Automatic compilation from high-level biologically-oriented programming language to genetic regulatory networks.

<h4>Background</h4>The field of synthetic biology promises to revolutionize our ability to engineer biological systems, providing important benefits for a variety of applications. Recent advances in DNA synthesis and automated DNA assembly technologies suggest that it is now possible to...

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Autores principales:	Jacob Beal, Ting Lu, Ron Weiss
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/65cd7173162445b9a26171b19c8c40d4
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spelling	oai:doaj.org-article:65cd7173162445b9a26171b19c8c40d42021-11-18T06:48:34ZAutomatic compilation from high-level biologically-oriented programming language to genetic regulatory networks.1932-620310.1371/journal.pone.0022490https://doaj.org/article/65cd7173162445b9a26171b19c8c40d42011-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21850228/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>The field of synthetic biology promises to revolutionize our ability to engineer biological systems, providing important benefits for a variety of applications. Recent advances in DNA synthesis and automated DNA assembly technologies suggest that it is now possible to construct synthetic systems of significant complexity. However, while a variety of novel genetic devices and small engineered gene networks have been successfully demonstrated, the regulatory complexity of synthetic systems that have been reported recently has somewhat plateaued due to a variety of factors, including the complexity of biology itself and the lag in our ability to design and optimize sophisticated biological circuitry.<h4>Methodology/principal findings</h4>To address the gap between DNA synthesis and circuit design capabilities, we present a platform that enables synthetic biologists to express desired behavior using a convenient high-level biologically-oriented programming language, Proto. The high level specification is compiled, using a regulatory motif based mechanism, to a gene network, optimized, and then converted to a computational simulation for numerical verification. Through several example programs we illustrate the automated process of biological system design with our platform, and show that our compiler optimizations can yield significant reductions in the number of genes (~ 50%) and latency of the optimized engineered gene networks.<h4>Conclusions/significance</h4>Our platform provides a convenient and accessible tool for the automated design of sophisticated synthetic biological systems, bridging an important gap between DNA synthesis and circuit design capabilities. Our platform is user-friendly and features biologically relevant compiler optimizations, providing an important foundation for the development of sophisticated biological systems.Jacob BealTing LuRon WeissPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 8, p e22490 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Jacob Beal Ting Lu Ron Weiss Automatic compilation from high-level biologically-oriented programming language to genetic regulatory networks.
description	<h4>Background</h4>The field of synthetic biology promises to revolutionize our ability to engineer biological systems, providing important benefits for a variety of applications. Recent advances in DNA synthesis and automated DNA assembly technologies suggest that it is now possible to construct synthetic systems of significant complexity. However, while a variety of novel genetic devices and small engineered gene networks have been successfully demonstrated, the regulatory complexity of synthetic systems that have been reported recently has somewhat plateaued due to a variety of factors, including the complexity of biology itself and the lag in our ability to design and optimize sophisticated biological circuitry.<h4>Methodology/principal findings</h4>To address the gap between DNA synthesis and circuit design capabilities, we present a platform that enables synthetic biologists to express desired behavior using a convenient high-level biologically-oriented programming language, Proto. The high level specification is compiled, using a regulatory motif based mechanism, to a gene network, optimized, and then converted to a computational simulation for numerical verification. Through several example programs we illustrate the automated process of biological system design with our platform, and show that our compiler optimizations can yield significant reductions in the number of genes (~ 50%) and latency of the optimized engineered gene networks.<h4>Conclusions/significance</h4>Our platform provides a convenient and accessible tool for the automated design of sophisticated synthetic biological systems, bridging an important gap between DNA synthesis and circuit design capabilities. Our platform is user-friendly and features biologically relevant compiler optimizations, providing an important foundation for the development of sophisticated biological systems.
format	article
author	Jacob Beal Ting Lu Ron Weiss
author_facet	Jacob Beal Ting Lu Ron Weiss
author_sort	Jacob Beal
title	Automatic compilation from high-level biologically-oriented programming language to genetic regulatory networks.
title_short	Automatic compilation from high-level biologically-oriented programming language to genetic regulatory networks.
title_full	Automatic compilation from high-level biologically-oriented programming language to genetic regulatory networks.
title_fullStr	Automatic compilation from high-level biologically-oriented programming language to genetic regulatory networks.
title_full_unstemmed	Automatic compilation from high-level biologically-oriented programming language to genetic regulatory networks.
title_sort	automatic compilation from high-level biologically-oriented programming language to genetic regulatory networks.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/65cd7173162445b9a26171b19c8c40d4
work_keys_str_mv	AT jacobbeal automaticcompilationfromhighlevelbiologicallyorientedprogramminglanguagetogeneticregulatorynetworks AT tinglu automaticcompilationfromhighlevelbiologicallyorientedprogramminglanguagetogeneticregulatorynetworks AT ronweiss automaticcompilationfromhighlevelbiologicallyorientedprogramminglanguagetogeneticregulatorynetworks
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Automatic compilation from high-level biologically-oriented programming language to genetic regulatory networks.

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