Related Experiment Video
Updated: May 18, 2026

3D Modeling of Dendritic Spines with Synaptic Plasticity
Published on: May 18, 2020
SGNS2: a compartmentalized stochastic chemical kinetics simulator for dynamic cell populations
Jason Lloyd-Price1, Abhishekh Gupta, Andre S Ribeiro
1Department of Signal Processing, Tampere University of Technology, 33101 Tampere, Finland. jason.lloyd-price@tut.fi
Motivation:
Cell growth and division affect the kinetics of internal cellular processes and the phenotype diversity of cell populations. Since the effects are complex, e.g. different cellular components are partitioned differently in cell division, to account for them in silico, one needs to simulate these processes in great detail.
Results:
We present SGNS2, a simulator of chemical reaction systems according to the Stochastic Simulation Algorithm with multi-delayed reactions within hierarchical, interlinked compartments which can be created, destroyed and divided at runtime. In division, molecules are randomly segregated into the daughter cells following a specified distribution corresponding to one of several partitioning schemes, applicable on a per-molecule-type basis. We exemplify its use with six models including a stochastic model of the disposal mechanism of unwanted protein aggregates in Escherichia coli, a model of phenotypic diversity in populations with different levels of synchrony, a model of a bacteriophage's infection of a cell population and a model of prokaryotic gene expression at the nucleotide and codon levels.
Availability:
SGNS2, instructions and examples available at www.cs.tut.fi/~lloydpri/sgns2/ (open source under New BSD license).
Contact:
jason.lloyd-price@tut.fi.
Supplementary Information:
Supplementary data are available at Bioinformatics online.
Related Concept Videos
Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving
In individual population analyses, different algorithms are employed, such as Cauchy's method, which uses a...
Two-Compartment Open Model: Overview
The...
Pharmacokinetic Models: Comparison and Selection Criterion
Physiological models take a detailed approach by considering specific molecular processes. They can predict drug distribution, metabolism, and elimination changes, providing a comprehensive understanding of how drugs interact with the body.
Compartment Models: Two-Compartment Model
Compartment Models: Single-Compartment Model
Mechanistic Models: Overview of Compartment Models

