and Chaouiya C. EpiLog: A software for the logical modelling of epithelial dynamics [version 2; peer review: 3 approved]. F1000Research 2019, 7:1145