analytical models

An Improvement in Partial Order Reduction Using Behavioral Analysis

Efficacy of partial order reduction in reducing state space relies on adequate extraction of the independence relation among possible behaviors. However, traditional approaches by statically analyzing system model structures are often not able to …

Design and Test of Genetic Circuits Using tt iBioSim

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 …

Utilizing stochastic model checking to analyze genetic circuits

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 …

iSSA: An incremental stochastic simulation algorithm for genetic circuits

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 …