Eugene--a domain specific language for specifying and constraining synthetic biological parts, devices, and systems.

<h4>Background</h4>Synthetic biological systems are currently created by an ad-hoc, iterative process of specification, design, and assembly. These systems would greatly benefit from a more formalized and rigorous specification of the desired system components as well as constraints on t...

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Autores principales:	Lesia Bilitchenko, Adam Liu, Sherine Cheung, Emma Weeding, Bing Xia, Mariana Leguia, J Christopher Anderson, Douglas Densmore
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/f39b23c1bcc6424cb5919f11d479d881
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spelling	oai:doaj.org-article:f39b23c1bcc6424cb5919f11d479d8812021-11-18T06:54:36ZEugene--a domain specific language for specifying and constraining synthetic biological parts, devices, and systems.1932-620310.1371/journal.pone.0018882https://doaj.org/article/f39b23c1bcc6424cb5919f11d479d8812011-04-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21559524/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>Synthetic biological systems are currently created by an ad-hoc, iterative process of specification, design, and assembly. These systems would greatly benefit from a more formalized and rigorous specification of the desired system components as well as constraints on their composition. Therefore, the creation of robust and efficient design flows and tools is imperative. We present a human readable language (Eugene) that allows for the specification of synthetic biological designs based on biological parts, as well as provides a very expressive constraint system to drive the automatic creation of composite Parts (Devices) from a collection of individual Parts.<h4>Results</h4>We illustrate Eugene's capabilities in three different areas: Device specification, design space exploration, and assembly and simulation integration. These results highlight Eugene's ability to create combinatorial design spaces and prune these spaces for simulation or physical assembly. Eugene creates functional designs quickly and cost-effectively.<h4>Conclusions</h4>Eugene is intended for forward engineering of DNA-based devices, and through its data types and execution semantics, reflects the desired abstraction hierarchy in synthetic biology. Eugene provides a powerful constraint system which can be used to drive the creation of new devices at runtime. It accomplishes all of this while being part of a larger tool chain which includes support for design, simulation, and physical device assembly.Lesia BilitchenkoAdam LiuSherine CheungEmma WeedingBing XiaMariana LeguiaJ Christopher AndersonDouglas DensmorePublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 4, p e18882 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Lesia Bilitchenko Adam Liu Sherine Cheung Emma Weeding Bing Xia Mariana Leguia J Christopher Anderson Douglas Densmore Eugene--a domain specific language for specifying and constraining synthetic biological parts, devices, and systems.
description	<h4>Background</h4>Synthetic biological systems are currently created by an ad-hoc, iterative process of specification, design, and assembly. These systems would greatly benefit from a more formalized and rigorous specification of the desired system components as well as constraints on their composition. Therefore, the creation of robust and efficient design flows and tools is imperative. We present a human readable language (Eugene) that allows for the specification of synthetic biological designs based on biological parts, as well as provides a very expressive constraint system to drive the automatic creation of composite Parts (Devices) from a collection of individual Parts.<h4>Results</h4>We illustrate Eugene's capabilities in three different areas: Device specification, design space exploration, and assembly and simulation integration. These results highlight Eugene's ability to create combinatorial design spaces and prune these spaces for simulation or physical assembly. Eugene creates functional designs quickly and cost-effectively.<h4>Conclusions</h4>Eugene is intended for forward engineering of DNA-based devices, and through its data types and execution semantics, reflects the desired abstraction hierarchy in synthetic biology. Eugene provides a powerful constraint system which can be used to drive the creation of new devices at runtime. It accomplishes all of this while being part of a larger tool chain which includes support for design, simulation, and physical device assembly.
format	article
author	Lesia Bilitchenko Adam Liu Sherine Cheung Emma Weeding Bing Xia Mariana Leguia J Christopher Anderson Douglas Densmore
author_facet	Lesia Bilitchenko Adam Liu Sherine Cheung Emma Weeding Bing Xia Mariana Leguia J Christopher Anderson Douglas Densmore
author_sort	Lesia Bilitchenko
title	Eugene--a domain specific language for specifying and constraining synthetic biological parts, devices, and systems.
title_short	Eugene--a domain specific language for specifying and constraining synthetic biological parts, devices, and systems.
title_full	Eugene--a domain specific language for specifying and constraining synthetic biological parts, devices, and systems.
title_fullStr	Eugene--a domain specific language for specifying and constraining synthetic biological parts, devices, and systems.
title_full_unstemmed	Eugene--a domain specific language for specifying and constraining synthetic biological parts, devices, and systems.
title_sort	eugene--a domain specific language for specifying and constraining synthetic biological parts, devices, and systems.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/f39b23c1bcc6424cb5919f11d479d881
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Eugene--a domain specific language for specifying and constraining synthetic biological parts, devices, and systems.

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