Closed jonrkarr closed 3 years ago
seeAlso: 10.1016/j.jbiotec.2017.06.1200, 10.1007/978-1-59745-525-1_2, 10.1093/bioinformatics/btl485, 10.5555/1218112.1218421
Original comment by: jonrkarr
Title should be "New algorithm for Pahle hybrid Gibson-Bruck Next Reaction method/Runge-Kutta method"
Original comment by: jonrkarr
Original comment by: jonrkarr
incorporated as KISAO_0000561
Original comment by: jonrkarr
name: Pahle hybrid Gibson-Bruck Next Reaction method/Runge-Kutta method
definition: Combines a deterministic numerical integration of ODEs with a stochastic simulation algorithm. The whole biochemical network is partitioned into a deterministic and a stochastic subnet internally. The deterministic subnet contains all reactions in which only species with high particle numbers take part. All reactions with at least one low-numbered species are in the stochastic subnet. The partitioning of the biochemical network can change dynamically during the simulation. The reaction probabilities of the stochastic subnet are approximated as constant during one stochastic step. A 4th-order Runge-Kutta method is used to numerically integrate the deterministic part of the system. The stochastic subnet is simulated by the Gibson-Bruck Next Reaction Method.
subClassOf: KISAO_0000231
isImplementedIn: COPASI
Reported by: jonrkarr