EpiLog: A software for the logical modelling of epithelial dynamics

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

Publication

EpiLog: A software for the logical modelling of epithelial dynamics

2019-03-11Journal article

dc.contributor.author	Varela, Pedro L.
dc.contributor.author	Ramos, Camila V.
dc.contributor.author	Monteiro, Pedro T.
dc.contributor.author	Chaouiya, Claudine
dc.date.accessioned	2020-03-11T15:50:45Z
dc.date.available	2020-03-11T15:50:45Z
dc.date.issued	2019-03-11
dc.description.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.	pt_PT
dc.description.version	info:eu-repo/semantics/publishedVersion	pt_PT
dc.identifier.citation	Varela PL, Ramos CV, Monteiro PT and Chaouiya C. EpiLog: A software for the logical modelling of epithelial dynamics [version 2; peer review: 3 approved]. F1000Research 2019, 7:1145	pt_PT
dc.identifier.doi	10.12688/f1000research.15613.2	pt_PT
dc.identifier.uri	http://hdl.handle.net/10400.7/938
dc.language.iso	eng	pt_PT
dc.peerreviewed	yes	pt_PT
dc.relation	CoMEDy - A COmputational Modelling platform for Epithelial DYnamics to explore the role of epithelial-mesenchymal transition and stemness acquisition in cancer recurrence
dc.relation	Towards a semi-automatic model revision of logical regulatory networks
dc.relation	MALIN: Modular modelling and Analysis of Large biological Interacting Networks
dc.rights.uri	http://creativecommons.org/licenses/by/4.0/	pt_PT
dc.subject	Logical modelling, Multicellular regulatory networks, Cellular automaton, Hexagonal grid	pt_PT
dc.title	EpiLog: A software for the logical modelling of epithelial dynamics	pt_PT
dc.type	journal article
dspace.entity.type	Publication
oaire.awardTitle	CoMEDy - A COmputational Modelling platform for Epithelial DYnamics to explore the role of epithelial-mesenchymal transition and stemness acquisition in cancer recurrence
oaire.awardTitle	Towards a semi-automatic model revision of logical regulatory networks
oaire.awardTitle	MALIN: Modular modelling and Analysis of Large biological Interacting Networks
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oaire.citation.startPage	1145	pt_PT
oaire.citation.title	F1000Research	pt_PT
oaire.citation.volume	7	pt_PT
oaire.fundingStream	3599-PPCDT
oaire.fundingStream	5876
oaire.fundingStream	Investigador FCT
oaire.fundingStream	3599-PPCDT
project.funder.identifier	http://doi.org/10.13039/501100001871
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project.funder.identifier	http://doi.org/10.13039/501100001871
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project.funder.name	Fundação para a Ciência e a Tecnologia
project.funder.name	Fundação para a Ciência e a Tecnologia
project.funder.name	Fundação para a Ciência e a Tecnologia
project.funder.name	Fundação para a Ciência e a Tecnologia
rcaap.rights	openAccess	pt_PT
rcaap.type	article	pt_PT
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