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SED-ML / KiSAO

Ontology of algorithms for analyzing biological models, their parameters, and their outputs
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Pahle hybrid Gibson-Bruck Next Reaction method/RK-45 method #71

Closed jonrkarr closed 3 years ago

jonrkarr commented 3 years ago

name: Pahle hybrid Gibson-Bruck Next Reaction method/RK-45 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. The deterministic subnet is integrated with RK-45. The stochastic subnet is simulated by the Gibson-Bruck Next Reaction Method.

subClassOf: KISAO_0000231

seeAlso: 10.1016/j.jbiotec.2017.06.1200, 10.1007/978-1-59745-525-1_2, 10.1093/bioinformatics/btl485, 10.5555/1218112.1218421

isImplementedIn: COPASI

Reported by: jonrkarr

jonrkarr commented 3 years ago

Original comment by: jonrkarr

jonrkarr commented 3 years ago

incorporated as KISAO_0000563

Original comment by: jonrkarr