EpiLog: A software for the logical modelling of epithelial dynamics.

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

doi:10.12688/f1000research.15613.1

Abstract

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.

Highlights

Pattern formation emerges from the interplay of interaction networks, at the cellular and multi-cellular levels[1]
The consideration of ensembles of communicating cells is often required to recapitulate observed patterns (e.g. 4,5). This motivated the development of EpiLog, which implements an extension of the logical framework to hexagonal grids embodying simple epithelia
Summary To the best of our knowledge, EpiLog is the first software tool for the definition, simulation and visualisation of qualitative, logical (Boolean and multivalued) models over hexagonal grids. It provides a graphical user interface and tools to conveniently support the study of epithelial pattern formation, relying on a logical framework

Summary

Introduction

Pattern formation emerges from the interplay of interaction networks, at the cellular and multi-cellular levels[1]. To uncover the complex mechanisms at stake, computational modelling is very needed. In this context, cellular automaton approaches are well suited[2]. The logical formalism has proved efficient to explore cellular regulatory networks driving developmental processes (for a recent review on the logical modelling approach, see 3). The consideration of ensembles of communicating cells is often required to recapitulate observed patterns (e.g. 4,5). This motivated the development of EpiLog, which implements an extension of the logical framework to hexagonal grids embodying simple epithelia

Methods

Discussion

Conclusion