molecular biophysics

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 …

Learning Genetic Regulatory Network Connectivity from Time Series Data

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 …