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Streamlining the Design-to-Build Transition with Build-Optimization Software Tools
Scaling-up
capabilities for the design, build, and test of synthetic
biology constructs holds great promise for the development of new
applications in fuels, chemical production, or cellular-behavior engineering.
Construct design is an essential component in this process; however,
not every designed DNA sequence can be readily manufactured, even
using state-of-the-art DNA synthesis methods. Current biological computer-aided
design and manufacture tools (bioCAD/CAM) do not adequately consider
the limitations of DNA synthesis technologies when generating their
outputs. Designed sequences that violate DNA synthesis constraints
may require substantial sequence redesign or lead to price-premiums
and temporal delays, which adversely impact the efficiency of the
DNA manufacturing process. We
have developed a suite of build-optimization software tools (BOOST)
to streamline the design-build transition in synthetic biology engineering
workflows. BOOST incorporates knowledge of DNA synthesis success determinants
into the design process to output ready-to-build sequences, preempting
the need for sequence redesign. The BOOST web application
is available at https://boost.jgi.doe.gov and its Application Program Interfaces (API) enable
integration into automated, customized DNA design processes. The herein
presented results highlight the effectiveness of BOOST in reducing
DNA synthesis costs and timelines
SBOL: A community standard for communicating designs in synthetic biology
<p>Abstract</p>
<p>The Synthetic Biology Open Language (SBOL) is a proposed data standard for exchanging designs within the synthetic biology community. SBOL represents synthetic biology designs in a community-adopted, formalized format for exchange between software tools, research groups, and commercial service providers. The re-use of previously validated designs is critical to the evolution of synthetic biology from a research discipline to an engineering practice. As a community-driven standard, SBOL adapts as synthetic biology evolves, providing specific capabilities for different aspects of the synthetic biology workflow. The SBOL Developers Group has implemented SBOL 1.1 as an XML/RDF serialization and provides software libraries and specification documentation to help developers implement SBOL in their own software. This paper also reports on early successes, including a demonstration of the utility of SBOL for information exchange between three different tools from three academic sites.</p>
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