stochastic logic

Systems Biology Markup Language (SBML) Level 3 Package: Distributions, Version 1, Release 1

Biological models often contain elements that have inexact numerical values, since they are based on values that are stochastic in nature or data that contains uncertainty. The Systems Biology Markup Language (SBML) Level 3 Core specification does …

Stochastic Analysis of an Genetic Sensor

STAMINA: STochastic Approximate Model-Checker for INfinite-State Analysis

Stochastic model checking is a technique for analyzing systems that possess probabilistic characteristics. However, its scalability is limited as probabilistic models of real-world applications typically have very large or infinite state space. This …

Approximation techniques for stochastic analysis of biological systems

This book presents outstanding contributions in an exciting, new and multidisciplinary research area: the application of formal, automated reasoning techniques to analyse complex models in systems biology and systems medicine. Automated reasoning is …

Stochastic Model Checking of Genetic Circuits

Synthetic genetic circuits have a number of exciting potential applications such as cleaning up toxic waste, hunting and killing tumor cells, and producing drugs and bio-fuels more efficiently. When designing and analyzing genetic circuits, …

Hierarchical Stochastic Simulation of Genetic Circuits

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 …

Hierarchical stochastic simulation of genetic circuits

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 …

Hierarchical Stochastic Simulation Algorithm for SBML Models of Genetic Circuits

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 …

Stochastic Analysis of Synthetic Genetic Circuits

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 …

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 …