This stochastic simulation method implements Gillespie’s direct method as described in Gillespie76.
Support for discrete events has been added to this method.
Max Internal Steps
Specifies the maximum number of internal steps the integrator may take
before the next reporting time. Must be a positive integer. Default:
1000000.
Use Random Seed
Can be 0 or 1. If set to 0 (default), a random seed is chosen
before each simulation run, so the results differ between runs. If set
to 1, the specified random seed is used, and runs with the same seed
will produce identical results.
Random Seed
An unsigned integer used as the random seed if “Use Random Seed” is set
to 1. Default value is 1.
This stochastic simulation method uses the algorithm developed by Gibson and Bruck [Gibson00]. For each reaction, a tentative stochastic reaction time is calculated, and the reaction with the shortest reaction time is executed. All reactions are organized in a priority queue to efficiently find the fastest reaction. Additionally, a dependency graph is used so that only those reaction times affected by the executed reaction need to be recalculated at each step.
Note: This simulation method requires all reactions to be irreversible. COPASI provides a tool that can convert all reversible reactions to irreversible ones. The algorithm operates on discrete particle numbers rather than concentrations, and particle numbers in the system must not exceed $2^{64}-1$ (approximately $1.84 \cdot 10^{19}$).
The current implementation of the Next-Reaction Method is inefficient for models containing assignment rules, leading to increased calculation times.
There are also some restrictions with global quantities:
Max Internal Steps
Specifies the maximum number of internal steps the integrator may take before
the next reporting time. Must be a positive integer. Default: 1000000.
Subtype
This parameter is ignored in the current version of COPASI.
Use Random Seed
Can be 0 or 1. If set to 0 (default), a random seed is chosen before
each simulation run, so the results differ between runs. If set to 1, the
specified random seed is used, and runs with the same seed will produce
identical results.
Random Seed
An unsigned integer used as the random seed if “Use Random Seed” is set to 1.
Default value is 1.
This stochastic simulation method implements the τ-leap method as described in Gillespie01.
Max Internal Steps
Specifies the maximum number of internal steps the integrator may take
before the next reporting time. Must be a positive integer. Default:
10000.
Use Random Seed
Can be 0 or 1. If set to 0 (default), a random seed is chosen
before each simulation run, so the results differ between runs. If set
to 1, the specified random seed is used, and runs with the same seed
will produce identical results.
Random Seed
An unsigned integer used as the random seed if “Use Random Seed” is set
to 1. Default value is 1.
This stochastic simulation method implements the Adaptive SSA/τ-leap method as described in Cao07.
Max Internal Steps
Specifies the maximum number of internal steps the integrator may take
before the next reporting time. Must be a positive integer. Default:
10000000.
Use Random Seed
Can be 0 or 1. If set to 0 (default), a random seed is chosen
before each simulation run, so the results differ between runs. If set
to 1, the specified random seed is used, and runs with the same seed
will produce identical results.
Random Seed
An unsigned integer used as the random seed if “Use Random Seed” is set
to 1. Default value is 1.
