Varela Pedro L, Ramos Camila V, Monteiro Pedro T, Chaouiya Claudine
Instituto Superior Técnico, Universidade de Lisboa, Lisbon, P-1049-001, Portugal.
INESC-ID, Lisbon, P-1000-029, Portugal.
F1000Res. 2018 Jul 27;7:1145. doi: 10.12688/f1000research.15613.2. eCollection 2018.
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.
细胞反应受调控网络支配，这些调控网络会受到来自周围细胞的外部信号以及其他微环境线索的影响。逻辑（布尔或多值）框架已被证明非常适合在细胞水平研究此类过程，通过指定相关信号通路和基因调控网络的定性模型。在此，我们描述并阐释EpiLog的主要特征，EpiLog是一种将逻辑框架扩展到组织水平的计算工具。EpiLog在二维网格上定义了一组六边形细胞，代表单层上皮组织。基本上，它定义了一种细胞自动机，其中细胞行为由受外部信号影响的相关逻辑模型驱动。EpiLog可在网页http://epilog-tool.org上免费获取。它用Java实现（需要版本≥1.7），源代码在https://github.com/epilog-tool/epilog上根据GNU通用公共许可证v3.0提供。
