BioScape: A Modeling and Simulation Language for Bacteria-Materials Interactions

Autores
Compagnoni, Adriana; Sharma, Vishaka; Bao, Yifei; Libera, Matthew; Sukhishvili, Svetlana; Bidinger, Philippe; Boglio, Livio; Bonelli, Eduardo Augusto
Año de publicación
2013
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
We design BioScape, a concurrent language for the stochastic simulation of biological and bio-materials processes in a reactive environment in 3D space. BioScape is based on the Stochastic Pi-Calculus, and it is motivated by the need for individual-based, continuous motion, and continuous space simulation in modeling complex bacteria-materials interactions. Our driving example is a bio-triggered drug delivery system for infection-resistant medical implants. Our models in BioScape will help in identifying biological targets and materials strategies to treat biomaterials associated bacterial infections. The novel aspects of BioScape include syntactic primitives to declare the scope in space where species can move, diffusion rate, shape, and reaction distance, and an operational semantics that deals with the specifics of 3D locations, verifying reaction distance, and featuring random movement. We define a translation from BioScape to 3π and prove its soundness with respect to the operational semantics.
Fil: Compagnoni, Adriana. Stevens Institute of Technology; Estados Unidos
Fil: Sharma, Vishaka. Stevens Institute of Technology; Estados Unidos
Fil: Bao, Yifei. Stevens Institute of Technology; Estados Unidos
Fil: Libera, Matthew. Stevens Institute of Technology; Estados Unidos
Fil: Sukhishvili, Svetlana. Stevens Institute of Technology; Estados Unidos
Fil: Bidinger, Philippe. VERIMAG; Francia
Fil: Boglio, Livio. Universita Di Torino; Italia
Fil: Bonelli, Eduardo Augusto. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnologia; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Materia
BACTERIA-MATERIALS INTERACTION
STOCHASTIC PI-CALCULUS
STOCHASTIC SIMULATION
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-nd/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/3761
Acceder
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network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling BioScape: A Modeling and Simulation Language for Bacteria-Materials InteractionsCompagnoni, AdrianaSharma, VishakaBao, YifeiLibera, MatthewSukhishvili, SvetlanaBidinger, PhilippeBoglio, LivioBonelli, Eduardo AugustoBACTERIA-MATERIALS INTERACTIONSTOCHASTIC PI-CALCULUSSTOCHASTIC SIMULATIONhttps://purl.org/becyt/ford/1.2https://purl.org/becyt/ford/1We design BioScape, a concurrent language for the stochastic simulation of biological and bio-materials processes in a reactive environment in 3D space. BioScape is based on the Stochastic Pi-Calculus, and it is motivated by the need for individual-based, continuous motion, and continuous space simulation in modeling complex bacteria-materials interactions. Our driving example is a bio-triggered drug delivery system for infection-resistant medical implants. Our models in BioScape will help in identifying biological targets and materials strategies to treat biomaterials associated bacterial infections. The novel aspects of BioScape include syntactic primitives to declare the scope in space where species can move, diffusion rate, shape, and reaction distance, and an operational semantics that deals with the specifics of 3D locations, verifying reaction distance, and featuring random movement. We define a translation from BioScape to 3π and prove its soundness with respect to the operational semantics.Fil: Compagnoni, Adriana. Stevens Institute of Technology; Estados UnidosFil: Sharma, Vishaka. Stevens Institute of Technology; Estados UnidosFil: Bao, Yifei. Stevens Institute of Technology; Estados UnidosFil: Libera, Matthew. Stevens Institute of Technology; Estados UnidosFil: Sukhishvili, Svetlana. Stevens Institute of Technology; Estados UnidosFil: Bidinger, Philippe. VERIMAG; FranciaFil: Boglio, Livio. Universita Di Torino; ItaliaFil: Bonelli, Eduardo Augusto. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnologia; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaElsevier2013-03-11info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/3761Compagnoni, Adriana; Sharma, Vishaka; Bao, Yifei; Libera, Matthew; Sukhishvili, Svetlana; et al.; BioScape: A Modeling and Simulation Language for Bacteria-Materials Interactions; Elsevier; Electronic Notes in Theoretical Computer Science; 293; 11-3-2013; 35-491571-0661engProceedings of the Third International Workshop on Interactions Between Computer Science and Biology (CS2Bio'12)info:eu-repo/semantics/altIdentifier/url/http://www.sciencedirect.com/science/article/pii/S1571066113000194info:eu-repo/semantics/altIdentifier/doi/10.1016/j.entcs.2013.02.017info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-nd/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T10:27:54Zoai:ri.conicet.gov.ar:11336/3761instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-29 10:27:54.804CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv BioScape: A Modeling and Simulation Language for Bacteria-Materials Interactions
title BioScape: A Modeling and Simulation Language for Bacteria-Materials Interactions
spellingShingle BioScape: A Modeling and Simulation Language for Bacteria-Materials Interactions
Compagnoni, Adriana
BACTERIA-MATERIALS INTERACTION
STOCHASTIC PI-CALCULUS
STOCHASTIC SIMULATION
title_short BioScape: A Modeling and Simulation Language for Bacteria-Materials Interactions
title_full BioScape: A Modeling and Simulation Language for Bacteria-Materials Interactions
title_fullStr BioScape: A Modeling and Simulation Language for Bacteria-Materials Interactions
title_full_unstemmed BioScape: A Modeling and Simulation Language for Bacteria-Materials Interactions
title_sort BioScape: A Modeling and Simulation Language for Bacteria-Materials Interactions
dc.creator.none.fl_str_mv Compagnoni, Adriana
Sharma, Vishaka
Bao, Yifei
Libera, Matthew
Sukhishvili, Svetlana
Bidinger, Philippe
Boglio, Livio
Bonelli, Eduardo Augusto
author Compagnoni, Adriana
author_facet Compagnoni, Adriana
Sharma, Vishaka
Bao, Yifei
Libera, Matthew
Sukhishvili, Svetlana
Bidinger, Philippe
Boglio, Livio
Bonelli, Eduardo Augusto
author_role author
author2 Sharma, Vishaka
Bao, Yifei
Libera, Matthew
Sukhishvili, Svetlana
Bidinger, Philippe
Boglio, Livio
Bonelli, Eduardo Augusto
author2_role author
author
author
author
author
author
author
dc.subject.none.fl_str_mv BACTERIA-MATERIALS INTERACTION
STOCHASTIC PI-CALCULUS
STOCHASTIC SIMULATION
topic BACTERIA-MATERIALS INTERACTION
STOCHASTIC PI-CALCULUS
STOCHASTIC SIMULATION
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.2
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv We design BioScape, a concurrent language for the stochastic simulation of biological and bio-materials processes in a reactive environment in 3D space. BioScape is based on the Stochastic Pi-Calculus, and it is motivated by the need for individual-based, continuous motion, and continuous space simulation in modeling complex bacteria-materials interactions. Our driving example is a bio-triggered drug delivery system for infection-resistant medical implants. Our models in BioScape will help in identifying biological targets and materials strategies to treat biomaterials associated bacterial infections. The novel aspects of BioScape include syntactic primitives to declare the scope in space where species can move, diffusion rate, shape, and reaction distance, and an operational semantics that deals with the specifics of 3D locations, verifying reaction distance, and featuring random movement. We define a translation from BioScape to 3π and prove its soundness with respect to the operational semantics.
Fil: Compagnoni, Adriana. Stevens Institute of Technology; Estados Unidos
Fil: Sharma, Vishaka. Stevens Institute of Technology; Estados Unidos
Fil: Bao, Yifei. Stevens Institute of Technology; Estados Unidos
Fil: Libera, Matthew. Stevens Institute of Technology; Estados Unidos
Fil: Sukhishvili, Svetlana. Stevens Institute of Technology; Estados Unidos
Fil: Bidinger, Philippe. VERIMAG; Francia
Fil: Boglio, Livio. Universita Di Torino; Italia
Fil: Bonelli, Eduardo Augusto. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnologia; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
description We design BioScape, a concurrent language for the stochastic simulation of biological and bio-materials processes in a reactive environment in 3D space. BioScape is based on the Stochastic Pi-Calculus, and it is motivated by the need for individual-based, continuous motion, and continuous space simulation in modeling complex bacteria-materials interactions. Our driving example is a bio-triggered drug delivery system for infection-resistant medical implants. Our models in BioScape will help in identifying biological targets and materials strategies to treat biomaterials associated bacterial infections. The novel aspects of BioScape include syntactic primitives to declare the scope in space where species can move, diffusion rate, shape, and reaction distance, and an operational semantics that deals with the specifics of 3D locations, verifying reaction distance, and featuring random movement. We define a translation from BioScape to 3π and prove its soundness with respect to the operational semantics.
publishDate 2013
dc.date.none.fl_str_mv 2013-03-11
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/3761
Compagnoni, Adriana; Sharma, Vishaka; Bao, Yifei; Libera, Matthew; Sukhishvili, Svetlana; et al.; BioScape: A Modeling and Simulation Language for Bacteria-Materials Interactions; Elsevier; Electronic Notes in Theoretical Computer Science; 293; 11-3-2013; 35-49
1571-0661
url http://hdl.handle.net/11336/3761
identifier_str_mv Compagnoni, Adriana; Sharma, Vishaka; Bao, Yifei; Libera, Matthew; Sukhishvili, Svetlana; et al.; BioScape: A Modeling and Simulation Language for Bacteria-Materials Interactions; Elsevier; Electronic Notes in Theoretical Computer Science; 293; 11-3-2013; 35-49
1571-0661
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv Proceedings of the Third International Workshop on Interactions Between Computer Science and Biology (CS2Bio'12)
info:eu-repo/semantics/altIdentifier/url/http://www.sciencedirect.com/science/article/pii/S1571066113000194
info:eu-repo/semantics/altIdentifier/doi/10.1016/j.entcs.2013.02.017
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-nd/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-nd/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Elsevier
publisher.none.fl_str_mv Elsevier
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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score 13.070432

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