EpiLog supports the definition, simulation and visualisation of qualitative, logical models over hexagonal grids of cells. Such models conveniently support the study of epithelial pattern formation.
EpiLog defines hexagonal cellular automata, where the behaviour of each cell is governed by the associated (logical) cellular model subject to input signals from neighbouring cells or to other positional cues. Signalling is defined through appropriate logical functions, which qualitatively handle signal ranges and synergies.
Cellular models should be provided in the SBML-qual format, being generated using e.g. GINsim. Internal handling of logical models is made with the support of bioLQM.
To compile EpiLog all you will need is java7+ JDK and maven.
Grab the source from github:
git clone https://github.com/epilog-tool/epilog.git
To compile and package it, run:
mvn package assembly:single
Launch the jar package in the "target/" subdirectory:
java -jar target/EpiLog-<version>.jar
This code is available under GPL-3.0.
- Pedro T. Monteiro
- Pedro L. Varela
- Camila Ramos
Claudine Chaouiya & Pedro T. Monteiro
A. Fauré & C. Hernandez for insightful feedback and comments