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RSSALib: a library for stochastic simulation of complex biochemical reactions.

Vo Hong Thanh¹

¹Department of Computer Science, Aalto University, Finland.

Bioinformatics (Oxford, England)

|July 3, 2020

Summary

This summary is machine-generated.

This study introduces RSSALib, a new simulation library for stochastic chemical kinetics. It accelerates the analysis of biochemical reactions with complex kinetics and time delays using a novel algorithm.

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Area of Science:

Computational Biology
Biochemistry
Systems Biology

Background:

Stochastic chemical kinetics is crucial for understanding biological processes where randomness is significant.
Many practical models in this field are analytically intractable, necessitating simulation for analysis.

Purpose of the Study:

To present RSSALib, a simulation library designed to accelerate the analysis of biochemical reactions.
To implement a novel rejection-based stochastic simulation algorithm (RSSA) and its enhancements.

Main Methods:

Development and implementation of the RSSALib simulation library.
Utilizing a rejection-based stochastic simulation algorithm (RSSA) with various improvements.
Support for complex reaction kinetics and time delays.

Main Results:

RSSALib significantly accelerates the simulation and analysis of biochemical reactions.
The library accommodates complex reaction mechanisms, including those with time delays.
Provides both programmatic (API) and graphical (GUI) interfaces for ease of use and visualization.

Conclusions:

RSSALib offers an efficient tool for researchers studying stochasticity in biological systems.
The library's features facilitate the modeling of complex biochemical reaction networks.
Freely available open-source software to advance research in computational biology.