Should additional algorithms and algorithm parameters be exposed through KISAO? - Githubissues

biosimulators / Biosimulators_tellurium

tellurium biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container

https://docs.biosimulators.org/Biosimulators_tellurium

MIT License

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Should additional algorithms and algorithm parameters be exposed through KISAO? #5

Closed jonrkarr closed 4 years ago

jonrkarr commented 4 years ago

Question for tellurium/libRoadRunner developers:

Algorithms

euler
NLEQ1: KISAO_0000568

Algorithm parameters (tellurium name: default)

CVODE
- stiff: true
- multiple_steps: false
euler
- subdivision_steps: 1
RK45
- epsilon: 1e-12 Maximum error tolerance
Gillespie
- nonnegative: false
NLEQ1, NLEQ2
- allow_presimulation: false
- presimulation_maximum_steps: 100
- presimulation_time: 100
- allow_approx: false
- approx_tolerance: 1e-6
- approx_maximum_steps: 10000
- approx_time: 10000
- broyden_method: 0
- linearity: 3

jonrkarr commented 4 years ago

Moved to tellurium repo. See https://github.com/sys-bio/tellurium/issues/485.