<sec> <title>Background</title> <p>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.</p> </sec> <sec>
<title>Results</title> <p>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.</p> </sec> <sec>
<title>Conclusions</title> <p>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.</p>
</sec>
%0 Journal Article
%1 bilitchenko-eugene-dsl-synthetic-2011
%A Bilitchenko, Lesia
%A Liu, Adam
%A Cheung, Sherine
%A Weeding, Emma
%A Xia, Bing
%A Leguia, Mariana
%A Anderson, J. Christopher
%A Densmore, Douglas
%D 2011
%I Public Library of Science
%J PLoS ONE
%K domain dsl language specific
%N 4
%P e18882
%R 10.1371/journal.pone.0018882
%T Eugene – A Domain Specific Language for Specifying
and Constraining Synthetic Biological Parts, Devices,
and Systems
%U http://dx.doi.org/10.1371%2Fjournal.pone.0018882
%V 6
%X <sec> <title>Background</title> <p>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.</p> </sec> <sec>
<title>Results</title> <p>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.</p> </sec> <sec>
<title>Conclusions</title> <p>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.</p>
</sec>
@article{bilitchenko-eugene-dsl-synthetic-2011,
abstract = {<sec> <title>Background</title> <p>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.</p> </sec> <sec>
<title>Results</title> <p>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.</p> </sec> <sec>
<title>Conclusions</title> <p>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.</p>
</sec>},
added-at = {2014-02-13T19:07:04.000+0100},
author = {Bilitchenko, Lesia and Liu, Adam and Cheung, Sherine and Weeding, Emma and Xia, Bing and Leguia, Mariana and Anderson, J. Christopher and Densmore, Douglas},
biburl = {https://www.bibsonomy.org/bibtex/2285581c7beff2218482a48d1b0583428/mhwombat},
doi = {10.1371/journal.pone.0018882},
interhash = {4bf1dba0e014c2c8d36bdb0ded303c1f},
intrahash = {285581c7beff2218482a48d1b0583428},
journal = {PLoS ONE},
keywords = {domain dsl language specific},
month = {04},
number = 4,
pages = {e18882},
publisher = {Public Library of Science},
timestamp = {2016-07-12T19:25:30.000+0200},
title = {Eugene – {A} Domain Specific Language for Specifying
and Constraining Synthetic Biological Parts, Devices,
and Systems},
url = {http://dx.doi.org/10.1371%2Fjournal.pone.0018882},
volume = 6,
year = 2011
}