EpiLog: A software for the logical modelling of epithelial dynamics [version 1; referees: 2 approved]
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 invo...
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doaj-4b4f32e46a5a48649ad88d6067c2c0e62020-11-25T03:45:56ZengF1000 Research LtdF1000Research2046-14022018-07-01710.12688/f1000research.15613.117032EpiLog: A software for the logical modelling of epithelial dynamics [version 1; referees: 2 approved]Pedro L. Varela0Camila V. Ramos1Pedro T. Monteiro2Claudine Chaouiya3Instituto Superior Técnico, Universidade de Lisboa, Lisbon, P-1049-001, PortugalINESC-ID, Lisbon, P-1000-029, PortugalINESC-ID, Lisbon, P-1000-029, PortugalInstituto Gulbenkian de Ciência, Oeiras, P-2780-156, PortugalCellular 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.https://f1000research.com/articles/7-1145/v1 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Pedro L. Varela Camila V. Ramos Pedro T. Monteiro Claudine Chaouiya |
spellingShingle |
Pedro L. Varela Camila V. Ramos Pedro T. Monteiro Claudine Chaouiya EpiLog: A software for the logical modelling of epithelial dynamics [version 1; referees: 2 approved] F1000Research |
author_facet |
Pedro L. Varela Camila V. Ramos Pedro T. Monteiro Claudine Chaouiya |
author_sort |
Pedro L. Varela |
title |
EpiLog: A software for the logical modelling of epithelial dynamics [version 1; referees: 2 approved] |
title_short |
EpiLog: A software for the logical modelling of epithelial dynamics [version 1; referees: 2 approved] |
title_full |
EpiLog: A software for the logical modelling of epithelial dynamics [version 1; referees: 2 approved] |
title_fullStr |
EpiLog: A software for the logical modelling of epithelial dynamics [version 1; referees: 2 approved] |
title_full_unstemmed |
EpiLog: A software for the logical modelling of epithelial dynamics [version 1; referees: 2 approved] |
title_sort |
epilog: a software for the logical modelling of epithelial dynamics [version 1; referees: 2 approved] |
publisher |
F1000 Research Ltd |
series |
F1000Research |
issn |
2046-1402 |
publishDate |
2018-07-01 |
description |
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. |
url |
https://f1000research.com/articles/7-1145/v1 |
work_keys_str_mv |
AT pedrolvarela epilogasoftwareforthelogicalmodellingofepithelialdynamicsversion1referees2approved AT camilavramos epilogasoftwareforthelogicalmodellingofepithelialdynamicsversion1referees2approved AT pedrotmonteiro epilogasoftwareforthelogicalmodellingofepithelialdynamicsversion1referees2approved AT claudinechaouiya epilogasoftwareforthelogicalmodellingofepithelialdynamicsversion1referees2approved |
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