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dc.contributor.authorBilitchenko, Lesiaen_US
dc.contributor.authorLiu, Adamen_US
dc.contributor.authorCheung, Sherineen_US
dc.contributor.authorWeeding, Emmaen_US
dc.contributor.authorXia, Bingen_US
dc.contributor.authorLeguia, Marianaen_US
dc.contributor.authorAnderson, J. Christopheren_US
dc.contributor.authorDensmore, Douglasen_US
dc.coverage.spatialUnited Statesen_US
dc.date2011-03-24
dc.date.accessioned2018-03-21T15:08:40Z
dc.date.available2018-03-21T15:08:40Z
dc.date.issued2011-04-29
dc.identifierhttps://www.ncbi.nlm.nih.gov/pubmed/21559524
dc.identifier.citationBilitchenko L, Liu A, Cheung S, Weeding E, Xia B, Leguia M, et al. (2011) Eugene – A Domain Specific Language for Specifying and Constraining Synthetic Biological Parts, Devices, and Systems. PLoS ONE 6(4): e18882. https://doi.org/10.1371/journal.pone.0018882
dc.identifier.issn1932-6203
dc.identifier.urihttps://hdl.handle.net/2144/27829
dc.description.abstractBACKGROUND: 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. RESULTS: 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. CONCLUSIONS: 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.en_US
dc.format.extente18882en_US
dc.languageeng
dc.relation.ispartofPLoS One
dc.rightsCopyright: © 2011 Bilitchenko et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.en_US
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.subjectScience & technologyen_US
dc.subjectAlgorithmsen_US
dc.subjectAutomationen_US
dc.subjectBiologyen_US
dc.subjectComputational biologyen_US
dc.subjectComputer simulationen_US
dc.subjectDNAen_US
dc.subjectHumansen_US
dc.subjectLanguageen_US
dc.subjectSoftwareen_US
dc.subjectSynthetic biologyen_US
dc.titleEugene--a domain specific language for specifying and constraining synthetic biological parts, devices, and systemsen_US
dc.typeArticleen_US
dc.identifier.doi10.1371/journal.pone.0018882
pubs.elements-sourcepubmeden_US
pubs.notesEmbargo: Not knownen_US
pubs.organisational-groupBoston Universityen_US
pubs.organisational-groupBoston University, College of Engineeringen_US
pubs.organisational-groupBoston University, College of Engineering, Department of Electrical & Computer Engineeringen_US
pubs.publication-statusPublished onlineen_US


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Copyright: © 2011 Bilitchenko et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Except where otherwise noted, this item's license is described as Copyright: © 2011 Bilitchenko et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.