iBioSim

Dynamic Modeling of Cellular Populations within iBioSim

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 …

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 …

Modeling and Visualization of Synthetic Genetic Circuits

The iBioSim tool is being developed to facilitate the construction and simulation of synthetic genetic circuits. In this project, we have created a user interface that is similar to those used to construct schematic diagrams which are familiar to …

iBioSim: a tool for the analysis and design of genetic circuits

Representing Genetic Networks as Labeled Hybrid Petri Nets for State Space Exploration and Markov Chain Analysis

This paper presents the bachelor’s thesis of Curtis Kendall Madsen which can be broken down into the following three goals. The first goal of this project is to develop a way to convert genetic networks into logical models. Once this is done, finding …