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A description of each command line argument and their default values |
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| Command line parameter |
Description |
Which methods use it |
Default value |
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| Filename |
NetCDF file name |
All |
None |
| Random Seed |
The random number generator's seed value. |
All |
Randomized (system dependent) |
| Epsilon (ε) |
Minimum number of molecules of both reactant & product species for approximation to a continuous Markov process |
All HyJCMSS simulation methods |
100 molecules |
| Lambda (λ) |
Minimum rate of reaction for approximation to a continuous Markov process |
All HyJCMSS simulation methods |
10 molecules/sec |
| MSR Tolerance |
Maximum relative effect of slow reactions per numerical integration of SDEs |
All HyJCMSS simulation methods |
1/ε |
| SDE Tolerance |
Maximum values of drift& diffusion error criteria |
Adaptive Methods |
1e-4 |
| SDE time step |
Maximum time step of numerical integrator |
Fixed Methods |
0.10 seconds or Save Time |
Salis et al. BMC Bioinformatics 2006 7:93 doi:10.1186/1471-2105-7-93 |
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