This thesis describes a hierarchical stochastic simulation algorithm which has been implemented within iBioSim, a tool used to model, analyze, and visualize genetic circuits. Many biological analysis tools flatten out hierarchy before simulation, but …
This paper describes a hierarchical stochastic simulation algorithm which has been implemented within iBioSim, a tool used to model, analyze, and visualize genetic circuits. Many biological analysis tools flatten out hierarchy before simulation, but …
Recently, we have begun to witness the potential of synthetic biology, noted here in the form of bacteria and yeast that have been genetically engineered to produce biofuels, manufacture drug precursors, and even invade tumor cells. The success of …
This paper describes a hierarchical stochastic simulation algorithm which has been implemented within iBioSim, a tool used to model, analyze, and visualize genetic circuits. Many biological analysis tools flatten out hierarchy before simulation, but …
Crucial to the success of synthetic biology is the development of platforms for genetic design automation (GDA). This chapter presents the current state-of-the-art in GDA tools. This chapter also briefly describes the standards used for data …
Over the past few decades, synthetic biology has generated great interest to biologists and engineers alike. Synthetic biology combines the research of biology with the engineering principles of standards, abstraction, and automated construction with …
As the complexity of synthetic genetic circuits increases, modeling is becoming a necessary first step to inform subsequent experimental efforts. In recent years, the design automation community has developed a wealth of computational tools for …
Circuit designers are increasingly more drawn to challenges in modeling and designing biological circuits and systems. While the principles of biological organization and architecture resemble those in systems that engineers are designing, the …
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 …