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 …
The iBioSim tool has been developed to facilitate the design of genetic circuits via a model-based design strategy. This paper illustrates the new features incorporated into the tool for DNA circuit design, design analysis, and design synthesis, all …
This paper presents pySBOL, a software library for computer-aided design of synthetic biological systems in the Python scripting language. This library provides an easy-to-use, object-oriented, application programming interface (API) with low barrier …
Standard representation of data is key for the reproducibility of designs in synthetic biology. The Synthetic Biology Open Language (SBOL) has already emerged as a data standard to represent information about genetic circuits, and it is based on …
As improvements in DNA synthesis technology and assembly methods make combinatorial assembly of genetic constructs increasingly accessible, methods for representing genetic constructs likewise need to improve to handle the exponential growth of …
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 …
Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. The field still faces substantial challenges, including long …
People who are engineering biological organisms often find it useful to communicate in diagrams, both about the structure of the nucleic acid sequences that they are engineering and about the functional relationships between sequence features and …