SynBioSuite: A Tool for Improving the Workflow for Genetic Design and Modeling.

Synthetic biology research has led to the development of many software tools for designing, constructing, editing, simulating, and sharing genetic parts and circuits. Among these tools are SBOLCanvas, iBioSim, and SynBioHub, which can be used in conjunction to create a genetic circuit design following the design-build-test-learn process. However, although automation works within these tools, most of these software tools are not integrated, and the process of transferring information between them is a very manual, error-prone process.

A Comparison of Weighted Stochastic Simulation Methods for the Analysis of Genetic Circuits.

Rare events are of particular interest in synthetic biology because rare biochemical events may be catastrophic to a biological system by, for example, triggering irreversible events such as off-target drug delivery. To estimate the probability of rare events efficiently, several weighted stochastic simulation methods have been developed. Under optimal parameters and model conditions, these methods can greatly improve simulation efficiency in comparison to traditional stochastic simulation.

Stochastic Hazard Analysis of Genetic Circuits in iBioSim and STAMINA.

In synthetic biology, combinational circuits are used to program cells for various new applications like biosensors, drug delivery systems, and biofuels. Similar to asynchronous electronic circuits, some combinational genetic circuits may show unwanted switching variations () caused by multiple input changes. Depending on the biological circuit, glitches can cause irreversible effects and jeopardize the circuit's functionality.