Estimating Attractor Reachability in Asynchronous Logical Models

Detalhes bibliográficos
Autor(a) principal: Mendes, Nuno D.
Data de Publicação: 2018
Outros Autores: Henriques, Rui, Remy, Elisabeth, Carneiro, Jorge, Monteiro, Pedro T., Chaouiya, Claudine
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Texto Completo: http://hdl.handle.net/10400.7/897
Resumo: This deposit is composed by the main article. The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fphys.2018.01161/full#supplementary-material.
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spelling Estimating Attractor Reachability in Asynchronous Logical Modelsregulatory networklogical modelingdiscrete asynchronous dynamicsattractorsreachabilityThis deposit is composed by the main article. The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fphys.2018.01161/full#supplementary-material.Logical models are well-suited to capture salient dynamical properties of regulatory networks. For networks controlling cell fate decisions, cell fates are associated with model attractors (stable states or cyclic attractors) whose identification and reachability properties are particularly relevant. While synchronous updates assume unlikely instantaneous or identical rates associated with component changes, the consideration of asynchronous updates is more realistic but, for large models, may hinder the analysis of the resulting non-deterministic concurrent dynamics. This complexity hampers the study of asymptotical behaviors, and most existing approaches suffer from efficiency bottlenecks, being generally unable to handle cyclical attractors and quantify attractor reachability. Here, we propose two algorithms providing probability estimates of attractor reachability in asynchronous dynamics. The first algorithm, named Firefront, exhaustively explores the state space from an initial state, and provides quasi-exact evaluations of the reachability probabilities of model attractors. The algorithm progresses in breadth, propagating the probabilities of each encountered state to its successors. Second, Avatar is an adapted Monte Carlo approach, better suited for models with large and intertwined transient and terminal cycles. Avatar iteratively explores the state space by randomly selecting trajectories and by using these random walks to estimate the likelihood of reaching an attractor. Unlike Monte Carlo simulations, Avatar is equipped to avoid getting trapped in transient cycles and to identify cyclic attractors. Firefront and Avatar are validated and compared to related methods, using as test cases logical models of synthetic and biological networks. Both algorithms are implemented as new functionalities of GINsim 3.0, a well-established software tool for logical modeling, providing executable GUI, Java API, and scripting facilities.This work was supported by Fundação para a Ciência e a Tecnologia (FCT, Portugal), grants PTDC/EIA-CCO/099229/2008, UID/CEC/50021/2013, IF/01333/2013, and PTDC/EEI-CTP/2914/2014.Frontiers MediaARCAMendes, Nuno D.Henriques, RuiRemy, ElisabethCarneiro, JorgeMonteiro, Pedro T.Chaouiya, Claudine2018-10-10T11:28:36Z2018-09-072018-09-07T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10400.7/897engMendes ND, Henriques R, Remy E, Carneiro J, Monteiro PT and Chaouiya C (2018) Estimating Attractor Reachability in Asynchronous Logical Models. Front. Physiol. 9:1161. doi: 10.3389/fphys.2018.0116110.3389/fphys.2018.01161info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2022-11-29T14:35:18Zoai:arca.igc.gulbenkian.pt:10400.7/897Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T16:12:06.330821Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse
dc.title.none.fl_str_mv Estimating Attractor Reachability in Asynchronous Logical Models
title Estimating Attractor Reachability in Asynchronous Logical Models
spellingShingle Estimating Attractor Reachability in Asynchronous Logical Models
Mendes, Nuno D.
regulatory network
logical modeling
discrete asynchronous dynamics
attractors
reachability
title_short Estimating Attractor Reachability in Asynchronous Logical Models
title_full Estimating Attractor Reachability in Asynchronous Logical Models
title_fullStr Estimating Attractor Reachability in Asynchronous Logical Models
title_full_unstemmed Estimating Attractor Reachability in Asynchronous Logical Models
title_sort Estimating Attractor Reachability in Asynchronous Logical Models
author Mendes, Nuno D.
author_facet Mendes, Nuno D.
Henriques, Rui
Remy, Elisabeth
Carneiro, Jorge
Monteiro, Pedro T.
Chaouiya, Claudine
author_role author
author2 Henriques, Rui
Remy, Elisabeth
Carneiro, Jorge
Monteiro, Pedro T.
Chaouiya, Claudine
author2_role author
author
author
author
author
dc.contributor.none.fl_str_mv ARCA
dc.contributor.author.fl_str_mv Mendes, Nuno D.
Henriques, Rui
Remy, Elisabeth
Carneiro, Jorge
Monteiro, Pedro T.
Chaouiya, Claudine
dc.subject.por.fl_str_mv regulatory network
logical modeling
discrete asynchronous dynamics
attractors
reachability
topic regulatory network
logical modeling
discrete asynchronous dynamics
attractors
reachability
description This deposit is composed by the main article. The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fphys.2018.01161/full#supplementary-material.
publishDate 2018
dc.date.none.fl_str_mv 2018-10-10T11:28:36Z
2018-09-07
2018-09-07T00:00:00Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://hdl.handle.net/10400.7/897
url http://hdl.handle.net/10400.7/897
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv Mendes ND, Henriques R, Remy E, Carneiro J, Monteiro PT and Chaouiya C (2018) Estimating Attractor Reachability in Asynchronous Logical Models. Front. Physiol. 9:1161. doi: 10.3389/fphys.2018.01161
10.3389/fphys.2018.01161
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Frontiers Media
publisher.none.fl_str_mv Frontiers Media
dc.source.none.fl_str_mv reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron:RCAAP
instname_str Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron_str RCAAP
institution RCAAP
reponame_str Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
collection Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
repository.name.fl_str_mv Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
repository.mail.fl_str_mv
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