Related Experiment Video
Updated: Nov 22, 2025

Sealable Femtoliter Chamber Arrays for Cell-free Biology
Published on: March 11, 2015
Stochastic Differential Equations for Practical Simulation of Gene Circuits
Jesús Picó1, Alejandro Vignoni2, Yadira Boada2,3
1Synthetic Biology and Biosystems Control Lab, I.U. de Automática e Informática Industrial (ai2), Universitat Politècnica de Valencia, Valencia, Spain. jpico@upv.es.
Abstract:
The Chemical Langevin Equation approach allows simple stochastic simulation of gene circuits under many practical situations where the number of molecules of the species involved is not extremely low. Here, we describe methods and a computational framework to simulate a population of cells containing gene circuits of interest. These methods account for both intrinsic and extrinsic noise sources, and allow us to have both individual cell-related species and population-related ones. The protocol covers aspects related to proper description of the system and setting the software tools. It also helps to deal with the optimization of data storage and the simulation precision versus computational time issue. Finally, it also gives practical tests to assess the validity of the underlying technical assumptions.
More Related Videos
08:25Continuous Measurement of Biological Noise in Escherichia Coli Using Time-lapse Microscopy
Published on: April 27, 2021
10:44Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline
Published on: December 7, 2021
Related Concept Videos
Mutation, Gene Flow, and Genetic Drift
Transmission-Line Differential Equations
Line Section Model
A circuit representing a line section of length Δx helps in understanding the transmission line parameters. The voltage V(x) and current i(x) are measured from...
Transfer Function to State Space
In an RLC...
Current Growth And Decay In RL Circuits
Exponential Equations for Modeling Growth
State Space Representation
Consider an RLC circuit, a...