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 Open Language (SBOL) Visual is a graphical standard for genetic engineering. It consists of symbols representing DNA subsequences, including regulatory elements and DNA assembly features. These symbols can be used to draw …
The simulation of biological systems prior to their physical implementation can save time, money, and potentially provide insights into alternate designs. This paper presents a simulation environment which allows for a visual design process …
When designing and analyzing genetic circuits, researchers are often interested in the probability of the system reaching a given state within a certain amount of time. Usually, this involves simulating the system to produce some time series data and …
Recent experimental advances facilitate the collection of time series data that indicate which genes in a cell are expressed. This information can be used to understand the genetic regulatory network that generates the data. Typically, Bayesian …
Researchers are now developing synthetic genetic circuits to manipulate the biochemical processes within living cells. In order to model and predict the behavior of these circuits, the designer must account for numerous reactions among many chemical …
Electronic design automation (EDA) tools have facilitated the design of ever more complex integrated circuits each year. Synthetic biology would also benefit from the development of genetic design automation (GDA) tools. Existing GDA tools require …