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EpiLog: A software for the logical modelling of epithelial dynamics
Pedro L Varela1,2,3, Camila V Ramos2,3, Pedro T Monteiro1,2
1Instituto Superior Técnico, Universidade de Lisboa, Lisbon, P-1049-001, Portugal.
F1000Research
|March 23, 2019
Summary
EpiLog is a new computational tool extending logical models from cell to tissue levels. This cellular automaton simulates epithelial tissue behavior based on logical rules and external signals.
Area of Science:
- Computational biology
- Systems biology
- Bioinformatics
Background:
- Cellular responses are regulated by complex networks influenced by micro-environmental cues.
- Logical (Boolean or multi-valued) frameworks are effective for modeling cellular-level signaling and gene regulatory networks.
Purpose of the Study:
- To introduce EpiLog, a computational tool that extends the logical framework for modeling biological processes to the tissue level.
- To provide a platform for simulating mono-layer epithelia using a cellular automaton approach.
Main Methods:
- EpiLog implements an extension of the logical framework to model tissue-level dynamics.
- It defines a 2D grid of hexagonal cells, forming a cellular automaton.
- Cell behaviors are governed by logical models influenced by external signals.
Main Results:
- EpiLog enables the simulation of cellular behaviors within a tissue context.
- The tool integrates logical models with a spatial grid for tissue-level analysis.
- It provides a computational framework for studying emergent properties in epithelial tissues.
Conclusions:
- EpiLog offers a novel approach to model tissue-level biological regulation.
- The tool facilitates the study of how micro-environmental signals impact epithelial tissue behavior.
- EpiLog is freely available, promoting accessibility for researchers in systems and computational biology.
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