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SED-ML / KiSAO

Ontology of algorithms for analyzing biological models, their parameters, and their outputs
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Maximal Timestep Method #10

Closed jonrkarr closed 3 years ago

jonrkarr commented 9 years ago

From KiSAO surveymonkey:

Q3: Algorithm name (e.g. tau-leaping method):

Maximal Timestep Method Q4: Short description:

Hybrid simulation algorithm integrating Gillespie exact simulation and Gillespie tau leap. Q5: Reference (e.g. article name, DOI, PubMed id):

PMID: 14990466 Q6: Your comment:

Hybrid simulation method used to simulate systems involving reactions with propensities varying by many orders of magnitude.

Q15: Algorithm ancestor:

hybrid Q16: Is this method a hybrid one or does it use other algorithms?

yes (please specify which algorithms it uses) Gillespie direct method Gillespie tau leap

Q17: Which characteristics does it possess?

Stochastic simulation of stiff systems Q18: Which parameters does it use?

Key parameter is Maximal Timestep. If Gillespie waiting time is longer than Maximal Timestep, slow reaction is not fired and tau-leap step is executed for fast reactions. Otherwise, slow reaction is fired and tau-leap is executed with shorter time step.

Q23: Your name:

Andrzej Kierzek Q24: Your e-mail:

a.kierzek@surrey.ac.uk

Reported by: gambardella

jonrkarr commented 9 years ago

Original comment by: gambardella