Computational models are essential to engineer predictable biological systems and to scale up this process for complex systems. Computational modeling often requires expert knowledge and data to build models. Clearly, manual creation of models is not scalable for large designs. Despite several automated model…
Computational models are essential to engineer predictable biological systems and to scale up this process for complex systems. Computational modeling often requires expert knowledge and data to build models. Clearly, manual creation of models is not scalable for large designs. Despite several automated model…
Most digital electronic circuits utilize a timing reference to synchronize the progression of signals and enable sequential memory elements. These designs may not be realizable in biological substrates due to the lack of a reliable high-frequency clock signal. Asynchronous designs eliminate the need for a clock with…
Most digital electronic circuits utilize a timing reference to synchronize the progression of signals and enable sequential memory elements. These designs may not be realizable in biological substrates due to the lack of a reliable high-frequency clock signal. Asynchronous designs eliminate the need for a clock with…
The Synthetic Biology Open Language (SBOL) is a standard that enables collaborative engineering of biological systems across different institutions and tools. SBOL is developed through careful consideration of recent synthetic biology trends, real use cases, and consensus among leading researchers in the field and…
The Synthetic Biology Open Language (SBOL) is a standard that enables collaborative engineering of biological systems across different institutions and tools. SBOL is developed through careful consideration of recent synthetic biology trends, real use cases, and consensus among leading researchers in the field and…
Raven calculates assembly plans for complex genetic constructs from thousands of parts. It integrates user feedback on failed intermediate assemblies to improve the final outcome.
Raven calculates assembly plans for complex genetic constructs from thousands of parts. It integrates user feedback on failed intermediate assemblies to improve the final outcome.
The synthetic biology research community describes a standard language for exchanging designs of biological 'parts'.
The synthetic biology research community describes a standard language for exchanging designs of biological 'parts'.
Pigeon is a Web-based tool that translates a textual description of a synthetic biology design into an image. It allows programmatic generation of design visualizations, is easy to learn, is easily extensible to new glyphs and notation, and can be connected to other software tools for visualizing their output. We…
Pigeon is a Web-based tool that translates a textual description of a synthetic biology design into an image. It allows programmatic generation of design visualizations, is easy to learn, is easily extensible to new glyphs and notation, and can be connected to other software tools for visualizing their output. We…
Biological Computer Aided Design (bioCAD) assists the de novo design and selection of existing genetic components to achieve a desired biological activity, as part of an integrated design-build-test cycle. To meet the emerging needs of Synthetic Biology, bioCAD tools must address the increasing prevalence of…
Biological Computer Aided Design (bioCAD) assists the de novo design and selection of existing genetic components to achieve a desired biological activity, as part of an integrated design-build-test cycle. To meet the emerging needs of Synthetic Biology, bioCAD tools must address the increasing prevalence of…
In this BioBricks Foundation Request for Comments (BBF RFC), we specify the Synthetic Biology Open Language (SBOL) Version 1.1.0 to enable the electronic exchange of information describing DNA components used in synthetic biology. We define: 1. the vocabulary, a set of preferred terms and 2. the core data model, a…
In this BioBricks Foundation Request for Comments (BBF RFC), we specify the Synthetic Biology Open Language (SBOL) Version 1.1.0 to enable the electronic exchange of information describing DNA components used in synthetic biology. We define: 1. the vocabulary, a set of preferred terms and 2. the core data model, a…
We present a workflow for the design and production of biological networks from high-level program specifications. The workflow is based on a sequence of intermediate models that incrementally translate high-level specifications into DNA samples that implement them. We identify algorithms for translating between…
Raising the level of abstraction for synthetic biology design requires solving several challenging problems, including mapping abstract designs to DNA sequences. In this paper we present the first formalism and algorithms to address this problem. The key steps of this transformation are feature matching, signal…
We present a workflow for the design and production of biological networks from high-level program specifications. The workflow is based on a sequence of intermediate models that incrementally translate high-level specifications into DNA samples that implement them. We identify algorithms for translating between…
Raising the level of abstraction for synthetic biology design requires solving several challenging problems, including mapping abstract designs to DNA sequences. In this paper we present the first formalism and algorithms to address this problem. The key steps of this transformation are feature matching, signal…
In this BioBricks Foundation Request for Comments (BBF RFC), we specify the Synthetic Biology Open Language (SBOL) Version 1.0.0 to enable the electronic exchange of information describing DNA components used in synthetic biology. We define: 1. the vocabulary, a set of preferred terms and 2. the core data…
In this BioBricks Foundation Request for Comments (BBF RFC), we specify the Synthetic Biology Open Language (SBOL) Version 1.0.0 to enable the electronic exchange of information describing DNA components used in synthetic biology. We define: 1. the vocabulary, a set of preferred terms and 2. the core data…
Background 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…
Background 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…