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A membrane computing simulator of trans-hierarchical antibiotic resistance evolution dynamics in nested ecological compartments (ARES)

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A membrane computing simulator of trans-hierarchical antibiotic resistance evolution dynamics in nested ecological compartments (ARES)

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dc.contributor.author Campos Frances, Marcelino es_ES
dc.contributor.author Llorens, Carlos es_ES
dc.contributor.author Sempere Luna, José María es_ES
dc.contributor.author Futami, Ricardo es_ES
dc.contributor.author Rodríguez, Irene es_ES
dc.contributor.author Carrasco, Purificación es_ES
dc.contributor.author Capilla, Rafael es_ES
dc.contributor.author Latorre, Amparo es_ES
dc.contributor.author Coque, Teresa M. es_ES
dc.contributor.author Moya, Andrés es_ES
dc.contributor.author Baquero, Fernando es_ES
dc.date.accessioned 2016-05-27T08:23:02Z
dc.date.available 2016-05-27T08:23:02Z
dc.date.issued 2015
dc.identifier.issn 1745-6150
dc.identifier.uri http://hdl.handle.net/10251/64840
dc.description.abstract In this article, we introduce ARES (Antibiotic Resistance Evolution Simulator) a software device that simulates P-system model scenarios with five types of nested computing membranes oriented to emulate a hierarchy of eco-biological compartments, i.e. a) peripheral ecosystem; b) local environment; c) reservoir of supplies; d) animal host; and e) host's associated bacterial organisms (microbiome). Computational objects emulating molecular entities such as plasmids, antibiotic resistance genes, antimicrobials, and/or other substances can be introduced into this framework and may interact and evolve together with the membranes, according to a set of pre-established rules and specifications. ARES has been implemented as an online server and offers additional tools for storage and model editing and downstream analysis es_ES
dc.description.sponsorship This work has also been supported by grants BFU2012-39816-C02-01 (co-financed by FEDER funds and the Ministry of Economy and Competitiveness, Spain) to AL and Prometeo/2009/092 (Ministry of Education, Government of Valencia, Spain) and Explora Ciencia y Explora Tecnologia/SAF2013-49788-EXP (Spanish Ministry of Economy and Competitiveness) to AM. IRF is recipient of a "Sara Borrell" postdoctoral fellowship (Ref. CD12/00492) from the Ministry of Economy and Competitiveness (Spain). We are also grateful to the Spanish Network for the Study of Plasmids and Extrachromosomal Elements (REDEEX) for encouraging and funding cooperation among Spanish microbiologists working on the biology of mobile genetic elements (Spanish Ministry of Science and Innovation, reference number BFU2011-14145-E). en_EN
dc.language Inglés es_ES
dc.publisher BioMed Central es_ES
dc.relation European Commission/EvoTAR-282004 es_ES
dc.relation.ispartof Biology Direct es_ES
dc.rights Reconocimiento (by) es_ES
dc.subject Membrane computing es_ES
dc.subject P-system es_ES
dc.subject Antibiotic resistance es_ES
dc.subject Essential nesting es_ES
dc.subject.classification ORGANIZACION DE EMPRESAS es_ES
dc.subject.classification LENGUAJES Y SISTEMAS INFORMATICOS es_ES
dc.title A membrane computing simulator of trans-hierarchical antibiotic resistance evolution dynamics in nested ecological compartments (ARES) es_ES
dc.type Artículo es_ES
dc.identifier.doi 10.1186/s13062-015-0070-9
dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/282004/EU/Evolution and Transfer of Antibiotic Resistance/ en_EN
dc.relation.projectID info:eu-repo/grantAgreement/ISCIII//PI10%2F02588/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/MINECO//PI12%2F01581/ES/Nodos de Alto Riesgo en Redes de Intercambio Génico de Poblaciones Bacterianas resistentes a antibióticos: Bases Teóricas y Experimentales de Futuras Estrategia/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/CAM//S2010%2FBMD-2414/ES/Programación de circuitos microbianos en medicina protectiva y terapéutica (PROMPT)/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/CIBER-BBN//CB06%2F02%2F0053/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/MINECO//BFU2012-39816-C02-01/ES/BIOLOGIA DE SISTEMAS DE LAS INTERACCIONES ENTRE LOS INSECTOS Y SUS SIMBIONTES/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/GVA//PROMETEO%2F2009%2F092/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/MINECO//SAF2013-49788-EXP/ES/INNOVACION EN MODELOS COMPUTACIONALES PREDICTIVOS EN EPIDEMIOLOGIA EXPERIMENTAL DE LA RESISTENCIA A LOS ANTIBIOTICOS/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/MINECO//CD12%2F00492/ES/CD12%2F00492/ es_ES
dc.rights.accessRights Abierto es_ES
dc.contributor.affiliation Universitat Politècnica de València. Departamento de Sistemas Informáticos y Computación - Departament de Sistemes Informàtics i Computació es_ES
dc.description.bibliographicCitation Campos Frances, M.; Llorens, C.; Sempere Luna, JM.; Futami, R.; Rodríguez, I.; Carrasco, P.; Capilla, R.... (2015). A membrane computing simulator of trans-hierarchical antibiotic resistance evolution dynamics in nested ecological compartments (ARES). Biology Direct. 10(41):1-13. https://doi.org/10.1186/s13062-015-0070-9 es_ES
dc.description.accrualMethod S es_ES
dc.relation.publisherversion http://dx.doi.org/10.1186/s13062-015-0070-9 es_ES
dc.description.upvformatpinicio 1 es_ES
dc.description.upvformatpfin 13 es_ES
dc.type.version info:eu-repo/semantics/publishedVersion es_ES
dc.description.volume 10 es_ES
dc.description.issue 41 es_ES
dc.relation.senia 295800 es_ES
dc.identifier.pmid 26243297 en_EN
dc.identifier.pmcid PMC4526193 en_EN
dc.contributor.funder Instituto de Salud Carlos III es_ES
dc.contributor.funder Ministerio de Economía y Competitividad es_ES
dc.contributor.funder Comunidad de Madrid es_ES
dc.contributor.funder Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina es_ES
dc.contributor.funder Generalitat Valenciana es_ES
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