Abstract
HSimulator is a multithread simulator for mass-action biochemical reaction systems placed in a well-mixed environment. HSimulator provides optimized implementation of a set of widespread state-of-the-art stochastic, deterministic, and hybrid simulation strategies including the first publicly available implementation of the Hybrid Rejection-based Stochastic Simulation Algorithm (HRSSA). HRSSA, the fastest hybrid algorithm to date, allows for an efficient simulation of the models while ensuring the exact simulation of a subset of the reaction network modeling slow reactions. Benchmarks show that HSimulator is often considerably faster than the other considered simulators. The software, running on Java v6.0 or higher, offers a simulation GUI for modeling and visually exploring biological processes and a Javadoc-documented Java library to support the development of custom applications. HSimulator is released under the COSBI Shared Source license agreement (COSBI-SSLA).
Highlights
Computational systems biology is becoming a fundamental tool of life-science research, which aims at developing models representing biological phenomena and reliable computational techniques for their simulation [1,2,3,4,5,6,7].We introduce HSimulator, a Java hybrid stochastic/ deterministic simulator for mass-action biochemical reaction systems placed in a well-mixed environment, where position and speed of molecular species are randomized and they do not affect reaction executions
Several algorithms have been introduced to decrease simulation runtime, such as the Reaction Method (NRM, [9]) and later the Rejectionbased Stochastic Simulation Algorithm (RSSA, [10]). The latter is tailored for complex biochemical reactions with timeconsuming propensity functions and it constitutes the state of the art of exact stochastic simulation
HSimulator is a cross-platform simulation software written in Java, offering a suite of state-of-the-art stochastic, deterministic, and hybrid simulation strategies for massaction well-stirred biochemical reaction systems
Summary
Computational systems biology is becoming a fundamental tool of life-science research, which aims at developing models representing biological phenomena and reliable computational techniques for their simulation [1,2,3,4,5,6,7].We introduce HSimulator, a Java hybrid stochastic/ deterministic simulator for mass-action biochemical reaction systems placed in a well-mixed environment, where position and speed of molecular species are randomized and they do not affect reaction executions. Where the species on the left of the arrow are reactants and the ones on the right are products. From the milestone work of Gillespie [8], where the Direct Method (DM) has been defined, exact stochastic simulation is the most accurate simulation approach. Several algorithms have been introduced to decrease simulation runtime, such as the Reaction Method (NRM, [9]) and later the Rejectionbased Stochastic Simulation Algorithm (RSSA, [10]). The latter is tailored for complex biochemical reactions with timeconsuming propensity functions and it constitutes the state of the art of exact stochastic simulation
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
