pymetadata 0.5.0__py3-none-any.whl

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  1. pymetadata/__init__.py +14 -0
  2. pymetadata/cache.py +52 -0
  3. pymetadata/chebi.py +92 -0
  4. pymetadata/console.py +18 -0
  5. pymetadata/core/__init__.py +1 -0
  6. pymetadata/core/annotation.py +396 -0
  7. pymetadata/core/creator.py +46 -0
  8. pymetadata/core/synonym.py +12 -0
  9. pymetadata/core/xref.py +66 -0
  10. pymetadata/examples/__init__.py +1 -0
  11. pymetadata/examples/cache_path_example.py +15 -0
  12. pymetadata/examples/omex_example.py +46 -0
  13. pymetadata/examples/results/test_from_files.omex +0 -0
  14. pymetadata/examples/results/test_from_omex.omex +0 -0
  15. pymetadata/examples/results/testomex/README.md +3 -0
  16. pymetadata/examples/results/testomex/manifest.xml +9 -0
  17. pymetadata/examples/results/testomex/models/omex_comp.xml +174 -0
  18. pymetadata/examples/results/testomex/models/omex_comp_flat.xml +215 -0
  19. pymetadata/examples/results/testomex/models/omex_minimal.xml +99 -0
  20. pymetadata/examples/test.omex +0 -0
  21. pymetadata/identifiers/__init__.py +1 -0
  22. pymetadata/identifiers/miriam.py +43 -0
  23. pymetadata/identifiers/registry.py +397 -0
  24. pymetadata/log.py +29 -0
  25. pymetadata/metadata/__init__.py +6 -0
  26. pymetadata/metadata/eco.py +15918 -0
  27. pymetadata/metadata/kisao.py +2731 -0
  28. pymetadata/metadata/sbo.py +3754 -0
  29. pymetadata/omex.py +771 -0
  30. pymetadata/omex_v2.py +30 -0
  31. pymetadata/ontologies/__init__.py +1 -0
  32. pymetadata/ontologies/ols.py +214 -0
  33. pymetadata/ontologies/ontology.py +312 -0
  34. pymetadata/py.typed +0 -0
  35. pymetadata/resources/chebi_webservice_wsdl.xml +509 -0
  36. pymetadata/resources/ontologies/README.md +4 -0
  37. pymetadata/resources/templates/ontology_enum.pytemplate +61 -0
  38. pymetadata/unichem.py +190 -0
  39. pymetadata-0.5.0.dist-info/METADATA +154 -0
  40. pymetadata-0.5.0.dist-info/RECORD +42 -0
  41. pymetadata-0.5.0.dist-info/WHEEL +4 -0
  42. pymetadata-0.5.0.dist-info/licenses/LICENSE +7 -0
pymetadata/metadata/kisao.py ADDED
@@ -0,0 +1,2731 @@
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+ """KISAO ontology."""
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+
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+ from enum import Enum
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+ from typing import Optional, Union
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+
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+
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+ KISAOType = Union[str, "KISAO"]
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+
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+ _terms = {
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+ "KISAO_0000000": "modelling and simulation algorithm",
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+ "KISAO_0000003": "weighted stochastic simulation algorithm",
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+ "KISAO_0000015": "Gillespie first reaction algorithm",
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+ "KISAO_0000017": "multi-state agent-based simulation method",
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+ "KISAO_0000019": "CVODE",
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+ "KISAO_0000020": "PVODE",
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+ "KISAO_0000021": "StochSim nearest-neighbour algorithm",
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+ "KISAO_0000022": "Elf and Ehrenberg method",
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+ "KISAO_0000027": "Gibson-Bruck next reaction algorithm",
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+ "KISAO_0000028": "slow-scale stochastic simulation algorithm",
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+ "KISAO_0000029": "Gillespie direct algorithm",
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+ "KISAO_0000030": "Euler forward method",
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+ "KISAO_0000031": "Euler backward method",
23
+ "KISAO_0000032": "explicit fourth-order Runge-Kutta method",
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+ "KISAO_0000033": "Rosenbrock method",
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+ "KISAO_0000038": "sorting stochastic simulation algorithm",
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+ "KISAO_0000039": "tau-leaping method",
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+ "KISAO_0000040": "Poisson tau-leaping method",
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+ "KISAO_0000045": "implicit tau-leaping method",
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+ "KISAO_0000046": "trapezoidal tau-leaping method",
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+ "KISAO_0000048": "adaptive explicit-implicit tau-leaping method",
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+ "KISAO_0000051": "Bortz-Kalos-Lebowitz algorithm",
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+ "KISAO_0000056": "Smoluchowski equation based method",
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+ "KISAO_0000057": "Brownian diffusion Smoluchowski method",
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+ "KISAO_0000058": "Greens function reaction dynamics",
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+ "KISAO_0000064": "Runge-Kutta based method",
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+ "KISAO_0000068": "deterministic cellular automata update algorithm",
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+ "KISAO_0000071": "LSODE",
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+ "KISAO_0000074": "binomial tau-leaping method",
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+ "KISAO_0000075": "Gillespie multi-particle method",
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+ "KISAO_0000076": "Stundzia and Lumsden method",
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+ "KISAO_0000081": "estimated midpoint tau-leaping method",
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+ "KISAO_0000082": "k-alpha leaping method",
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+ "KISAO_0000084": "nonnegative Poisson tau-leaping method",
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+ "KISAO_0000086": "Fehlberg method",
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+ "KISAO_0000087": "Dormand-Prince method",
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+ "KISAO_0000088": "LSODA",
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+ "KISAO_0000089": "LSODAR",
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+ "KISAO_0000090": "LSODI",
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+ "KISAO_0000091": "LSODIS",
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+ "KISAO_0000093": "LSODPK",
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+ "KISAO_0000094": "Livermore solver",
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+ "KISAO_0000095": "sub-volume stochastic reaction-diffusion algorithm",
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+ "KISAO_0000097": "modelling and simulation algorithm characteristic",
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+ "KISAO_0000098": "type of variable",
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+ "KISAO_0000099": "type of system behaviour",
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+ "KISAO_0000100": "type of progression time step",
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+ "KISAO_0000102": "spatial description",
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+ "KISAO_0000103": "deterministic system behaviour",
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+ "KISAO_0000104": "stochastic system behaviour",
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+ "KISAO_0000105": "discrete variable",
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+ "KISAO_0000106": "continuous variable",
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+ "KISAO_0000107": "progression with adaptive time step",
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+ "KISAO_0000108": "progression with fixed time step",
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+ "KISAO_0000201": "modelling and simulation algorithm parameter",
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+ "KISAO_0000203": "particle number lower limit",
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+ "KISAO_0000204": "particle number upper limit",
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+ "KISAO_0000205": "partitioning interval",
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+ "KISAO_0000209": "relative tolerance",
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+ "KISAO_0000211": "absolute tolerance",
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+ "KISAO_0000216": "use reduced model",
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+ "KISAO_0000219": "maximum Adams order",
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+ "KISAO_0000220": "maximum BDF order",
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+ "KISAO_0000223": "number of history bins",
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+ "KISAO_0000228": "tau-leaping epsilon",
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+ "KISAO_0000230": "minimum reactions per leap",
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+ "KISAO_0000231": "Pahle hybrid method",
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+ "KISAO_0000232": "LSOIBT",
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+ "KISAO_0000233": "LSODES",
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+ "KISAO_0000234": "LSODKR",
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+ "KISAO_0000235": "type of solution",
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+ "KISAO_0000236": "exact solution",
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+ "KISAO_0000237": "approximate solution",
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+ "KISAO_0000238": "type of method",
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+ "KISAO_0000239": "explicit method type",
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+ "KISAO_0000240": "implicit method type",
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+ "KISAO_0000241": "Gillespie-like method",
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+ "KISAO_0000242": "error control parameter",
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+ "KISAO_0000243": "method switching control parameter",
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+ "KISAO_0000244": "granularity control parameter",
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+ "KISAO_0000245": "has characteristic",
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+ "KISAO_0000246": "is hybrid of",
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+ "KISAO_0000248": "tau-leaping delta",
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+ "KISAO_0000249": "critical firing threshold",
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+ "KISAO_0000250": "is parameter of",
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+ "KISAO_0000252": "partitioning control parameter",
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+ "KISAO_0000253": "coarse-graining factor",
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+ "KISAO_0000254": "Brownian diffusion accuracy",
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+ "KISAO_0000255": "molecules per virtual box",
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+ "KISAO_0000256": "virtual box side length",
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+ "KISAO_0000257": "surface-bound epsilon",
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+ "KISAO_0000258": "neighbour distance",
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+ "KISAO_0000259": "has parameter",
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+ "KISAO_0000260": "virtual box size",
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+ "KISAO_0000261": "Euler method",
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+ "KISAO_0000263": "NFSim agent-based simulation method",
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+ "KISAO_0000264": "cellular automata update method",
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+ "KISAO_0000268": "is characteristic of",
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+ "KISAO_0000273": "hard-particle molecular dynamics",
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+ "KISAO_0000274": "first-passage Monte Carlo algorithm",
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+ "KISAO_0000276": "Gill method",
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+ "KISAO_0000278": "Metropolis Monte Carlo algorithm",
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+ "KISAO_0000279": "Adams-Bashforth method",
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+ "KISAO_0000280": "Adams-Moulton method",
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+ "KISAO_0000281": "multistep method",
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+ "KISAO_0000282": "KINSOL",
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+ "KISAO_0000283": "IDA",
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+ "KISAO_0000285": "finite volume method",
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+ "KISAO_0000286": "Euler-Maruyama method",
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+ "KISAO_0000287": "Milstein method",
120
+ "KISAO_0000288": "backward differentiation formula",
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+ "KISAO_0000289": "Adams method",
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+ "KISAO_0000290": "Merson method",
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+ "KISAO_0000296": "Hammer-Hollingsworth method",
124
+ "KISAO_0000297": "Lobatto method",
125
+ "KISAO_0000299": "Butcher-Kuntzmann method",
126
+ "KISAO_0000301": "Heun method",
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+ "KISAO_0000302": "embedded Runge-Kutta method",
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+ "KISAO_0000303": "Zonneveld method",
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+ "KISAO_0000304": "Radau method",
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+ "KISAO_0000305": "Verner method",
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+ "KISAO_0000306": "Lagrangian sliding fluid element algorithm",
132
+ "KISAO_0000307": "finite difference method",
133
+ "KISAO_0000308": "MacCormack method",
134
+ "KISAO_0000309": "Crank-Nicolson method",
135
+ "KISAO_0000310": "method of lines",
136
+ "KISAO_0000311": "type of domain geometry handling",
137
+ "KISAO_0000314": "S-System power-law canonical differential equations solver",
138
+ "KISAO_0000315": "lattice gas automata",
139
+ "KISAO_0000316": "enhanced Greens function reaction dynamics",
140
+ "KISAO_0000317": "E-Cell multi-algorithm simulation method",
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+ "KISAO_0000318": "Gauss-Legendre Runge-Kutta method",
142
+ "KISAO_0000319": "Monte Carlo method",
143
+ "KISAO_0000320": "BioRica hybrid method",
144
+ "KISAO_0000321": "Cash-Karp method",
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+ "KISAO_0000322": "hybridity",
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+ "KISAO_0000323": "equation-free probabilistic steady-state approximation",
147
+ "KISAO_0000324": "nested stochastic simulation algorithm",
148
+ "KISAO_0000325": "minimum fast/discrete reaction occurrences number",
149
+ "KISAO_0000326": "number of samples",
150
+ "KISAO_0000327": "maximum discrete number",
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+ "KISAO_0000328": "minimum fast rate",
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+ "KISAO_0000329": "constant-time kinetic Monte Carlo algorithm",
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+ "KISAO_0000330": "R-leaping algorithm",
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+ "KISAO_0000331": "exact R-leaping algorithm",
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+ "KISAO_0000332": "ER-leap initial leap",
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+ "KISAO_0000333": "accelerated stochastic simulation algorithm",
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+ "KISAO_0000334": "multiparticle lattice gas automata",
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+ "KISAO_0000335": "generalized stochastic simulation algorithm",
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+ "KISAO_0000336": "D-leaping method",
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+ "KISAO_0000337": "finite element method",
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+ "KISAO_0000338": "h-version of the finite element method",
162
+ "KISAO_0000339": "p-version of the finite element method",
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+ "KISAO_0000340": "h-p version of the finite element method",
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+ "KISAO_0000341": "mixed finite element method",
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+ "KISAO_0000342": "level set method",
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+ "KISAO_0000343": "generalized finite element method",
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+ "KISAO_0000345": "h-p cloud method",
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+ "KISAO_0000346": "mesh-based geometry handling",
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+ "KISAO_0000347": "meshless geometry handling",
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+ "KISAO_0000348": "extended finite element method",
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+ "KISAO_0000349": "method of finite spheres",
172
+ "KISAO_0000350": "probability-weighted dynamic Monte Carlo method",
173
+ "KISAO_0000351": "multinomial tau-leaping method",
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+ "KISAO_0000352": "hybrid method",
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+ "KISAO_0000353": "generalized minimal residual algorithm",
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+ "KISAO_0000354": "Krylov subspace projection method",
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+ "KISAO_0000355": "DASPK",
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+ "KISAO_0000356": "DASSL",
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+ "KISAO_0000357": "conjugate gradient method",
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+ "KISAO_0000358": "biconjugate gradient method",
181
+ "KISAO_0000359": "is similar to",
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+ "KISAO_0000360": "uses",
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+ "KISAO_0000361": "is generalization of",
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+ "KISAO_0000362": "implicit-state Doob-Gillespie algorithm",
185
+ "KISAO_0000363": "rule-based simulation method",
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+ "KISAO_0000364": "Adams predictor-corrector method",
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+ "KISAO_0000365": "NDSolve method",
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+ "KISAO_0000366": "symplecticness",
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+ "KISAO_0000367": "partitioned Runge-Kutta method",
190
+ "KISAO_0000369": "partial differential equation discretization method",
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+ "KISAO_0000370": "type of problem",
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+ "KISAO_0000371": "stochastic differential equation problem",
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+ "KISAO_0000372": "partial differential equation problem",
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+ "KISAO_0000373": "differential-algebraic equation problem",
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+ "KISAO_0000374": "ordinary differential equation problem",
196
+ "KISAO_0000375": "delay differential equation problem",
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+ "KISAO_0000376": "linearity of equation",
198
+ "KISAO_0000377": "one-step method",
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+ "KISAO_0000378": "implicit midpoint rule",
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+ "KISAO_0000379": "Bulirsch-Stoer algorithm",
201
+ "KISAO_0000380": "Richardson extrapolation based method",
202
+ "KISAO_0000381": "midpoint method",
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+ "KISAO_0000382": "modified midpoint method",
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+ "KISAO_0000383": "Bader-Deuflhard method",
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+ "KISAO_0000384": "semi-implicit midpoint rule",
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+ "KISAO_0000386": "scaled preconditioned generalized minimal residual method",
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+ "KISAO_0000388": "minimal residual method",
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+ "KISAO_0000389": "quasi-minimal residual method",
209
+ "KISAO_0000392": "biconjugate gradient stabilized method",
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+ "KISAO_0000393": "ingenious conjugate gradients-squared method",
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+ "KISAO_0000394": "quasi-minimal residual variant of biconjugate gradient stabilized method",
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+ "KISAO_0000395": "improved biconjugate gradient method",
213
+ "KISAO_0000396": "transpose-free quasi-minimal residual algorithm",
214
+ "KISAO_0000397": "preconditioning technique",
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+ "KISAO_0000398": "iterative method for solving a system of linear equations",
216
+ "KISAO_0000399": "is used by",
217
+ "KISAO_0000403": "homogeneousness of equation",
218
+ "KISAO_0000404": "symmetricity of matrix",
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+ "KISAO_0000405": "type of differential equation",
220
+ "KISAO_0000407": "steady state root-finding method",
221
+ "KISAO_0000408": "Newton-type method",
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+ "KISAO_0000409": "ordinary Newton method",
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+ "KISAO_0000410": "simplified Newton method",
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+ "KISAO_0000411": "Newton-like method",
225
+ "KISAO_0000412": "inexact Newton method",
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+ "KISAO_0000413": "exact Newton method",
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+ "KISAO_0000415": "maximum number of steps",
228
+ "KISAO_0000416": "partial least squares regression method",
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+ "KISAO_0000417": "hierarchical cluster-based partial least squares regression method",
230
+ "KISAO_0000418": "N-way partial least squares regression method",
231
+ "KISAO_0000419": "metamodelling method",
232
+ "KISAO_0000420": "number of partial least squares components",
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+ "KISAO_0000421": "type of validation",
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+ "KISAO_0000422": "number of N-way partial least squares regression factors",
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+ "KISAO_0000423": "partial least squares regression-like method",
236
+ "KISAO_0000424": "mean-centring of variables",
237
+ "KISAO_0000425": "standardising of variables",
238
+ "KISAO_0000427": "number of clusters",
239
+ "KISAO_0000428": "matrix for clusterization",
240
+ "KISAO_0000429": "clusterization parameter",
241
+ "KISAO_0000430": "variables preprocessing parameter",
242
+ "KISAO_0000432": "IDA-like method",
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+ "KISAO_0000433": "CVODE-like method",
244
+ "KISAO_0000434": "Higham-Hall method",
245
+ "KISAO_0000435": "embedded Runge-Kutta 5(4) method",
246
+ "KISAO_0000436": "Dormand-Prince 8(5,3) method",
247
+ "KISAO_0000437": "flux balance analysis",
248
+ "KISAO_0000447": "COAST",
249
+ "KISAO_0000448": "logical model simulation method",
250
+ "KISAO_0000449": "synchronous logical model simulation method",
251
+ "KISAO_0000450": "asynchronous logical model simulation method",
252
+ "KISAO_0000451": "type of updating policy",
253
+ "KISAO_0000452": "random updating policy",
254
+ "KISAO_0000453": "ordered updating policy",
255
+ "KISAO_0000454": "constant updating policy",
256
+ "KISAO_0000455": "prioritized updating policy",
257
+ "KISAO_0000467": "maximum step size",
258
+ "KISAO_0000468": "maximal timestep method",
259
+ "KISAO_0000469": "maximal timestep",
260
+ "KISAO_0000470": "optimization algorithm",
261
+ "KISAO_0000471": "local optimization algorithm",
262
+ "KISAO_0000472": "global optimization algorithm",
263
+ "KISAO_0000473": "Bayesian inference algorithm",
264
+ "KISAO_0000475": "integration method",
265
+ "KISAO_0000476": "iteration type",
266
+ "KISAO_0000477": "linear solver",
267
+ "KISAO_0000478": "preconditioner",
268
+ "KISAO_0000479": "upper half-bandwidth",
269
+ "KISAO_0000480": "lower half-bandwidth",
270
+ "KISAO_0000481": "interpolate solution",
271
+ "KISAO_0000482": "half-bandwith parameter",
272
+ "KISAO_0000483": "step size",
273
+ "KISAO_0000484": "maximum order",
274
+ "KISAO_0000485": "minimum step size",
275
+ "KISAO_0000486": "maximum iterations",
276
+ "KISAO_0000487": "minimum damping",
277
+ "KISAO_0000488": "seed",
278
+ "KISAO_0000491": "discrete event simulation algorithm",
279
+ "KISAO_0000492": "asynchronous updating policy",
280
+ "KISAO_0000493": "synchronous updating policy",
281
+ "KISAO_0000494": "fully asynchronous updating policy",
282
+ "KISAO_0000495": "random asynchronous updating policy",
283
+ "KISAO_0000496": "CVODES",
284
+ "KISAO_0000497": "KLU",
285
+ "KISAO_0000498": "number of runs",
286
+ "KISAO_0000499": "dynamic flux balance analysis",
287
+ "KISAO_0000500": "SOA-DFBA",
288
+ "KISAO_0000501": "DOA-DFBA",
289
+ "KISAO_0000502": "DA-DFBA",
290
+ "KISAO_0000503": "simulated annealing",
291
+ "KISAO_0000504": "random search",
292
+ "KISAO_0000505": "particle swarm",
293
+ "KISAO_0000506": "genetic algorithm",
294
+ "KISAO_0000507": "genetic algorithm SR",
295
+ "KISAO_0000508": "evolutionary programming",
296
+ "KISAO_0000509": "evolutionary strategy",
297
+ "KISAO_0000510": "truncated Newton",
298
+ "KISAO_0000511": "steepest descent",
299
+ "KISAO_0000512": "praxis",
300
+ "KISAO_0000513": "NL2SOL",
301
+ "KISAO_0000514": "Nelder-Mead",
302
+ "KISAO_0000515": "Levenberg-Marquardt",
303
+ "KISAO_0000516": "Hooke&Jeeves",
304
+ "KISAO_0000517": "number of generations",
305
+ "KISAO_0000518": "evolutionary algorithm parameter",
306
+ "KISAO_0000519": "population size",
307
+ "KISAO_0000520": "evolutionary algorithm",
308
+ "KISAO_0000521": "simulated annealing parameter",
309
+ "KISAO_0000522": "start temperature",
310
+ "KISAO_0000523": "cooling factor",
311
+ "KISAO_0000524": "partitioned leaping method",
312
+ "KISAO_0000525": "stop condition",
313
+ "KISAO_0000526": "flux variability analysis",
314
+ "KISAO_0000527": "geometric flux balance analysis",
315
+ "KISAO_0000528": "parsimonious enzyme usage flux balance analysis (minimum sum of absolute fluxes)",
316
+ "KISAO_0000529": "parallelism",
317
+ "KISAO_0000531": "fraction of optimum",
318
+ "KISAO_0000532": "loopless",
319
+ "KISAO_0000533": "pFBA factor",
320
+ "KISAO_0000534": "reactions",
321
+ "KISAO_0000535": "VODE",
322
+ "KISAO_0000536": "ZVODE",
323
+ "KISAO_0000537": "explicit Runge-Kutta method of order 3(2)",
324
+ "KISAO_0000538": "safety factor on new step selection",
325
+ "KISAO_0000539": "minimum factor to change step size by",
326
+ "KISAO_0000540": "maximum factor to change step size by",
327
+ "KISAO_0000541": "beta parameter for stabilized step size control",
328
+ "KISAO_0000542": "correction step should use internally generated full Jacobian",
329
+ "KISAO_0000543": "stability limit detection flag",
330
+ "KISAO_0000544": "IDAS",
331
+ "KISAO_0000545": "include sensitivity variables in error control mechanism",
332
+ "KISAO_0000546": "convex optimization algorithm",
333
+ "KISAO_0000547": "linear programming",
334
+ "KISAO_0000548": "quadratic programming",
335
+ "KISAO_0000549": "non-linear programming",
336
+ "KISAO_0000550": "simplex method",
337
+ "KISAO_0000551": "primal-dual interior point method",
338
+ "KISAO_0000552": "optimization method",
339
+ "KISAO_0000553": "optimization solver",
340
+ "KISAO_0000554": "parsimonius flux balance analysis (minimum number of active fluxes)",
341
+ "KISAO_0000555": "absolute quadrature tolerance",
342
+ "KISAO_0000556": "relative quadrature tolerance",
343
+ "KISAO_0000557": "absolute steady-state tolerance",
344
+ "KISAO_0000558": "relative steady-state tolerance",
345
+ "KISAO_0000559": "initial step size",
346
+ "KISAO_0000560": "LSODA/LSODAR hybrid method",
347
+ "KISAO_0000561": "Pahle hybrid Gibson-Bruck Next Reaction method/Runge-Kutta method",
348
+ "KISAO_0000562": "Pahle hybrid Gibson-Bruck Next Reaction method/LSODA method",
349
+ "KISAO_0000563": "Pahle hybrid Gibson-Bruck Next Reaction method/RK-45 method",
350
+ "KISAO_0000564": "stochastic Runge-Kutta method",
351
+ "KISAO_0000565": "absolute tolerance for root finding",
352
+ "KISAO_0000566": "stochastic second order Runge-Kutta method",
353
+ "KISAO_0000567": "force physical correctness",
354
+ "KISAO_0000568": "NLEQ1",
355
+ "KISAO_0000569": "NLEQ2",
356
+ "KISAO_0000570": "auto reduce tolerances",
357
+ "KISAO_0000571": "absolute tolerance adjustment factor",
358
+ "KISAO_0000572": "level of superimposed noise",
359
+ "KISAO_0000573": "probabilistic logical model simulation method",
360
+ "KISAO_0000574": "species transition probabilities",
361
+ "KISAO_0000575": "hybrid tau-leaping method",
362
+ "KISAO_0000576": "quadratic MOMA",
363
+ "KISAO_0000577": "flux minimization weight",
364
+ "KISAO_0000578": "nested algorithm",
365
+ "KISAO_0000579": "linear MOMA",
366
+ "KISAO_0000580": "ROOM",
367
+ "KISAO_0000581": "BKMC",
368
+ "KISAO_0000582": "Spatiocyte method",
369
+ "KISAO_0000583": "minimum order",
370
+ "KISAO_0000584": "initial order",
371
+ "KISAO_0000585": "TOMS731",
372
+ "KISAO_0000586": "Gibson-Bruck next reaction algorithm with indexed priority queue",
373
+ "KISAO_0000587": "IMEX",
374
+ "KISAO_0000588": "flux sampling",
375
+ "KISAO_0000589": "ACB flux sampling method",
376
+ "KISAO_0000590": "ACHR flux sampling method",
377
+ "KISAO_0000591": "mdFBA",
378
+ "KISAO_0000592": "dynamic rFBA",
379
+ "KISAO_0000593": "MOMA",
380
+ "KISAO_0000594": "order",
381
+ "KISAO_0000595": "rFBA",
382
+ "KISAO_0000596": "srFBA",
383
+ "KISAO_0000597": "tolerance",
384
+ "KISAO_0000598": "hybrid Gibson - Milstein method",
385
+ "KISAO_0000599": "hybrid Gibson - Euler-Maruyama method",
386
+ "KISAO_0000600": "hybrid adaptive Gibson - Milstein method",
387
+ "KISAO_0000601": "number of trials",
388
+ "KISAO_0000602": "minimum species threshold for continuous approximation",
389
+ "KISAO_0000603": "minimum reaction rate for continuous approximation",
390
+ "KISAO_0000604": "MSR tolerance",
391
+ "KISAO_0000605": "SDE tolerance",
392
+ "KISAO_0000606": "hierarchical stochastic simulation algorithm",
393
+ "KISAO_0000607": "hierarchical Fehlberg method",
394
+ "KISAO_0000608": "hierarchical flux balance analysis",
395
+ "KISAO_0000609": "embedded Runge-Kutta Prince-Dormand (8,9) method",
396
+ "KISAO_0000610": "composite-rejection stochastic simulation algorithm",
397
+ "KISAO_0000611": "incremental stochastic simulation algorithm",
398
+ "KISAO_0000612": "implicit 4th order Runge-Kutta method at Gaussian points",
399
+ "KISAO_0000613": "stochastic simulation algorithm with normally-distributed next reaction times",
400
+ "KISAO_0000614": "implementation",
401
+ "KISAO_0000615": "fully-implicit regular grid finite volume method with a variable time step",
402
+ "KISAO_0000616": "semi-implicit regular grid finite volume method with a fixed time step",
403
+ "KISAO_0000617": "IDA-CVODE hybrid method",
404
+ "KISAO_0000618": "bunker",
405
+ "KISAO_0000619": "emc-sim",
406
+ "KISAO_0000620": "parsimonius flux balance analysis",
407
+ "KISAO_0000621": "stochastic simulation leaping method",
408
+ "KISAO_0000622": "flux balance method",
409
+ "KISAO_0000623": "flux balance problem",
410
+ "KISAO_0000624": "method for solving a system of linear equations",
411
+ "KISAO_0000625": "dense direct solver",
412
+ "KISAO_0000626": "band direct solver",
413
+ "KISAO_0000627": "diagonal approximate Jacobian solver",
414
+ "KISAO_0000628": "modelling and simulation algorithm parameter value",
415
+ "KISAO_0000629": "null",
416
+ "KISAO_0000630": "general steady state method",
417
+ "KISAO_0000631": "iterative root-finding method",
418
+ "KISAO_0000632": "functional iteration root-finding method",
419
+ "KISAO_0000633": "computational function",
420
+ "KISAO_0000634": "scaled property",
421
+ "KISAO_0000635": "unscaled property",
422
+ "KISAO_0000636": "primary property",
423
+ "KISAO_0000637": "derived property",
424
+ "KISAO_0000638": "level",
425
+ "KISAO_0000639": "flux",
426
+ "KISAO_0000640": "lower bound",
427
+ "KISAO_0000641": "bound",
428
+ "KISAO_0000642": "minimum flux",
429
+ "KISAO_0000643": "upper bound",
430
+ "KISAO_0000644": "maximum flux",
431
+ "KISAO_0000645": "objective value",
432
+ "KISAO_0000646": "propensity",
433
+ "KISAO_0000647": "derivative",
434
+ "KISAO_0000648": "step",
435
+ "KISAO_0000649": "shadow price",
436
+ "KISAO_0000650": "sensitivity",
437
+ "KISAO_0000651": "reduced costs",
438
+ "KISAO_0000652": "concentration rate",
439
+ "KISAO_0000653": "particle number rate",
440
+ "KISAO_0000654": "amount rate",
441
+ "KISAO_0000655": "rate",
442
+ "KISAO_0000656": "use adaptive time steps",
443
+ "KISAO_0000657": "sequential logical simulation method",
444
+ "KISAO_0000658": "logical model analysis method",
445
+ "KISAO_0000659": "Naldi MDD logical model stable state search method",
446
+ "KISAO_0000660": "logical model stable state search method",
447
+ "KISAO_0000661": "logical model trap space identification method",
448
+ "KISAO_0000662": "Klarner ASP logical model trap space identification method",
449
+ "KISAO_0000663": "BDD logical model trap space identification method",
450
+ "KISAO_0000664": "Second order backward implicit product Euler scheme",
451
+ "KISAO_0000665": "maximum number of iterations for root finding",
452
+ "KISAO_0000666": "Jacobian epsilon",
453
+ "KISAO_0000667": "memory size",
454
+ "KISAO_0000668": "Numerical Recipes in C 'stiff' Rosenbrock method",
455
+ "KISAO_0000669": "Resource Balance Analysis",
456
+ "KISAO_0000670": "use multiple steps",
457
+ "KISAO_0000671": "use stiff method",
458
+ "KISAO_0000672": "Numerical Recipes in C 'quality-controlled Runge-Kutta' method",
459
+ "KISAO_0000673": "skip reactions that produce negative species amounts",
460
+ "KISAO_0000674": "presimulate",
461
+ "KISAO_0000675": "Broyden method",
462
+ "KISAO_0000676": "degree of linearity",
463
+ "KISAO_0000677": "maximum number of steps for presimulation",
464
+ "KISAO_0000678": "maximum number of steps for approximation",
465
+ "KISAO_0000679": "maximum time for approximation",
466
+ "KISAO_0000680": "duration",
467
+ "KISAO_0000681": "maximum time",
468
+ "KISAO_0000682": "allow approximation",
469
+ "KISAO_0000683": "relative tolerance for approximation",
470
+ "KISAO_0000684": "number of steps per output",
471
+ "KISAO_0000685": "biological state optimization method",
472
+ "KISAO_0000686": "Enzyme Cost Minimization",
473
+ "KISAO_0000687": "Max-min Driving Force method",
474
+ "KISAO_0000688": "type of system described",
475
+ "KISAO_0000689": "mathematical system",
476
+ "KISAO_0000690": "biological system",
477
+ "KISAO_0000691": "metabolic system",
478
+ "KISAO_0000692": "cellular system",
479
+ "KISAO_0000693": "biochemical system",
480
+ "KISAO_0000694": "ODE solver",
481
+ "KISAO_0000695": "parameters for",
482
+ "KISAO_0000696": "steady state root-finding problem",
483
+ "KISAO_0000697": "SDE solver",
484
+ "KISAO_0000698": "particle coordinates",
485
+ "KISAO_0000699": "DAE Solver",
486
+ "KISAO_0000800": "systems property",
487
+ "KISAO_0000801": "concentration control coefficient matrix (unscaled)",
488
+ "KISAO_0000802": "control coefficient (scaled)",
489
+ "KISAO_0000803": "control coefficient (unscaled)",
490
+ "KISAO_0000804": "elasticity matrix (unscaled)",
491
+ "KISAO_0000805": "elasticity coefficient (unscaled)",
492
+ "KISAO_0000806": "elasticity matrix (scaled)",
493
+ "KISAO_0000807": "elasticity coefficient (scaled)",
494
+ "KISAO_0000808": "reduced stoichiometry matrix",
495
+ "KISAO_0000809": "reduced Jacobian matrix",
496
+ "KISAO_0000810": "reduced eigenvalue matrix",
497
+ "KISAO_0000811": "stoichiometry matrix",
498
+ "KISAO_0000812": "Jacobian matrix",
499
+ "KISAO_0000813": "Eigenvalue matrix",
500
+ "KISAO_0000814": "flux control coefficient matrix (unscaled)",
501
+ "KISAO_0000815": "flux control coefficient matrix (scaled)",
502
+ "KISAO_0000816": "link matrix",
503
+ "KISAO_0000817": "kernel matrix",
504
+ "KISAO_0000818": "L0 matrix",
505
+ "KISAO_0000819": "Nr matrix",
506
+ "KISAO_0000820": "model and simulation property characteristic",
507
+ "KISAO_0000821": "intensive property",
508
+ "KISAO_0000822": "extensive property",
509
+ "KISAO_0000824": "aggregation function",
510
+ "KISAO_0000825": "mean ignoring NaN",
511
+ "KISAO_0000826": "standard deviation ignoring NaN",
512
+ "KISAO_0000827": "standard error ignoring NaN",
513
+ "KISAO_0000828": "maximum ignoring NaN",
514
+ "KISAO_0000829": "minimum ignoring NaN",
515
+ "KISAO_0000830": "maximum",
516
+ "KISAO_0000831": "model and simulation property",
517
+ "KISAO_0000832": "time",
518
+ "KISAO_0000834": "rate of change",
519
+ "KISAO_0000835": "concentration control coefficient matrix (scaled)",
520
+ "KISAO_0000836": "amount",
521
+ "KISAO_0000837": "particle number",
522
+ "KISAO_0000838": "concentration",
523
+ "KISAO_0000839": "temperature",
524
+ "KISAO_0000840": "minimum",
525
+ "KISAO_0000841": "mean",
526
+ "KISAO_0000842": "standard deviation",
527
+ "KISAO_0000843": "standard error",
528
+ "KISAO_0000844": "sum ignoring NaN",
529
+ "KISAO_0000845": "sum",
530
+ "KISAO_0000846": "product ignoring NaN",
531
+ "KISAO_0000847": "product",
532
+ "KISAO_0000848": "cumulative sum ignoring NaN",
533
+ "KISAO_0000849": "cumulative sum",
534
+ "KISAO_0000850": "cumulative product ignoring NaN",
535
+ "KISAO_0000851": "cumulative product",
536
+ "KISAO_0000852": "count ignoring NaN",
537
+ "KISAO_0000853": "count",
538
+ "KISAO_0000854": "length ignoring NaN",
539
+ "KISAO_0000855": "length",
540
+ "KISAO_0000856": "median ignoring NaN",
541
+ "KISAO_0000857": "median",
542
+ "KISAO_0000858": "variance ignoring NaN",
543
+ "KISAO_0000859": "variance",
544
+ }
545
+
546
+ pattern = r"^KISAO_\d{7}$"
547
+
548
+
549
+ class KISAO(str, Enum):
550
+ """Enum for KISAO ontology."""
551
+
552
+ # modelling and simulation algorithm
553
+ KISAO_0000000 = "KISAO_0000000"
554
+ MODELLING_AND_SIMULATION_ALGORITHM = "KISAO_0000000"
555
+
556
+ # weighted stochastic simulation algorithm
557
+ KISAO_0000003 = "KISAO_0000003"
558
+ WEIGHTED_STOCHASTIC_SIMULATION_ALGORITHM = "KISAO_0000003"
559
+
560
+ # Gillespie first reaction algorithm
561
+ KISAO_0000015 = "KISAO_0000015"
562
+ GILLESPIE_FIRST_REACTION_ALGORITHM = "KISAO_0000015"
563
+
564
+ # multi-state agent-based simulation method
565
+ KISAO_0000017 = "KISAO_0000017"
566
+ MULTI_STATE_AGENT_BASED_SIMULATION_METHOD = "KISAO_0000017"
567
+
568
+ # CVODE
569
+ KISAO_0000019 = "KISAO_0000019"
570
+ CVODE = "KISAO_0000019"
571
+
572
+ # PVODE
573
+ KISAO_0000020 = "KISAO_0000020"
574
+ PVODE = "KISAO_0000020"
575
+
576
+ # StochSim nearest-neighbour algorithm
577
+ KISAO_0000021 = "KISAO_0000021"
578
+ STOCHSIM_NEAREST_NEIGHBOUR_ALGORITHM = "KISAO_0000021"
579
+
580
+ # Elf and Ehrenberg method
581
+ KISAO_0000022 = "KISAO_0000022"
582
+ ELF_AND_EHRENBERG_METHOD = "KISAO_0000022"
583
+
584
+ # Gibson-Bruck next reaction algorithm
585
+ KISAO_0000027 = "KISAO_0000027"
586
+ GIBSON_BRUCK_NEXT_REACTION_ALGORITHM = "KISAO_0000027"
587
+
588
+ # slow-scale stochastic simulation algorithm
589
+ KISAO_0000028 = "KISAO_0000028"
590
+ SLOW_SCALE_STOCHASTIC_SIMULATION_ALGORITHM = "KISAO_0000028"
591
+
592
+ # Gillespie direct algorithm
593
+ KISAO_0000029 = "KISAO_0000029"
594
+ GILLESPIE_DIRECT_ALGORITHM = "KISAO_0000029"
595
+
596
+ # Euler forward method
597
+ KISAO_0000030 = "KISAO_0000030"
598
+ EULER_FORWARD_METHOD = "KISAO_0000030"
599
+
600
+ # Euler backward method
601
+ KISAO_0000031 = "KISAO_0000031"
602
+ EULER_BACKWARD_METHOD = "KISAO_0000031"
603
+
604
+ # explicit fourth-order Runge-Kutta method
605
+ KISAO_0000032 = "KISAO_0000032"
606
+ EXPLICIT_FOURTH_ORDER_RUNGE_KUTTA_METHOD = "KISAO_0000032"
607
+
608
+ # Rosenbrock method
609
+ KISAO_0000033 = "KISAO_0000033"
610
+ ROSENBROCK_METHOD = "KISAO_0000033"
611
+
612
+ # sorting stochastic simulation algorithm
613
+ KISAO_0000038 = "KISAO_0000038"
614
+ SORTING_STOCHASTIC_SIMULATION_ALGORITHM = "KISAO_0000038"
615
+
616
+ # tau-leaping method
617
+ KISAO_0000039 = "KISAO_0000039"
618
+ TAU_LEAPING_METHOD = "KISAO_0000039"
619
+
620
+ # Poisson tau-leaping method
621
+ KISAO_0000040 = "KISAO_0000040"
622
+ POISSON_TAU_LEAPING_METHOD = "KISAO_0000040"
623
+
624
+ # implicit tau-leaping method
625
+ KISAO_0000045 = "KISAO_0000045"
626
+ IMPLICIT_TAU_LEAPING_METHOD = "KISAO_0000045"
627
+
628
+ # trapezoidal tau-leaping method
629
+ KISAO_0000046 = "KISAO_0000046"
630
+ TRAPEZOIDAL_TAU_LEAPING_METHOD = "KISAO_0000046"
631
+
632
+ # adaptive explicit-implicit tau-leaping method
633
+ KISAO_0000048 = "KISAO_0000048"
634
+ ADAPTIVE_EXPLICIT_IMPLICIT_TAU_LEAPING_METHOD = "KISAO_0000048"
635
+
636
+ # Bortz-Kalos-Lebowitz algorithm
637
+ KISAO_0000051 = "KISAO_0000051"
638
+ BORTZ_KALOS_LEBOWITZ_ALGORITHM = "KISAO_0000051"
639
+
640
+ # Smoluchowski equation based method
641
+ KISAO_0000056 = "KISAO_0000056"
642
+ SMOLUCHOWSKI_EQUATION_BASED_METHOD = "KISAO_0000056"
643
+
644
+ # Brownian diffusion Smoluchowski method
645
+ KISAO_0000057 = "KISAO_0000057"
646
+ BROWNIAN_DIFFUSION_SMOLUCHOWSKI_METHOD = "KISAO_0000057"
647
+
648
+ # Greens function reaction dynamics
649
+ KISAO_0000058 = "KISAO_0000058"
650
+ GREENS_FUNCTION_REACTION_DYNAMICS = "KISAO_0000058"
651
+
652
+ # Runge-Kutta based method
653
+ KISAO_0000064 = "KISAO_0000064"
654
+ RUNGE_KUTTA_BASED_METHOD = "KISAO_0000064"
655
+
656
+ # deterministic cellular automata update algorithm
657
+ KISAO_0000068 = "KISAO_0000068"
658
+ DETERMINISTIC_CELLULAR_AUTOMATA_UPDATE_ALGORITHM = "KISAO_0000068"
659
+
660
+ # LSODE
661
+ KISAO_0000071 = "KISAO_0000071"
662
+ LSODE = "KISAO_0000071"
663
+
664
+ # binomial tau-leaping method
665
+ KISAO_0000074 = "KISAO_0000074"
666
+ BINOMIAL_TAU_LEAPING_METHOD = "KISAO_0000074"
667
+
668
+ # Gillespie multi-particle method
669
+ KISAO_0000075 = "KISAO_0000075"
670
+ GILLESPIE_MULTI_PARTICLE_METHOD = "KISAO_0000075"
671
+
672
+ # Stundzia and Lumsden method
673
+ KISAO_0000076 = "KISAO_0000076"
674
+ STUNDZIA_AND_LUMSDEN_METHOD = "KISAO_0000076"
675
+
676
+ # estimated midpoint tau-leaping method
677
+ KISAO_0000081 = "KISAO_0000081"
678
+ ESTIMATED_MIDPOINT_TAU_LEAPING_METHOD = "KISAO_0000081"
679
+
680
+ # k-alpha leaping method
681
+ KISAO_0000082 = "KISAO_0000082"
682
+ K_ALPHA_LEAPING_METHOD = "KISAO_0000082"
683
+
684
+ # nonnegative Poisson tau-leaping method
685
+ KISAO_0000084 = "KISAO_0000084"
686
+ NONNEGATIVE_POISSON_TAU_LEAPING_METHOD = "KISAO_0000084"
687
+
688
+ # Fehlberg method
689
+ KISAO_0000086 = "KISAO_0000086"
690
+ FEHLBERG_METHOD = "KISAO_0000086"
691
+
692
+ # Dormand-Prince method
693
+ KISAO_0000087 = "KISAO_0000087"
694
+ DORMAND_PRINCE_METHOD = "KISAO_0000087"
695
+
696
+ # LSODA
697
+ KISAO_0000088 = "KISAO_0000088"
698
+ LSODA = "KISAO_0000088"
699
+
700
+ # LSODAR
701
+ KISAO_0000089 = "KISAO_0000089"
702
+ LSODAR = "KISAO_0000089"
703
+
704
+ # LSODI
705
+ KISAO_0000090 = "KISAO_0000090"
706
+ LSODI = "KISAO_0000090"
707
+
708
+ # LSODIS
709
+ KISAO_0000091 = "KISAO_0000091"
710
+ LSODIS = "KISAO_0000091"
711
+
712
+ # LSODPK
713
+ KISAO_0000093 = "KISAO_0000093"
714
+ LSODPK = "KISAO_0000093"
715
+
716
+ # Livermore solver
717
+ KISAO_0000094 = "KISAO_0000094"
718
+ LIVERMORE_SOLVER = "KISAO_0000094"
719
+
720
+ # sub-volume stochastic reaction-diffusion algorithm
721
+ KISAO_0000095 = "KISAO_0000095"
722
+ SUB_VOLUME_STOCHASTIC_REACTION_DIFFUSION_ALGORITHM = "KISAO_0000095"
723
+
724
+ # modelling and simulation algorithm characteristic
725
+ KISAO_0000097 = "KISAO_0000097"
726
+ MODELLING_AND_SIMULATION_ALGORITHM_CHARACTERISTIC = "KISAO_0000097"
727
+
728
+ # type of variable
729
+ KISAO_0000098 = "KISAO_0000098"
730
+ TYPE_OF_VARIABLE = "KISAO_0000098"
731
+
732
+ # type of system behaviour
733
+ KISAO_0000099 = "KISAO_0000099"
734
+ TYPE_OF_SYSTEM_BEHAVIOUR = "KISAO_0000099"
735
+
736
+ # type of progression time step
737
+ KISAO_0000100 = "KISAO_0000100"
738
+ TYPE_OF_PROGRESSION_TIME_STEP = "KISAO_0000100"
739
+
740
+ # spatial description
741
+ KISAO_0000102 = "KISAO_0000102"
742
+ SPATIAL_DESCRIPTION = "KISAO_0000102"
743
+
744
+ # deterministic system behaviour
745
+ KISAO_0000103 = "KISAO_0000103"
746
+ DETERMINISTIC_SYSTEM_BEHAVIOUR = "KISAO_0000103"
747
+
748
+ # stochastic system behaviour
749
+ KISAO_0000104 = "KISAO_0000104"
750
+ STOCHASTIC_SYSTEM_BEHAVIOUR = "KISAO_0000104"
751
+
752
+ # discrete variable
753
+ KISAO_0000105 = "KISAO_0000105"
754
+ DISCRETE_VARIABLE = "KISAO_0000105"
755
+
756
+ # continuous variable
757
+ KISAO_0000106 = "KISAO_0000106"
758
+ CONTINUOUS_VARIABLE = "KISAO_0000106"
759
+
760
+ # progression with adaptive time step
761
+ KISAO_0000107 = "KISAO_0000107"
762
+ PROGRESSION_WITH_ADAPTIVE_TIME_STEP = "KISAO_0000107"
763
+
764
+ # progression with fixed time step
765
+ KISAO_0000108 = "KISAO_0000108"
766
+ PROGRESSION_WITH_FIXED_TIME_STEP = "KISAO_0000108"
767
+
768
+ # modelling and simulation algorithm parameter
769
+ KISAO_0000201 = "KISAO_0000201"
770
+ MODELLING_AND_SIMULATION_ALGORITHM_PARAMETER = "KISAO_0000201"
771
+
772
+ # particle number lower limit
773
+ KISAO_0000203 = "KISAO_0000203"
774
+ PARTICLE_NUMBER_LOWER_LIMIT = "KISAO_0000203"
775
+
776
+ # particle number upper limit
777
+ KISAO_0000204 = "KISAO_0000204"
778
+ PARTICLE_NUMBER_UPPER_LIMIT = "KISAO_0000204"
779
+
780
+ # partitioning interval
781
+ KISAO_0000205 = "KISAO_0000205"
782
+ PARTITIONING_INTERVAL = "KISAO_0000205"
783
+
784
+ # relative tolerance
785
+ KISAO_0000209 = "KISAO_0000209"
786
+ RELATIVE_TOLERANCE = "KISAO_0000209"
787
+
788
+ # absolute tolerance
789
+ KISAO_0000211 = "KISAO_0000211"
790
+ ABSOLUTE_TOLERANCE = "KISAO_0000211"
791
+
792
+ # use reduced model
793
+ KISAO_0000216 = "KISAO_0000216"
794
+ USE_REDUCED_MODEL = "KISAO_0000216"
795
+
796
+ # maximum Adams order
797
+ KISAO_0000219 = "KISAO_0000219"
798
+ MAXIMUM_ADAMS_ORDER = "KISAO_0000219"
799
+
800
+ # maximum BDF order
801
+ KISAO_0000220 = "KISAO_0000220"
802
+ MAXIMUM_BDF_ORDER = "KISAO_0000220"
803
+
804
+ # number of history bins
805
+ KISAO_0000223 = "KISAO_0000223"
806
+ NUMBER_OF_HISTORY_BINS = "KISAO_0000223"
807
+
808
+ # tau-leaping epsilon
809
+ KISAO_0000228 = "KISAO_0000228"
810
+ TAU_LEAPING_EPSILON = "KISAO_0000228"
811
+
812
+ # minimum reactions per leap
813
+ KISAO_0000230 = "KISAO_0000230"
814
+ MINIMUM_REACTIONS_PER_LEAP = "KISAO_0000230"
815
+
816
+ # Pahle hybrid method
817
+ KISAO_0000231 = "KISAO_0000231"
818
+ PAHLE_HYBRID_METHOD = "KISAO_0000231"
819
+
820
+ # LSOIBT
821
+ KISAO_0000232 = "KISAO_0000232"
822
+ LSOIBT = "KISAO_0000232"
823
+
824
+ # LSODES
825
+ KISAO_0000233 = "KISAO_0000233"
826
+ LSODES = "KISAO_0000233"
827
+
828
+ # LSODKR
829
+ KISAO_0000234 = "KISAO_0000234"
830
+ LSODKR = "KISAO_0000234"
831
+
832
+ # type of solution
833
+ KISAO_0000235 = "KISAO_0000235"
834
+ TYPE_OF_SOLUTION = "KISAO_0000235"
835
+
836
+ # exact solution
837
+ KISAO_0000236 = "KISAO_0000236"
838
+ EXACT_SOLUTION = "KISAO_0000236"
839
+
840
+ # approximate solution
841
+ KISAO_0000237 = "KISAO_0000237"
842
+ APPROXIMATE_SOLUTION = "KISAO_0000237"
843
+
844
+ # type of method
845
+ KISAO_0000238 = "KISAO_0000238"
846
+ TYPE_OF_METHOD = "KISAO_0000238"
847
+
848
+ # explicit method type
849
+ KISAO_0000239 = "KISAO_0000239"
850
+ EXPLICIT_METHOD_TYPE = "KISAO_0000239"
851
+
852
+ # implicit method type
853
+ KISAO_0000240 = "KISAO_0000240"
854
+ IMPLICIT_METHOD_TYPE = "KISAO_0000240"
855
+
856
+ # Gillespie-like method
857
+ KISAO_0000241 = "KISAO_0000241"
858
+ GILLESPIE_LIKE_METHOD = "KISAO_0000241"
859
+
860
+ # error control parameter
861
+ KISAO_0000242 = "KISAO_0000242"
862
+ ERROR_CONTROL_PARAMETER = "KISAO_0000242"
863
+
864
+ # method switching control parameter
865
+ KISAO_0000243 = "KISAO_0000243"
866
+ METHOD_SWITCHING_CONTROL_PARAMETER = "KISAO_0000243"
867
+
868
+ # granularity control parameter
869
+ KISAO_0000244 = "KISAO_0000244"
870
+ GRANULARITY_CONTROL_PARAMETER = "KISAO_0000244"
871
+
872
+ # has characteristic
873
+ KISAO_0000245 = "KISAO_0000245"
874
+ HAS_CHARACTERISTIC = "KISAO_0000245"
875
+
876
+ # is hybrid of
877
+ KISAO_0000246 = "KISAO_0000246"
878
+ IS_HYBRID_OF = "KISAO_0000246"
879
+
880
+ # tau-leaping delta
881
+ KISAO_0000248 = "KISAO_0000248"
882
+ TAU_LEAPING_DELTA = "KISAO_0000248"
883
+
884
+ # critical firing threshold
885
+ KISAO_0000249 = "KISAO_0000249"
886
+ CRITICAL_FIRING_THRESHOLD = "KISAO_0000249"
887
+
888
+ # is parameter of
889
+ KISAO_0000250 = "KISAO_0000250"
890
+ IS_PARAMETER_OF = "KISAO_0000250"
891
+
892
+ # partitioning control parameter
893
+ KISAO_0000252 = "KISAO_0000252"
894
+ PARTITIONING_CONTROL_PARAMETER = "KISAO_0000252"
895
+
896
+ # coarse-graining factor
897
+ KISAO_0000253 = "KISAO_0000253"
898
+ COARSE_GRAINING_FACTOR = "KISAO_0000253"
899
+
900
+ # Brownian diffusion accuracy
901
+ KISAO_0000254 = "KISAO_0000254"
902
+ BROWNIAN_DIFFUSION_ACCURACY = "KISAO_0000254"
903
+
904
+ # molecules per virtual box
905
+ KISAO_0000255 = "KISAO_0000255"
906
+ MOLECULES_PER_VIRTUAL_BOX = "KISAO_0000255"
907
+
908
+ # virtual box side length
909
+ KISAO_0000256 = "KISAO_0000256"
910
+ VIRTUAL_BOX_SIDE_LENGTH = "KISAO_0000256"
911
+
912
+ # surface-bound epsilon
913
+ KISAO_0000257 = "KISAO_0000257"
914
+ SURFACE_BOUND_EPSILON = "KISAO_0000257"
915
+
916
+ # neighbour distance
917
+ KISAO_0000258 = "KISAO_0000258"
918
+ NEIGHBOUR_DISTANCE = "KISAO_0000258"
919
+
920
+ # has parameter
921
+ KISAO_0000259 = "KISAO_0000259"
922
+ HAS_PARAMETER = "KISAO_0000259"
923
+
924
+ # virtual box size
925
+ KISAO_0000260 = "KISAO_0000260"
926
+ VIRTUAL_BOX_SIZE = "KISAO_0000260"
927
+
928
+ # Euler method
929
+ KISAO_0000261 = "KISAO_0000261"
930
+ EULER_METHOD = "KISAO_0000261"
931
+
932
+ # NFSim agent-based simulation method
933
+ KISAO_0000263 = "KISAO_0000263"
934
+ NFSIM_AGENT_BASED_SIMULATION_METHOD = "KISAO_0000263"
935
+
936
+ # cellular automata update method
937
+ KISAO_0000264 = "KISAO_0000264"
938
+ CELLULAR_AUTOMATA_UPDATE_METHOD = "KISAO_0000264"
939
+
940
+ # is characteristic of
941
+ KISAO_0000268 = "KISAO_0000268"
942
+ IS_CHARACTERISTIC_OF = "KISAO_0000268"
943
+
944
+ # hard-particle molecular dynamics
945
+ KISAO_0000273 = "KISAO_0000273"
946
+ HARD_PARTICLE_MOLECULAR_DYNAMICS = "KISAO_0000273"
947
+
948
+ # first-passage Monte Carlo algorithm
949
+ KISAO_0000274 = "KISAO_0000274"
950
+ FIRST_PASSAGE_MONTE_CARLO_ALGORITHM = "KISAO_0000274"
951
+
952
+ # Gill method
953
+ KISAO_0000276 = "KISAO_0000276"
954
+ GILL_METHOD = "KISAO_0000276"
955
+
956
+ # Metropolis Monte Carlo algorithm
957
+ KISAO_0000278 = "KISAO_0000278"
958
+ METROPOLIS_MONTE_CARLO_ALGORITHM = "KISAO_0000278"
959
+
960
+ # Adams-Bashforth method
961
+ KISAO_0000279 = "KISAO_0000279"
962
+ ADAMS_BASHFORTH_METHOD = "KISAO_0000279"
963
+
964
+ # Adams-Moulton method
965
+ KISAO_0000280 = "KISAO_0000280"
966
+ ADAMS_MOULTON_METHOD = "KISAO_0000280"
967
+
968
+ # multistep method
969
+ KISAO_0000281 = "KISAO_0000281"
970
+ MULTISTEP_METHOD = "KISAO_0000281"
971
+
972
+ # KINSOL
973
+ KISAO_0000282 = "KISAO_0000282"
974
+ KINSOL = "KISAO_0000282"
975
+
976
+ # IDA
977
+ KISAO_0000283 = "KISAO_0000283"
978
+ IDA = "KISAO_0000283"
979
+
980
+ # finite volume method
981
+ KISAO_0000285 = "KISAO_0000285"
982
+ FINITE_VOLUME_METHOD = "KISAO_0000285"
983
+
984
+ # Euler-Maruyama method
985
+ KISAO_0000286 = "KISAO_0000286"
986
+ EULER_MARUYAMA_METHOD = "KISAO_0000286"
987
+
988
+ # Milstein method
989
+ KISAO_0000287 = "KISAO_0000287"
990
+ MILSTEIN_METHOD = "KISAO_0000287"
991
+
992
+ # backward differentiation formula
993
+ KISAO_0000288 = "KISAO_0000288"
994
+ BACKWARD_DIFFERENTIATION_FORMULA = "KISAO_0000288"
995
+
996
+ # Adams method
997
+ KISAO_0000289 = "KISAO_0000289"
998
+ ADAMS_METHOD = "KISAO_0000289"
999
+
1000
+ # Merson method
1001
+ KISAO_0000290 = "KISAO_0000290"
1002
+ MERSON_METHOD = "KISAO_0000290"
1003
+
1004
+ # Hammer-Hollingsworth method
1005
+ KISAO_0000296 = "KISAO_0000296"
1006
+ HAMMER_HOLLINGSWORTH_METHOD = "KISAO_0000296"
1007
+
1008
+ # Lobatto method
1009
+ KISAO_0000297 = "KISAO_0000297"
1010
+ LOBATTO_METHOD = "KISAO_0000297"
1011
+
1012
+ # Butcher-Kuntzmann method
1013
+ KISAO_0000299 = "KISAO_0000299"
1014
+ BUTCHER_KUNTZMANN_METHOD = "KISAO_0000299"
1015
+
1016
+ # Heun method
1017
+ KISAO_0000301 = "KISAO_0000301"
1018
+ HEUN_METHOD = "KISAO_0000301"
1019
+
1020
+ # embedded Runge-Kutta method
1021
+ KISAO_0000302 = "KISAO_0000302"
1022
+ EMBEDDED_RUNGE_KUTTA_METHOD = "KISAO_0000302"
1023
+
1024
+ # Zonneveld method
1025
+ KISAO_0000303 = "KISAO_0000303"
1026
+ ZONNEVELD_METHOD = "KISAO_0000303"
1027
+
1028
+ # Radau method
1029
+ KISAO_0000304 = "KISAO_0000304"
1030
+ RADAU_METHOD = "KISAO_0000304"
1031
+
1032
+ # Verner method
1033
+ KISAO_0000305 = "KISAO_0000305"
1034
+ VERNER_METHOD = "KISAO_0000305"
1035
+
1036
+ # Lagrangian sliding fluid element algorithm
1037
+ KISAO_0000306 = "KISAO_0000306"
1038
+ LAGRANGIAN_SLIDING_FLUID_ELEMENT_ALGORITHM = "KISAO_0000306"
1039
+
1040
+ # finite difference method
1041
+ KISAO_0000307 = "KISAO_0000307"
1042
+ FINITE_DIFFERENCE_METHOD = "KISAO_0000307"
1043
+
1044
+ # MacCormack method
1045
+ KISAO_0000308 = "KISAO_0000308"
1046
+ MACCORMACK_METHOD = "KISAO_0000308"
1047
+
1048
+ # Crank-Nicolson method
1049
+ KISAO_0000309 = "KISAO_0000309"
1050
+ CRANK_NICOLSON_METHOD = "KISAO_0000309"
1051
+
1052
+ # method of lines
1053
+ KISAO_0000310 = "KISAO_0000310"
1054
+ METHOD_OF_LINES = "KISAO_0000310"
1055
+
1056
+ # type of domain geometry handling
1057
+ KISAO_0000311 = "KISAO_0000311"
1058
+ TYPE_OF_DOMAIN_GEOMETRY_HANDLING = "KISAO_0000311"
1059
+
1060
+ # S-System power-law canonical differential equations solver
1061
+ KISAO_0000314 = "KISAO_0000314"
1062
+ S_SYSTEM_POWER_LAW_CANONICAL_DIFFERENTIAL_EQUATIONS_SOLVER = "KISAO_0000314"
1063
+
1064
+ # lattice gas automata
1065
+ KISAO_0000315 = "KISAO_0000315"
1066
+ LATTICE_GAS_AUTOMATA = "KISAO_0000315"
1067
+
1068
+ # enhanced Greens function reaction dynamics
1069
+ KISAO_0000316 = "KISAO_0000316"
1070
+ ENHANCED_GREENS_FUNCTION_REACTION_DYNAMICS = "KISAO_0000316"
1071
+
1072
+ # E-Cell multi-algorithm simulation method
1073
+ KISAO_0000317 = "KISAO_0000317"
1074
+ E_CELL_MULTI_ALGORITHM_SIMULATION_METHOD = "KISAO_0000317"
1075
+
1076
+ # Gauss-Legendre Runge-Kutta method
1077
+ KISAO_0000318 = "KISAO_0000318"
1078
+ GAUSS_LEGENDRE_RUNGE_KUTTA_METHOD = "KISAO_0000318"
1079
+
1080
+ # Monte Carlo method
1081
+ KISAO_0000319 = "KISAO_0000319"
1082
+ MONTE_CARLO_METHOD = "KISAO_0000319"
1083
+
1084
+ # BioRica hybrid method
1085
+ KISAO_0000320 = "KISAO_0000320"
1086
+ BIORICA_HYBRID_METHOD = "KISAO_0000320"
1087
+
1088
+ # Cash-Karp method
1089
+ KISAO_0000321 = "KISAO_0000321"
1090
+ CASH_KARP_METHOD = "KISAO_0000321"
1091
+
1092
+ # hybridity
1093
+ KISAO_0000322 = "KISAO_0000322"
1094
+ HYBRIDITY = "KISAO_0000322"
1095
+
1096
+ # equation-free probabilistic steady-state approximation
1097
+ KISAO_0000323 = "KISAO_0000323"
1098
+ EQUATION_FREE_PROBABILISTIC_STEADY_STATE_APPROXIMATION = "KISAO_0000323"
1099
+
1100
+ # nested stochastic simulation algorithm
1101
+ KISAO_0000324 = "KISAO_0000324"
1102
+ NESTED_STOCHASTIC_SIMULATION_ALGORITHM = "KISAO_0000324"
1103
+
1104
+ # minimum fast/discrete reaction occurrences number
1105
+ KISAO_0000325 = "KISAO_0000325"
1106
+ MINIMUM_FAST_DISCRETE_REACTION_OCCURRENCES_NUMBER = "KISAO_0000325"
1107
+
1108
+ # number of samples
1109
+ KISAO_0000326 = "KISAO_0000326"
1110
+ NUMBER_OF_SAMPLES = "KISAO_0000326"
1111
+
1112
+ # maximum discrete number
1113
+ KISAO_0000327 = "KISAO_0000327"
1114
+ MAXIMUM_DISCRETE_NUMBER = "KISAO_0000327"
1115
+
1116
+ # minimum fast rate
1117
+ KISAO_0000328 = "KISAO_0000328"
1118
+ MINIMUM_FAST_RATE = "KISAO_0000328"
1119
+
1120
+ # constant-time kinetic Monte Carlo algorithm
1121
+ KISAO_0000329 = "KISAO_0000329"
1122
+ CONSTANT_TIME_KINETIC_MONTE_CARLO_ALGORITHM = "KISAO_0000329"
1123
+
1124
+ # R-leaping algorithm
1125
+ KISAO_0000330 = "KISAO_0000330"
1126
+ R_LEAPING_ALGORITHM = "KISAO_0000330"
1127
+
1128
+ # exact R-leaping algorithm
1129
+ KISAO_0000331 = "KISAO_0000331"
1130
+ EXACT_R_LEAPING_ALGORITHM = "KISAO_0000331"
1131
+
1132
+ # ER-leap initial leap
1133
+ KISAO_0000332 = "KISAO_0000332"
1134
+ ER_LEAP_INITIAL_LEAP = "KISAO_0000332"
1135
+
1136
+ # accelerated stochastic simulation algorithm
1137
+ KISAO_0000333 = "KISAO_0000333"
1138
+ ACCELERATED_STOCHASTIC_SIMULATION_ALGORITHM = "KISAO_0000333"
1139
+
1140
+ # multiparticle lattice gas automata
1141
+ KISAO_0000334 = "KISAO_0000334"
1142
+ MULTIPARTICLE_LATTICE_GAS_AUTOMATA = "KISAO_0000334"
1143
+
1144
+ # generalized stochastic simulation algorithm
1145
+ KISAO_0000335 = "KISAO_0000335"
1146
+ GENERALIZED_STOCHASTIC_SIMULATION_ALGORITHM = "KISAO_0000335"
1147
+
1148
+ # D-leaping method
1149
+ KISAO_0000336 = "KISAO_0000336"
1150
+ D_LEAPING_METHOD = "KISAO_0000336"
1151
+
1152
+ # finite element method
1153
+ KISAO_0000337 = "KISAO_0000337"
1154
+ FINITE_ELEMENT_METHOD = "KISAO_0000337"
1155
+
1156
+ # h-version of the finite element method
1157
+ KISAO_0000338 = "KISAO_0000338"
1158
+ H_VERSION_OF_THE_FINITE_ELEMENT_METHOD = "KISAO_0000338"
1159
+
1160
+ # p-version of the finite element method
1161
+ KISAO_0000339 = "KISAO_0000339"
1162
+ P_VERSION_OF_THE_FINITE_ELEMENT_METHOD = "KISAO_0000339"
1163
+
1164
+ # h-p version of the finite element method
1165
+ KISAO_0000340 = "KISAO_0000340"
1166
+ H_P_VERSION_OF_THE_FINITE_ELEMENT_METHOD = "KISAO_0000340"
1167
+
1168
+ # mixed finite element method
1169
+ KISAO_0000341 = "KISAO_0000341"
1170
+ MIXED_FINITE_ELEMENT_METHOD = "KISAO_0000341"
1171
+
1172
+ # level set method
1173
+ KISAO_0000342 = "KISAO_0000342"
1174
+ LEVEL_SET_METHOD = "KISAO_0000342"
1175
+
1176
+ # generalized finite element method
1177
+ KISAO_0000343 = "KISAO_0000343"
1178
+ GENERALIZED_FINITE_ELEMENT_METHOD = "KISAO_0000343"
1179
+
1180
+ # h-p cloud method
1181
+ KISAO_0000345 = "KISAO_0000345"
1182
+ H_P_CLOUD_METHOD = "KISAO_0000345"
1183
+
1184
+ # mesh-based geometry handling
1185
+ KISAO_0000346 = "KISAO_0000346"
1186
+ MESH_BASED_GEOMETRY_HANDLING = "KISAO_0000346"
1187
+
1188
+ # meshless geometry handling
1189
+ KISAO_0000347 = "KISAO_0000347"
1190
+ MESHLESS_GEOMETRY_HANDLING = "KISAO_0000347"
1191
+
1192
+ # extended finite element method
1193
+ KISAO_0000348 = "KISAO_0000348"
1194
+ EXTENDED_FINITE_ELEMENT_METHOD = "KISAO_0000348"
1195
+
1196
+ # method of finite spheres
1197
+ KISAO_0000349 = "KISAO_0000349"
1198
+ METHOD_OF_FINITE_SPHERES = "KISAO_0000349"
1199
+
1200
+ # probability-weighted dynamic Monte Carlo method
1201
+ KISAO_0000350 = "KISAO_0000350"
1202
+ PROBABILITY_WEIGHTED_DYNAMIC_MONTE_CARLO_METHOD = "KISAO_0000350"
1203
+
1204
+ # multinomial tau-leaping method
1205
+ KISAO_0000351 = "KISAO_0000351"
1206
+ MULTINOMIAL_TAU_LEAPING_METHOD = "KISAO_0000351"
1207
+
1208
+ # hybrid method
1209
+ KISAO_0000352 = "KISAO_0000352"
1210
+ HYBRID_METHOD = "KISAO_0000352"
1211
+
1212
+ # generalized minimal residual algorithm
1213
+ KISAO_0000353 = "KISAO_0000353"
1214
+ GENERALIZED_MINIMAL_RESIDUAL_ALGORITHM = "KISAO_0000353"
1215
+
1216
+ # Krylov subspace projection method
1217
+ KISAO_0000354 = "KISAO_0000354"
1218
+ KRYLOV_SUBSPACE_PROJECTION_METHOD = "KISAO_0000354"
1219
+
1220
+ # DASPK
1221
+ KISAO_0000355 = "KISAO_0000355"
1222
+ DASPK = "KISAO_0000355"
1223
+
1224
+ # DASSL
1225
+ KISAO_0000356 = "KISAO_0000356"
1226
+ DASSL = "KISAO_0000356"
1227
+
1228
+ # conjugate gradient method
1229
+ KISAO_0000357 = "KISAO_0000357"
1230
+ CONJUGATE_GRADIENT_METHOD = "KISAO_0000357"
1231
+
1232
+ # biconjugate gradient method
1233
+ KISAO_0000358 = "KISAO_0000358"
1234
+ BICONJUGATE_GRADIENT_METHOD = "KISAO_0000358"
1235
+
1236
+ # is similar to
1237
+ KISAO_0000359 = "KISAO_0000359"
1238
+ IS_SIMILAR_TO = "KISAO_0000359"
1239
+
1240
+ # uses
1241
+ KISAO_0000360 = "KISAO_0000360"
1242
+ USES = "KISAO_0000360"
1243
+
1244
+ # is generalization of
1245
+ KISAO_0000361 = "KISAO_0000361"
1246
+ IS_GENERALIZATION_OF = "KISAO_0000361"
1247
+
1248
+ # implicit-state Doob-Gillespie algorithm
1249
+ KISAO_0000362 = "KISAO_0000362"
1250
+ IMPLICIT_STATE_DOOB_GILLESPIE_ALGORITHM = "KISAO_0000362"
1251
+
1252
+ # rule-based simulation method
1253
+ KISAO_0000363 = "KISAO_0000363"
1254
+ RULE_BASED_SIMULATION_METHOD = "KISAO_0000363"
1255
+
1256
+ # Adams predictor-corrector method
1257
+ KISAO_0000364 = "KISAO_0000364"
1258
+ ADAMS_PREDICTOR_CORRECTOR_METHOD = "KISAO_0000364"
1259
+
1260
+ # NDSolve method
1261
+ KISAO_0000365 = "KISAO_0000365"
1262
+ NDSOLVE_METHOD = "KISAO_0000365"
1263
+
1264
+ # symplecticness
1265
+ KISAO_0000366 = "KISAO_0000366"
1266
+ SYMPLECTICNESS = "KISAO_0000366"
1267
+
1268
+ # partitioned Runge-Kutta method
1269
+ KISAO_0000367 = "KISAO_0000367"
1270
+ PARTITIONED_RUNGE_KUTTA_METHOD = "KISAO_0000367"
1271
+
1272
+ # partial differential equation discretization method
1273
+ KISAO_0000369 = "KISAO_0000369"
1274
+ PARTIAL_DIFFERENTIAL_EQUATION_DISCRETIZATION_METHOD = "KISAO_0000369"
1275
+
1276
+ # type of problem
1277
+ KISAO_0000370 = "KISAO_0000370"
1278
+ TYPE_OF_PROBLEM = "KISAO_0000370"
1279
+
1280
+ # stochastic differential equation problem
1281
+ KISAO_0000371 = "KISAO_0000371"
1282
+ STOCHASTIC_DIFFERENTIAL_EQUATION_PROBLEM = "KISAO_0000371"
1283
+
1284
+ # partial differential equation problem
1285
+ KISAO_0000372 = "KISAO_0000372"
1286
+ PARTIAL_DIFFERENTIAL_EQUATION_PROBLEM = "KISAO_0000372"
1287
+
1288
+ # differential-algebraic equation problem
1289
+ KISAO_0000373 = "KISAO_0000373"
1290
+ DIFFERENTIAL_ALGEBRAIC_EQUATION_PROBLEM = "KISAO_0000373"
1291
+
1292
+ # ordinary differential equation problem
1293
+ KISAO_0000374 = "KISAO_0000374"
1294
+ ORDINARY_DIFFERENTIAL_EQUATION_PROBLEM = "KISAO_0000374"
1295
+
1296
+ # delay differential equation problem
1297
+ KISAO_0000375 = "KISAO_0000375"
1298
+ DELAY_DIFFERENTIAL_EQUATION_PROBLEM = "KISAO_0000375"
1299
+
1300
+ # linearity of equation
1301
+ KISAO_0000376 = "KISAO_0000376"
1302
+ LINEARITY_OF_EQUATION = "KISAO_0000376"
1303
+
1304
+ # one-step method
1305
+ KISAO_0000377 = "KISAO_0000377"
1306
+ ONE_STEP_METHOD = "KISAO_0000377"
1307
+
1308
+ # implicit midpoint rule
1309
+ KISAO_0000378 = "KISAO_0000378"
1310
+ IMPLICIT_MIDPOINT_RULE = "KISAO_0000378"
1311
+
1312
+ # Bulirsch-Stoer algorithm
1313
+ KISAO_0000379 = "KISAO_0000379"
1314
+ BULIRSCH_STOER_ALGORITHM = "KISAO_0000379"
1315
+
1316
+ # Richardson extrapolation based method
1317
+ KISAO_0000380 = "KISAO_0000380"
1318
+ RICHARDSON_EXTRAPOLATION_BASED_METHOD = "KISAO_0000380"
1319
+
1320
+ # midpoint method
1321
+ KISAO_0000381 = "KISAO_0000381"
1322
+ MIDPOINT_METHOD = "KISAO_0000381"
1323
+
1324
+ # modified midpoint method
1325
+ KISAO_0000382 = "KISAO_0000382"
1326
+ MODIFIED_MIDPOINT_METHOD = "KISAO_0000382"
1327
+
1328
+ # Bader-Deuflhard method
1329
+ KISAO_0000383 = "KISAO_0000383"
1330
+ BADER_DEUFLHARD_METHOD = "KISAO_0000383"
1331
+
1332
+ # semi-implicit midpoint rule
1333
+ KISAO_0000384 = "KISAO_0000384"
1334
+ SEMI_IMPLICIT_MIDPOINT_RULE = "KISAO_0000384"
1335
+
1336
+ # scaled preconditioned generalized minimal residual method
1337
+ KISAO_0000386 = "KISAO_0000386"
1338
+ SCALED_PRECONDITIONED_GENERALIZED_MINIMAL_RESIDUAL_METHOD = "KISAO_0000386"
1339
+
1340
+ # minimal residual method
1341
+ KISAO_0000388 = "KISAO_0000388"
1342
+ MINIMAL_RESIDUAL_METHOD = "KISAO_0000388"
1343
+
1344
+ # quasi-minimal residual method
1345
+ KISAO_0000389 = "KISAO_0000389"
1346
+ QUASI_MINIMAL_RESIDUAL_METHOD = "KISAO_0000389"
1347
+
1348
+ # biconjugate gradient stabilized method
1349
+ KISAO_0000392 = "KISAO_0000392"
1350
+ BICONJUGATE_GRADIENT_STABILIZED_METHOD = "KISAO_0000392"
1351
+
1352
+ # ingenious conjugate gradients-squared method
1353
+ KISAO_0000393 = "KISAO_0000393"
1354
+ INGENIOUS_CONJUGATE_GRADIENTS_SQUARED_METHOD = "KISAO_0000393"
1355
+
1356
+ # quasi-minimal residual variant of biconjugate gradient stabilized method
1357
+ KISAO_0000394 = "KISAO_0000394"
1358
+ QUASI_MINIMAL_RESIDUAL_VARIANT_OF_BICONJUGATE_GRADIENT_STABILIZED_METHOD = (
1359
+ "KISAO_0000394"
1360
+ )
1361
+
1362
+ # improved biconjugate gradient method
1363
+ KISAO_0000395 = "KISAO_0000395"
1364
+ IMPROVED_BICONJUGATE_GRADIENT_METHOD = "KISAO_0000395"
1365
+
1366
+ # transpose-free quasi-minimal residual algorithm
1367
+ KISAO_0000396 = "KISAO_0000396"
1368
+ TRANSPOSE_FREE_QUASI_MINIMAL_RESIDUAL_ALGORITHM = "KISAO_0000396"
1369
+
1370
+ # preconditioning technique
1371
+ KISAO_0000397 = "KISAO_0000397"
1372
+ PRECONDITIONING_TECHNIQUE = "KISAO_0000397"
1373
+
1374
+ # iterative method for solving a system of linear equations
1375
+ KISAO_0000398 = "KISAO_0000398"
1376
+ ITERATIVE_METHOD_FOR_SOLVING_A_SYSTEM_OF_LINEAR_EQUATIONS = "KISAO_0000398"
1377
+
1378
+ # is used by
1379
+ KISAO_0000399 = "KISAO_0000399"
1380
+ IS_USED_BY = "KISAO_0000399"
1381
+
1382
+ # homogeneousness of equation
1383
+ KISAO_0000403 = "KISAO_0000403"
1384
+ HOMOGENEOUSNESS_OF_EQUATION = "KISAO_0000403"
1385
+
1386
+ # symmetricity of matrix
1387
+ KISAO_0000404 = "KISAO_0000404"
1388
+ SYMMETRICITY_OF_MATRIX = "KISAO_0000404"
1389
+
1390
+ # type of differential equation
1391
+ KISAO_0000405 = "KISAO_0000405"
1392
+ TYPE_OF_DIFFERENTIAL_EQUATION = "KISAO_0000405"
1393
+
1394
+ # steady state root-finding method
1395
+ KISAO_0000407 = "KISAO_0000407"
1396
+ STEADY_STATE_ROOT_FINDING_METHOD = "KISAO_0000407"
1397
+
1398
+ # Newton-type method
1399
+ KISAO_0000408 = "KISAO_0000408"
1400
+ NEWTON_TYPE_METHOD = "KISAO_0000408"
1401
+
1402
+ # ordinary Newton method
1403
+ KISAO_0000409 = "KISAO_0000409"
1404
+ ORDINARY_NEWTON_METHOD = "KISAO_0000409"
1405
+
1406
+ # simplified Newton method
1407
+ KISAO_0000410 = "KISAO_0000410"
1408
+ SIMPLIFIED_NEWTON_METHOD = "KISAO_0000410"
1409
+
1410
+ # Newton-like method
1411
+ KISAO_0000411 = "KISAO_0000411"
1412
+ NEWTON_LIKE_METHOD = "KISAO_0000411"
1413
+
1414
+ # inexact Newton method
1415
+ KISAO_0000412 = "KISAO_0000412"
1416
+ INEXACT_NEWTON_METHOD = "KISAO_0000412"
1417
+
1418
+ # exact Newton method
1419
+ KISAO_0000413 = "KISAO_0000413"
1420
+ EXACT_NEWTON_METHOD = "KISAO_0000413"
1421
+
1422
+ # maximum number of steps
1423
+ KISAO_0000415 = "KISAO_0000415"
1424
+ MAXIMUM_NUMBER_OF_STEPS = "KISAO_0000415"
1425
+
1426
+ # partial least squares regression method
1427
+ KISAO_0000416 = "KISAO_0000416"
1428
+ PARTIAL_LEAST_SQUARES_REGRESSION_METHOD = "KISAO_0000416"
1429
+
1430
+ # hierarchical cluster-based partial least squares regression method
1431
+ KISAO_0000417 = "KISAO_0000417"
1432
+ HIERARCHICAL_CLUSTER_BASED_PARTIAL_LEAST_SQUARES_REGRESSION_METHOD = "KISAO_0000417"
1433
+
1434
+ # N-way partial least squares regression method
1435
+ KISAO_0000418 = "KISAO_0000418"
1436
+ N_WAY_PARTIAL_LEAST_SQUARES_REGRESSION_METHOD = "KISAO_0000418"
1437
+
1438
+ # metamodelling method
1439
+ KISAO_0000419 = "KISAO_0000419"
1440
+ METAMODELLING_METHOD = "KISAO_0000419"
1441
+
1442
+ # number of partial least squares components
1443
+ KISAO_0000420 = "KISAO_0000420"
1444
+ NUMBER_OF_PARTIAL_LEAST_SQUARES_COMPONENTS = "KISAO_0000420"
1445
+
1446
+ # type of validation
1447
+ KISAO_0000421 = "KISAO_0000421"
1448
+ TYPE_OF_VALIDATION = "KISAO_0000421"
1449
+
1450
+ # number of N-way partial least squares regression factors
1451
+ KISAO_0000422 = "KISAO_0000422"
1452
+ NUMBER_OF_N_WAY_PARTIAL_LEAST_SQUARES_REGRESSION_FACTORS = "KISAO_0000422"
1453
+
1454
+ # partial least squares regression-like method
1455
+ KISAO_0000423 = "KISAO_0000423"
1456
+ PARTIAL_LEAST_SQUARES_REGRESSION_LIKE_METHOD = "KISAO_0000423"
1457
+
1458
+ # mean-centring of variables
1459
+ KISAO_0000424 = "KISAO_0000424"
1460
+ MEAN_CENTRING_OF_VARIABLES = "KISAO_0000424"
1461
+
1462
+ # standardising of variables
1463
+ KISAO_0000425 = "KISAO_0000425"
1464
+ STANDARDISING_OF_VARIABLES = "KISAO_0000425"
1465
+
1466
+ # number of clusters
1467
+ KISAO_0000427 = "KISAO_0000427"
1468
+ NUMBER_OF_CLUSTERS = "KISAO_0000427"
1469
+
1470
+ # matrix for clusterization
1471
+ KISAO_0000428 = "KISAO_0000428"
1472
+ MATRIX_FOR_CLUSTERIZATION = "KISAO_0000428"
1473
+
1474
+ # clusterization parameter
1475
+ KISAO_0000429 = "KISAO_0000429"
1476
+ CLUSTERIZATION_PARAMETER = "KISAO_0000429"
1477
+
1478
+ # variables preprocessing parameter
1479
+ KISAO_0000430 = "KISAO_0000430"
1480
+ VARIABLES_PREPROCESSING_PARAMETER = "KISAO_0000430"
1481
+
1482
+ # IDA-like method
1483
+ KISAO_0000432 = "KISAO_0000432"
1484
+ IDA_LIKE_METHOD = "KISAO_0000432"
1485
+
1486
+ # CVODE-like method
1487
+ KISAO_0000433 = "KISAO_0000433"
1488
+ CVODE_LIKE_METHOD = "KISAO_0000433"
1489
+
1490
+ # Higham-Hall method
1491
+ KISAO_0000434 = "KISAO_0000434"
1492
+ HIGHAM_HALL_METHOD = "KISAO_0000434"
1493
+
1494
+ # embedded Runge-Kutta 5(4) method
1495
+ KISAO_0000435 = "KISAO_0000435"
1496
+ EMBEDDED_RUNGE_KUTTA_5_4__METHOD = "KISAO_0000435"
1497
+
1498
+ # Dormand-Prince 8(5,3) method
1499
+ KISAO_0000436 = "KISAO_0000436"
1500
+ DORMAND_PRINCE_8_5_3__METHOD = "KISAO_0000436"
1501
+
1502
+ # flux balance analysis
1503
+ KISAO_0000437 = "KISAO_0000437"
1504
+ FLUX_BALANCE_ANALYSIS = "KISAO_0000437"
1505
+
1506
+ # COAST
1507
+ KISAO_0000447 = "KISAO_0000447"
1508
+ COAST = "KISAO_0000447"
1509
+
1510
+ # logical model simulation method
1511
+ KISAO_0000448 = "KISAO_0000448"
1512
+ LOGICAL_MODEL_SIMULATION_METHOD = "KISAO_0000448"
1513
+
1514
+ # synchronous logical model simulation method
1515
+ KISAO_0000449 = "KISAO_0000449"
1516
+ SYNCHRONOUS_LOGICAL_MODEL_SIMULATION_METHOD = "KISAO_0000449"
1517
+
1518
+ # asynchronous logical model simulation method
1519
+ KISAO_0000450 = "KISAO_0000450"
1520
+ ASYNCHRONOUS_LOGICAL_MODEL_SIMULATION_METHOD = "KISAO_0000450"
1521
+
1522
+ # type of updating policy
1523
+ KISAO_0000451 = "KISAO_0000451"
1524
+ TYPE_OF_UPDATING_POLICY = "KISAO_0000451"
1525
+
1526
+ # random updating policy
1527
+ KISAO_0000452 = "KISAO_0000452"
1528
+ RANDOM_UPDATING_POLICY = "KISAO_0000452"
1529
+
1530
+ # ordered updating policy
1531
+ KISAO_0000453 = "KISAO_0000453"
1532
+ ORDERED_UPDATING_POLICY = "KISAO_0000453"
1533
+
1534
+ # constant updating policy
1535
+ KISAO_0000454 = "KISAO_0000454"
1536
+ CONSTANT_UPDATING_POLICY = "KISAO_0000454"
1537
+
1538
+ # prioritized updating policy
1539
+ KISAO_0000455 = "KISAO_0000455"
1540
+ PRIORITIZED_UPDATING_POLICY = "KISAO_0000455"
1541
+
1542
+ # maximum step size
1543
+ KISAO_0000467 = "KISAO_0000467"
1544
+ MAXIMUM_STEP_SIZE = "KISAO_0000467"
1545
+
1546
+ # maximal timestep method
1547
+ KISAO_0000468 = "KISAO_0000468"
1548
+ MAXIMAL_TIMESTEP_METHOD = "KISAO_0000468"
1549
+
1550
+ # maximal timestep
1551
+ KISAO_0000469 = "KISAO_0000469"
1552
+ MAXIMAL_TIMESTEP = "KISAO_0000469"
1553
+
1554
+ # optimization algorithm
1555
+ KISAO_0000470 = "KISAO_0000470"
1556
+ OPTIMIZATION_ALGORITHM = "KISAO_0000470"
1557
+
1558
+ # local optimization algorithm
1559
+ KISAO_0000471 = "KISAO_0000471"
1560
+ LOCAL_OPTIMIZATION_ALGORITHM = "KISAO_0000471"
1561
+
1562
+ # global optimization algorithm
1563
+ KISAO_0000472 = "KISAO_0000472"
1564
+ GLOBAL_OPTIMIZATION_ALGORITHM = "KISAO_0000472"
1565
+
1566
+ # Bayesian inference algorithm
1567
+ KISAO_0000473 = "KISAO_0000473"
1568
+ BAYESIAN_INFERENCE_ALGORITHM = "KISAO_0000473"
1569
+
1570
+ # integration method
1571
+ KISAO_0000475 = "KISAO_0000475"
1572
+ INTEGRATION_METHOD = "KISAO_0000475"
1573
+
1574
+ # iteration type
1575
+ KISAO_0000476 = "KISAO_0000476"
1576
+ ITERATION_TYPE = "KISAO_0000476"
1577
+
1578
+ # linear solver
1579
+ KISAO_0000477 = "KISAO_0000477"
1580
+ LINEAR_SOLVER = "KISAO_0000477"
1581
+
1582
+ # preconditioner
1583
+ KISAO_0000478 = "KISAO_0000478"
1584
+ PRECONDITIONER = "KISAO_0000478"
1585
+
1586
+ # upper half-bandwidth
1587
+ KISAO_0000479 = "KISAO_0000479"
1588
+ UPPER_HALF_BANDWIDTH = "KISAO_0000479"
1589
+
1590
+ # lower half-bandwidth
1591
+ KISAO_0000480 = "KISAO_0000480"
1592
+ LOWER_HALF_BANDWIDTH = "KISAO_0000480"
1593
+
1594
+ # interpolate solution
1595
+ KISAO_0000481 = "KISAO_0000481"
1596
+ INTERPOLATE_SOLUTION = "KISAO_0000481"
1597
+
1598
+ # half-bandwith parameter
1599
+ KISAO_0000482 = "KISAO_0000482"
1600
+ HALF_BANDWITH_PARAMETER = "KISAO_0000482"
1601
+
1602
+ # step size
1603
+ KISAO_0000483 = "KISAO_0000483"
1604
+ STEP_SIZE = "KISAO_0000483"
1605
+
1606
+ # maximum order
1607
+ KISAO_0000484 = "KISAO_0000484"
1608
+ MAXIMUM_ORDER = "KISAO_0000484"
1609
+
1610
+ # minimum step size
1611
+ KISAO_0000485 = "KISAO_0000485"
1612
+ MINIMUM_STEP_SIZE = "KISAO_0000485"
1613
+
1614
+ # maximum iterations
1615
+ KISAO_0000486 = "KISAO_0000486"
1616
+ MAXIMUM_ITERATIONS = "KISAO_0000486"
1617
+
1618
+ # minimum damping
1619
+ KISAO_0000487 = "KISAO_0000487"
1620
+ MINIMUM_DAMPING = "KISAO_0000487"
1621
+
1622
+ # seed
1623
+ KISAO_0000488 = "KISAO_0000488"
1624
+ SEED = "KISAO_0000488"
1625
+
1626
+ # discrete event simulation algorithm
1627
+ KISAO_0000491 = "KISAO_0000491"
1628
+ DISCRETE_EVENT_SIMULATION_ALGORITHM = "KISAO_0000491"
1629
+
1630
+ # asynchronous updating policy
1631
+ KISAO_0000492 = "KISAO_0000492"
1632
+ ASYNCHRONOUS_UPDATING_POLICY = "KISAO_0000492"
1633
+
1634
+ # synchronous updating policy
1635
+ KISAO_0000493 = "KISAO_0000493"
1636
+ SYNCHRONOUS_UPDATING_POLICY = "KISAO_0000493"
1637
+
1638
+ # fully asynchronous updating policy
1639
+ KISAO_0000494 = "KISAO_0000494"
1640
+ FULLY_ASYNCHRONOUS_UPDATING_POLICY = "KISAO_0000494"
1641
+
1642
+ # random asynchronous updating policy
1643
+ KISAO_0000495 = "KISAO_0000495"
1644
+ RANDOM_ASYNCHRONOUS_UPDATING_POLICY = "KISAO_0000495"
1645
+
1646
+ # CVODES
1647
+ KISAO_0000496 = "KISAO_0000496"
1648
+ CVODES = "KISAO_0000496"
1649
+
1650
+ # KLU
1651
+ KISAO_0000497 = "KISAO_0000497"
1652
+ KLU = "KISAO_0000497"
1653
+
1654
+ # number of runs
1655
+ KISAO_0000498 = "KISAO_0000498"
1656
+ NUMBER_OF_RUNS = "KISAO_0000498"
1657
+
1658
+ # dynamic flux balance analysis
1659
+ KISAO_0000499 = "KISAO_0000499"
1660
+ DYNAMIC_FLUX_BALANCE_ANALYSIS = "KISAO_0000499"
1661
+
1662
+ # SOA-DFBA
1663
+ KISAO_0000500 = "KISAO_0000500"
1664
+ SOA_DFBA = "KISAO_0000500"
1665
+
1666
+ # DOA-DFBA
1667
+ KISAO_0000501 = "KISAO_0000501"
1668
+ DOA_DFBA = "KISAO_0000501"
1669
+
1670
+ # DA-DFBA
1671
+ KISAO_0000502 = "KISAO_0000502"
1672
+ DA_DFBA = "KISAO_0000502"
1673
+
1674
+ # simulated annealing
1675
+ KISAO_0000503 = "KISAO_0000503"
1676
+ SIMULATED_ANNEALING = "KISAO_0000503"
1677
+
1678
+ # random search
1679
+ KISAO_0000504 = "KISAO_0000504"
1680
+ RANDOM_SEARCH = "KISAO_0000504"
1681
+
1682
+ # particle swarm
1683
+ KISAO_0000505 = "KISAO_0000505"
1684
+ PARTICLE_SWARM = "KISAO_0000505"
1685
+
1686
+ # genetic algorithm
1687
+ KISAO_0000506 = "KISAO_0000506"
1688
+ GENETIC_ALGORITHM = "KISAO_0000506"
1689
+
1690
+ # genetic algorithm SR
1691
+ KISAO_0000507 = "KISAO_0000507"
1692
+ GENETIC_ALGORITHM_SR = "KISAO_0000507"
1693
+
1694
+ # evolutionary programming
1695
+ KISAO_0000508 = "KISAO_0000508"
1696
+ EVOLUTIONARY_PROGRAMMING = "KISAO_0000508"
1697
+
1698
+ # evolutionary strategy
1699
+ KISAO_0000509 = "KISAO_0000509"
1700
+ EVOLUTIONARY_STRATEGY = "KISAO_0000509"
1701
+
1702
+ # truncated Newton
1703
+ KISAO_0000510 = "KISAO_0000510"
1704
+ TRUNCATED_NEWTON = "KISAO_0000510"
1705
+
1706
+ # steepest descent
1707
+ KISAO_0000511 = "KISAO_0000511"
1708
+ STEEPEST_DESCENT = "KISAO_0000511"
1709
+
1710
+ # praxis
1711
+ KISAO_0000512 = "KISAO_0000512"
1712
+ PRAXIS = "KISAO_0000512"
1713
+
1714
+ # NL2SOL
1715
+ KISAO_0000513 = "KISAO_0000513"
1716
+ NL2SOL = "KISAO_0000513"
1717
+
1718
+ # Nelder-Mead
1719
+ KISAO_0000514 = "KISAO_0000514"
1720
+ NELDER_MEAD = "KISAO_0000514"
1721
+
1722
+ # Levenberg-Marquardt
1723
+ KISAO_0000515 = "KISAO_0000515"
1724
+ LEVENBERG_MARQUARDT = "KISAO_0000515"
1725
+
1726
+ # Hooke&Jeeves
1727
+ KISAO_0000516 = "KISAO_0000516"
1728
+ HOOKE_JEEVES = "KISAO_0000516"
1729
+
1730
+ # number of generations
1731
+ KISAO_0000517 = "KISAO_0000517"
1732
+ NUMBER_OF_GENERATIONS = "KISAO_0000517"
1733
+
1734
+ # evolutionary algorithm parameter
1735
+ KISAO_0000518 = "KISAO_0000518"
1736
+ EVOLUTIONARY_ALGORITHM_PARAMETER = "KISAO_0000518"
1737
+
1738
+ # population size
1739
+ KISAO_0000519 = "KISAO_0000519"
1740
+ POPULATION_SIZE = "KISAO_0000519"
1741
+
1742
+ # evolutionary algorithm
1743
+ KISAO_0000520 = "KISAO_0000520"
1744
+ EVOLUTIONARY_ALGORITHM = "KISAO_0000520"
1745
+
1746
+ # simulated annealing parameter
1747
+ KISAO_0000521 = "KISAO_0000521"
1748
+ SIMULATED_ANNEALING_PARAMETER = "KISAO_0000521"
1749
+
1750
+ # start temperature
1751
+ KISAO_0000522 = "KISAO_0000522"
1752
+ START_TEMPERATURE = "KISAO_0000522"
1753
+
1754
+ # cooling factor
1755
+ KISAO_0000523 = "KISAO_0000523"
1756
+ COOLING_FACTOR = "KISAO_0000523"
1757
+
1758
+ # partitioned leaping method
1759
+ KISAO_0000524 = "KISAO_0000524"
1760
+ PARTITIONED_LEAPING_METHOD = "KISAO_0000524"
1761
+
1762
+ # stop condition
1763
+ KISAO_0000525 = "KISAO_0000525"
1764
+ STOP_CONDITION = "KISAO_0000525"
1765
+
1766
+ # flux variability analysis
1767
+ KISAO_0000526 = "KISAO_0000526"
1768
+ FLUX_VARIABILITY_ANALYSIS = "KISAO_0000526"
1769
+
1770
+ # geometric flux balance analysis
1771
+ KISAO_0000527 = "KISAO_0000527"
1772
+ GEOMETRIC_FLUX_BALANCE_ANALYSIS = "KISAO_0000527"
1773
+
1774
+ # parsimonious enzyme usage flux balance analysis (minimum sum of absolute fluxes)
1775
+ KISAO_0000528 = "KISAO_0000528"
1776
+ PARSIMONIOUS_ENZYME_USAGE_FLUX_BALANCE_ANALYSIS__MINIMUM_SUM_OF_ABSOLUTE_FLUXES_ = (
1777
+ "KISAO_0000528"
1778
+ )
1779
+
1780
+ # parallelism
1781
+ KISAO_0000529 = "KISAO_0000529"
1782
+ PARALLELISM = "KISAO_0000529"
1783
+
1784
+ # fraction of optimum
1785
+ KISAO_0000531 = "KISAO_0000531"
1786
+ FRACTION_OF_OPTIMUM = "KISAO_0000531"
1787
+
1788
+ # loopless
1789
+ KISAO_0000532 = "KISAO_0000532"
1790
+ LOOPLESS = "KISAO_0000532"
1791
+
1792
+ # pFBA factor
1793
+ KISAO_0000533 = "KISAO_0000533"
1794
+ PFBA_FACTOR = "KISAO_0000533"
1795
+
1796
+ # reactions
1797
+ KISAO_0000534 = "KISAO_0000534"
1798
+ REACTIONS = "KISAO_0000534"
1799
+
1800
+ # VODE
1801
+ KISAO_0000535 = "KISAO_0000535"
1802
+ VODE = "KISAO_0000535"
1803
+
1804
+ # ZVODE
1805
+ KISAO_0000536 = "KISAO_0000536"
1806
+ ZVODE = "KISAO_0000536"
1807
+
1808
+ # explicit Runge-Kutta method of order 3(2)
1809
+ KISAO_0000537 = "KISAO_0000537"
1810
+ EXPLICIT_RUNGE_KUTTA_METHOD_OF_ORDER_3_2_ = "KISAO_0000537"
1811
+
1812
+ # safety factor on new step selection
1813
+ KISAO_0000538 = "KISAO_0000538"
1814
+ SAFETY_FACTOR_ON_NEW_STEP_SELECTION = "KISAO_0000538"
1815
+
1816
+ # minimum factor to change step size by
1817
+ KISAO_0000539 = "KISAO_0000539"
1818
+ MINIMUM_FACTOR_TO_CHANGE_STEP_SIZE_BY = "KISAO_0000539"
1819
+
1820
+ # maximum factor to change step size by
1821
+ KISAO_0000540 = "KISAO_0000540"
1822
+ MAXIMUM_FACTOR_TO_CHANGE_STEP_SIZE_BY = "KISAO_0000540"
1823
+
1824
+ # beta parameter for stabilized step size control
1825
+ KISAO_0000541 = "KISAO_0000541"
1826
+ BETA_PARAMETER_FOR_STABILIZED_STEP_SIZE_CONTROL = "KISAO_0000541"
1827
+
1828
+ # correction step should use internally generated full Jacobian
1829
+ KISAO_0000542 = "KISAO_0000542"
1830
+ CORRECTION_STEP_SHOULD_USE_INTERNALLY_GENERATED_FULL_JACOBIAN = "KISAO_0000542"
1831
+
1832
+ # stability limit detection flag
1833
+ KISAO_0000543 = "KISAO_0000543"
1834
+ STABILITY_LIMIT_DETECTION_FLAG = "KISAO_0000543"
1835
+
1836
+ # IDAS
1837
+ KISAO_0000544 = "KISAO_0000544"
1838
+ IDAS = "KISAO_0000544"
1839
+
1840
+ # include sensitivity variables in error control mechanism
1841
+ KISAO_0000545 = "KISAO_0000545"
1842
+ INCLUDE_SENSITIVITY_VARIABLES_IN_ERROR_CONTROL_MECHANISM = "KISAO_0000545"
1843
+
1844
+ # convex optimization algorithm
1845
+ KISAO_0000546 = "KISAO_0000546"
1846
+ CONVEX_OPTIMIZATION_ALGORITHM = "KISAO_0000546"
1847
+
1848
+ # linear programming
1849
+ KISAO_0000547 = "KISAO_0000547"
1850
+ LINEAR_PROGRAMMING = "KISAO_0000547"
1851
+
1852
+ # quadratic programming
1853
+ KISAO_0000548 = "KISAO_0000548"
1854
+ QUADRATIC_PROGRAMMING = "KISAO_0000548"
1855
+
1856
+ # non-linear programming
1857
+ KISAO_0000549 = "KISAO_0000549"
1858
+ NON_LINEAR_PROGRAMMING = "KISAO_0000549"
1859
+
1860
+ # simplex method
1861
+ KISAO_0000550 = "KISAO_0000550"
1862
+ SIMPLEX_METHOD = "KISAO_0000550"
1863
+
1864
+ # primal-dual interior point method
1865
+ KISAO_0000551 = "KISAO_0000551"
1866
+ PRIMAL_DUAL_INTERIOR_POINT_METHOD = "KISAO_0000551"
1867
+
1868
+ # optimization method
1869
+ KISAO_0000552 = "KISAO_0000552"
1870
+ OPTIMIZATION_METHOD = "KISAO_0000552"
1871
+
1872
+ # optimization solver
1873
+ KISAO_0000553 = "KISAO_0000553"
1874
+ OPTIMIZATION_SOLVER = "KISAO_0000553"
1875
+
1876
+ # parsimonius flux balance analysis (minimum number of active fluxes)
1877
+ KISAO_0000554 = "KISAO_0000554"
1878
+ PARSIMONIUS_FLUX_BALANCE_ANALYSIS__MINIMUM_NUMBER_OF_ACTIVE_FLUXES_ = (
1879
+ "KISAO_0000554"
1880
+ )
1881
+
1882
+ # absolute quadrature tolerance
1883
+ KISAO_0000555 = "KISAO_0000555"
1884
+ ABSOLUTE_QUADRATURE_TOLERANCE = "KISAO_0000555"
1885
+
1886
+ # relative quadrature tolerance
1887
+ KISAO_0000556 = "KISAO_0000556"
1888
+ RELATIVE_QUADRATURE_TOLERANCE = "KISAO_0000556"
1889
+
1890
+ # absolute steady-state tolerance
1891
+ KISAO_0000557 = "KISAO_0000557"
1892
+ ABSOLUTE_STEADY_STATE_TOLERANCE = "KISAO_0000557"
1893
+
1894
+ # relative steady-state tolerance
1895
+ KISAO_0000558 = "KISAO_0000558"
1896
+ RELATIVE_STEADY_STATE_TOLERANCE = "KISAO_0000558"
1897
+
1898
+ # initial step size
1899
+ KISAO_0000559 = "KISAO_0000559"
1900
+ INITIAL_STEP_SIZE = "KISAO_0000559"
1901
+
1902
+ # LSODA/LSODAR hybrid method
1903
+ KISAO_0000560 = "KISAO_0000560"
1904
+ LSODA_LSODAR_HYBRID_METHOD = "KISAO_0000560"
1905
+
1906
+ # Pahle hybrid Gibson-Bruck Next Reaction method/Runge-Kutta method
1907
+ KISAO_0000561 = "KISAO_0000561"
1908
+ PAHLE_HYBRID_GIBSON_BRUCK_NEXT_REACTION_METHOD_RUNGE_KUTTA_METHOD = "KISAO_0000561"
1909
+
1910
+ # Pahle hybrid Gibson-Bruck Next Reaction method/LSODA method
1911
+ KISAO_0000562 = "KISAO_0000562"
1912
+ PAHLE_HYBRID_GIBSON_BRUCK_NEXT_REACTION_METHOD_LSODA_METHOD = "KISAO_0000562"
1913
+
1914
+ # Pahle hybrid Gibson-Bruck Next Reaction method/RK-45 method
1915
+ KISAO_0000563 = "KISAO_0000563"
1916
+ PAHLE_HYBRID_GIBSON_BRUCK_NEXT_REACTION_METHOD_RK_45_METHOD = "KISAO_0000563"
1917
+
1918
+ # stochastic Runge-Kutta method
1919
+ KISAO_0000564 = "KISAO_0000564"
1920
+ STOCHASTIC_RUNGE_KUTTA_METHOD = "KISAO_0000564"
1921
+
1922
+ # absolute tolerance for root finding
1923
+ KISAO_0000565 = "KISAO_0000565"
1924
+ ABSOLUTE_TOLERANCE_FOR_ROOT_FINDING = "KISAO_0000565"
1925
+
1926
+ # stochastic second order Runge-Kutta method
1927
+ KISAO_0000566 = "KISAO_0000566"
1928
+ STOCHASTIC_SECOND_ORDER_RUNGE_KUTTA_METHOD = "KISAO_0000566"
1929
+
1930
+ # force physical correctness
1931
+ KISAO_0000567 = "KISAO_0000567"
1932
+ FORCE_PHYSICAL_CORRECTNESS = "KISAO_0000567"
1933
+
1934
+ # NLEQ1
1935
+ KISAO_0000568 = "KISAO_0000568"
1936
+ NLEQ1 = "KISAO_0000568"
1937
+
1938
+ # NLEQ2
1939
+ KISAO_0000569 = "KISAO_0000569"
1940
+ NLEQ2 = "KISAO_0000569"
1941
+
1942
+ # auto reduce tolerances
1943
+ KISAO_0000570 = "KISAO_0000570"
1944
+ AUTO_REDUCE_TOLERANCES = "KISAO_0000570"
1945
+
1946
+ # absolute tolerance adjustment factor
1947
+ KISAO_0000571 = "KISAO_0000571"
1948
+ ABSOLUTE_TOLERANCE_ADJUSTMENT_FACTOR = "KISAO_0000571"
1949
+
1950
+ # level of superimposed noise
1951
+ KISAO_0000572 = "KISAO_0000572"
1952
+ LEVEL_OF_SUPERIMPOSED_NOISE = "KISAO_0000572"
1953
+
1954
+ # probabilistic logical model simulation method
1955
+ KISAO_0000573 = "KISAO_0000573"
1956
+ PROBABILISTIC_LOGICAL_MODEL_SIMULATION_METHOD = "KISAO_0000573"
1957
+
1958
+ # species transition probabilities
1959
+ KISAO_0000574 = "KISAO_0000574"
1960
+ SPECIES_TRANSITION_PROBABILITIES = "KISAO_0000574"
1961
+
1962
+ # hybrid tau-leaping method
1963
+ KISAO_0000575 = "KISAO_0000575"
1964
+ HYBRID_TAU_LEAPING_METHOD = "KISAO_0000575"
1965
+
1966
+ # quadratic MOMA
1967
+ KISAO_0000576 = "KISAO_0000576"
1968
+ QUADRATIC_MOMA = "KISAO_0000576"
1969
+
1970
+ # flux minimization weight
1971
+ KISAO_0000577 = "KISAO_0000577"
1972
+ FLUX_MINIMIZATION_WEIGHT = "KISAO_0000577"
1973
+
1974
+ # nested algorithm
1975
+ KISAO_0000578 = "KISAO_0000578"
1976
+ NESTED_ALGORITHM = "KISAO_0000578"
1977
+
1978
+ # linear MOMA
1979
+ KISAO_0000579 = "KISAO_0000579"
1980
+ LINEAR_MOMA = "KISAO_0000579"
1981
+
1982
+ # ROOM
1983
+ KISAO_0000580 = "KISAO_0000580"
1984
+ ROOM = "KISAO_0000580"
1985
+
1986
+ # BKMC
1987
+ KISAO_0000581 = "KISAO_0000581"
1988
+ BKMC = "KISAO_0000581"
1989
+
1990
+ # Spatiocyte method
1991
+ KISAO_0000582 = "KISAO_0000582"
1992
+ SPATIOCYTE_METHOD = "KISAO_0000582"
1993
+
1994
+ # minimum order
1995
+ KISAO_0000583 = "KISAO_0000583"
1996
+ MINIMUM_ORDER = "KISAO_0000583"
1997
+
1998
+ # initial order
1999
+ KISAO_0000584 = "KISAO_0000584"
2000
+ INITIAL_ORDER = "KISAO_0000584"
2001
+
2002
+ # TOMS731
2003
+ KISAO_0000585 = "KISAO_0000585"
2004
+ TOMS731 = "KISAO_0000585"
2005
+
2006
+ # Gibson-Bruck next reaction algorithm with indexed priority queue
2007
+ KISAO_0000586 = "KISAO_0000586"
2008
+ GIBSON_BRUCK_NEXT_REACTION_ALGORITHM_WITH_INDEXED_PRIORITY_QUEUE = "KISAO_0000586"
2009
+
2010
+ # IMEX
2011
+ KISAO_0000587 = "KISAO_0000587"
2012
+ IMEX = "KISAO_0000587"
2013
+
2014
+ # flux sampling
2015
+ KISAO_0000588 = "KISAO_0000588"
2016
+ FLUX_SAMPLING = "KISAO_0000588"
2017
+
2018
+ # ACB flux sampling method
2019
+ KISAO_0000589 = "KISAO_0000589"
2020
+ ACB_FLUX_SAMPLING_METHOD = "KISAO_0000589"
2021
+
2022
+ # ACHR flux sampling method
2023
+ KISAO_0000590 = "KISAO_0000590"
2024
+ ACHR_FLUX_SAMPLING_METHOD = "KISAO_0000590"
2025
+
2026
+ # mdFBA
2027
+ KISAO_0000591 = "KISAO_0000591"
2028
+ MDFBA = "KISAO_0000591"
2029
+
2030
+ # dynamic rFBA
2031
+ KISAO_0000592 = "KISAO_0000592"
2032
+ DYNAMIC_RFBA = "KISAO_0000592"
2033
+
2034
+ # MOMA
2035
+ KISAO_0000593 = "KISAO_0000593"
2036
+ MOMA = "KISAO_0000593"
2037
+
2038
+ # order
2039
+ KISAO_0000594 = "KISAO_0000594"
2040
+ ORDER = "KISAO_0000594"
2041
+
2042
+ # rFBA
2043
+ KISAO_0000595 = "KISAO_0000595"
2044
+ RFBA = "KISAO_0000595"
2045
+
2046
+ # srFBA
2047
+ KISAO_0000596 = "KISAO_0000596"
2048
+ SRFBA = "KISAO_0000596"
2049
+
2050
+ # tolerance
2051
+ KISAO_0000597 = "KISAO_0000597"
2052
+ TOLERANCE = "KISAO_0000597"
2053
+
2054
+ # hybrid Gibson - Milstein method
2055
+ KISAO_0000598 = "KISAO_0000598"
2056
+ HYBRID_GIBSON___MILSTEIN_METHOD = "KISAO_0000598"
2057
+
2058
+ # hybrid Gibson - Euler-Maruyama method
2059
+ KISAO_0000599 = "KISAO_0000599"
2060
+ HYBRID_GIBSON___EULER_MARUYAMA_METHOD = "KISAO_0000599"
2061
+
2062
+ # hybrid adaptive Gibson - Milstein method
2063
+ KISAO_0000600 = "KISAO_0000600"
2064
+ HYBRID_ADAPTIVE_GIBSON___MILSTEIN_METHOD = "KISAO_0000600"
2065
+
2066
+ # number of trials
2067
+ KISAO_0000601 = "KISAO_0000601"
2068
+ NUMBER_OF_TRIALS = "KISAO_0000601"
2069
+
2070
+ # minimum species threshold for continuous approximation
2071
+ KISAO_0000602 = "KISAO_0000602"
2072
+ MINIMUM_SPECIES_THRESHOLD_FOR_CONTINUOUS_APPROXIMATION = "KISAO_0000602"
2073
+
2074
+ # minimum reaction rate for continuous approximation
2075
+ KISAO_0000603 = "KISAO_0000603"
2076
+ MINIMUM_REACTION_RATE_FOR_CONTINUOUS_APPROXIMATION = "KISAO_0000603"
2077
+
2078
+ # MSR tolerance
2079
+ KISAO_0000604 = "KISAO_0000604"
2080
+ MSR_TOLERANCE = "KISAO_0000604"
2081
+
2082
+ # SDE tolerance
2083
+ KISAO_0000605 = "KISAO_0000605"
2084
+ SDE_TOLERANCE = "KISAO_0000605"
2085
+
2086
+ # hierarchical stochastic simulation algorithm
2087
+ KISAO_0000606 = "KISAO_0000606"
2088
+ HIERARCHICAL_STOCHASTIC_SIMULATION_ALGORITHM = "KISAO_0000606"
2089
+
2090
+ # hierarchical Fehlberg method
2091
+ KISAO_0000607 = "KISAO_0000607"
2092
+ HIERARCHICAL_FEHLBERG_METHOD = "KISAO_0000607"
2093
+
2094
+ # hierarchical flux balance analysis
2095
+ KISAO_0000608 = "KISAO_0000608"
2096
+ HIERARCHICAL_FLUX_BALANCE_ANALYSIS = "KISAO_0000608"
2097
+
2098
+ # embedded Runge-Kutta Prince-Dormand (8,9) method
2099
+ KISAO_0000609 = "KISAO_0000609"
2100
+ EMBEDDED_RUNGE_KUTTA_PRINCE_DORMAND__8_9__METHOD = "KISAO_0000609"
2101
+
2102
+ # composite-rejection stochastic simulation algorithm
2103
+ KISAO_0000610 = "KISAO_0000610"
2104
+ COMPOSITE_REJECTION_STOCHASTIC_SIMULATION_ALGORITHM = "KISAO_0000610"
2105
+
2106
+ # incremental stochastic simulation algorithm
2107
+ KISAO_0000611 = "KISAO_0000611"
2108
+ INCREMENTAL_STOCHASTIC_SIMULATION_ALGORITHM = "KISAO_0000611"
2109
+
2110
+ # implicit 4th order Runge-Kutta method at Gaussian points
2111
+ KISAO_0000612 = "KISAO_0000612"
2112
+ IMPLICIT_4TH_ORDER_RUNGE_KUTTA_METHOD_AT_GAUSSIAN_POINTS = "KISAO_0000612"
2113
+
2114
+ # stochastic simulation algorithm with normally-distributed next reaction times
2115
+ KISAO_0000613 = "KISAO_0000613"
2116
+ STOCHASTIC_SIMULATION_ALGORITHM_WITH_NORMALLY_DISTRIBUTED_NEXT_REACTION_TIMES = (
2117
+ "KISAO_0000613"
2118
+ )
2119
+
2120
+ # implementation
2121
+ KISAO_0000614 = "KISAO_0000614"
2122
+ IMPLEMENTATION = "KISAO_0000614"
2123
+
2124
+ # fully-implicit regular grid finite volume method with a variable time step
2125
+ KISAO_0000615 = "KISAO_0000615"
2126
+ FULLY_IMPLICIT_REGULAR_GRID_FINITE_VOLUME_METHOD_WITH_A_VARIABLE_TIME_STEP = (
2127
+ "KISAO_0000615"
2128
+ )
2129
+
2130
+ # semi-implicit regular grid finite volume method with a fixed time step
2131
+ KISAO_0000616 = "KISAO_0000616"
2132
+ SEMI_IMPLICIT_REGULAR_GRID_FINITE_VOLUME_METHOD_WITH_A_FIXED_TIME_STEP = (
2133
+ "KISAO_0000616"
2134
+ )
2135
+
2136
+ # IDA-CVODE hybrid method
2137
+ KISAO_0000617 = "KISAO_0000617"
2138
+ IDA_CVODE_HYBRID_METHOD = "KISAO_0000617"
2139
+
2140
+ # bunker
2141
+ KISAO_0000618 = "KISAO_0000618"
2142
+ BUNKER = "KISAO_0000618"
2143
+
2144
+ # emc-sim
2145
+ KISAO_0000619 = "KISAO_0000619"
2146
+ EMC_SIM = "KISAO_0000619"
2147
+
2148
+ # parsimonius flux balance analysis
2149
+ KISAO_0000620 = "KISAO_0000620"
2150
+ PARSIMONIUS_FLUX_BALANCE_ANALYSIS = "KISAO_0000620"
2151
+
2152
+ # stochastic simulation leaping method
2153
+ KISAO_0000621 = "KISAO_0000621"
2154
+ STOCHASTIC_SIMULATION_LEAPING_METHOD = "KISAO_0000621"
2155
+
2156
+ # flux balance method
2157
+ KISAO_0000622 = "KISAO_0000622"
2158
+ FLUX_BALANCE_METHOD = "KISAO_0000622"
2159
+
2160
+ # flux balance problem
2161
+ KISAO_0000623 = "KISAO_0000623"
2162
+ FLUX_BALANCE_PROBLEM = "KISAO_0000623"
2163
+
2164
+ # method for solving a system of linear equations
2165
+ KISAO_0000624 = "KISAO_0000624"
2166
+ METHOD_FOR_SOLVING_A_SYSTEM_OF_LINEAR_EQUATIONS = "KISAO_0000624"
2167
+
2168
+ # dense direct solver
2169
+ KISAO_0000625 = "KISAO_0000625"
2170
+ DENSE_DIRECT_SOLVER = "KISAO_0000625"
2171
+
2172
+ # band direct solver
2173
+ KISAO_0000626 = "KISAO_0000626"
2174
+ BAND_DIRECT_SOLVER = "KISAO_0000626"
2175
+
2176
+ # diagonal approximate Jacobian solver
2177
+ KISAO_0000627 = "KISAO_0000627"
2178
+ DIAGONAL_APPROXIMATE_JACOBIAN_SOLVER = "KISAO_0000627"
2179
+
2180
+ # modelling and simulation algorithm parameter value
2181
+ KISAO_0000628 = "KISAO_0000628"
2182
+ MODELLING_AND_SIMULATION_ALGORITHM_PARAMETER_VALUE = "KISAO_0000628"
2183
+
2184
+ # null
2185
+ KISAO_0000629 = "KISAO_0000629"
2186
+ NULL = "KISAO_0000629"
2187
+
2188
+ # general steady state method
2189
+ KISAO_0000630 = "KISAO_0000630"
2190
+ GENERAL_STEADY_STATE_METHOD = "KISAO_0000630"
2191
+
2192
+ # iterative root-finding method
2193
+ KISAO_0000631 = "KISAO_0000631"
2194
+ ITERATIVE_ROOT_FINDING_METHOD = "KISAO_0000631"
2195
+
2196
+ # functional iteration root-finding method
2197
+ KISAO_0000632 = "KISAO_0000632"
2198
+ FUNCTIONAL_ITERATION_ROOT_FINDING_METHOD = "KISAO_0000632"
2199
+
2200
+ # computational function
2201
+ KISAO_0000633 = "KISAO_0000633"
2202
+ COMPUTATIONAL_FUNCTION = "KISAO_0000633"
2203
+
2204
+ # scaled property
2205
+ KISAO_0000634 = "KISAO_0000634"
2206
+ SCALED_PROPERTY = "KISAO_0000634"
2207
+
2208
+ # unscaled property
2209
+ KISAO_0000635 = "KISAO_0000635"
2210
+ UNSCALED_PROPERTY = "KISAO_0000635"
2211
+
2212
+ # primary property
2213
+ KISAO_0000636 = "KISAO_0000636"
2214
+ PRIMARY_PROPERTY = "KISAO_0000636"
2215
+
2216
+ # derived property
2217
+ KISAO_0000637 = "KISAO_0000637"
2218
+ DERIVED_PROPERTY = "KISAO_0000637"
2219
+
2220
+ # level
2221
+ KISAO_0000638 = "KISAO_0000638"
2222
+ LEVEL = "KISAO_0000638"
2223
+
2224
+ # flux
2225
+ KISAO_0000639 = "KISAO_0000639"
2226
+ FLUX = "KISAO_0000639"
2227
+
2228
+ # lower bound
2229
+ KISAO_0000640 = "KISAO_0000640"
2230
+ LOWER_BOUND = "KISAO_0000640"
2231
+
2232
+ # bound
2233
+ KISAO_0000641 = "KISAO_0000641"
2234
+ BOUND = "KISAO_0000641"
2235
+
2236
+ # minimum flux
2237
+ KISAO_0000642 = "KISAO_0000642"
2238
+ MINIMUM_FLUX = "KISAO_0000642"
2239
+
2240
+ # upper bound
2241
+ KISAO_0000643 = "KISAO_0000643"
2242
+ UPPER_BOUND = "KISAO_0000643"
2243
+
2244
+ # maximum flux
2245
+ KISAO_0000644 = "KISAO_0000644"
2246
+ MAXIMUM_FLUX = "KISAO_0000644"
2247
+
2248
+ # objective value
2249
+ KISAO_0000645 = "KISAO_0000645"
2250
+ OBJECTIVE_VALUE = "KISAO_0000645"
2251
+
2252
+ # propensity
2253
+ KISAO_0000646 = "KISAO_0000646"
2254
+ PROPENSITY = "KISAO_0000646"
2255
+
2256
+ # derivative
2257
+ KISAO_0000647 = "KISAO_0000647"
2258
+ DERIVATIVE = "KISAO_0000647"
2259
+
2260
+ # step
2261
+ KISAO_0000648 = "KISAO_0000648"
2262
+ STEP = "KISAO_0000648"
2263
+
2264
+ # shadow price
2265
+ KISAO_0000649 = "KISAO_0000649"
2266
+ SHADOW_PRICE = "KISAO_0000649"
2267
+
2268
+ # sensitivity
2269
+ KISAO_0000650 = "KISAO_0000650"
2270
+ SENSITIVITY = "KISAO_0000650"
2271
+
2272
+ # reduced costs
2273
+ KISAO_0000651 = "KISAO_0000651"
2274
+ REDUCED_COSTS = "KISAO_0000651"
2275
+
2276
+ # concentration rate
2277
+ KISAO_0000652 = "KISAO_0000652"
2278
+ CONCENTRATION_RATE = "KISAO_0000652"
2279
+
2280
+ # particle number rate
2281
+ KISAO_0000653 = "KISAO_0000653"
2282
+ PARTICLE_NUMBER_RATE = "KISAO_0000653"
2283
+
2284
+ # amount rate
2285
+ KISAO_0000654 = "KISAO_0000654"
2286
+ AMOUNT_RATE = "KISAO_0000654"
2287
+
2288
+ # rate
2289
+ KISAO_0000655 = "KISAO_0000655"
2290
+ RATE = "KISAO_0000655"
2291
+
2292
+ # use adaptive time steps
2293
+ KISAO_0000656 = "KISAO_0000656"
2294
+ USE_ADAPTIVE_TIME_STEPS = "KISAO_0000656"
2295
+
2296
+ # sequential logical simulation method
2297
+ KISAO_0000657 = "KISAO_0000657"
2298
+ SEQUENTIAL_LOGICAL_SIMULATION_METHOD = "KISAO_0000657"
2299
+
2300
+ # logical model analysis method
2301
+ KISAO_0000658 = "KISAO_0000658"
2302
+ LOGICAL_MODEL_ANALYSIS_METHOD = "KISAO_0000658"
2303
+
2304
+ # Naldi MDD logical model stable state search method
2305
+ KISAO_0000659 = "KISAO_0000659"
2306
+ NALDI_MDD_LOGICAL_MODEL_STABLE_STATE_SEARCH_METHOD = "KISAO_0000659"
2307
+
2308
+ # logical model stable state search method
2309
+ KISAO_0000660 = "KISAO_0000660"
2310
+ LOGICAL_MODEL_STABLE_STATE_SEARCH_METHOD = "KISAO_0000660"
2311
+
2312
+ # logical model trap space identification method
2313
+ KISAO_0000661 = "KISAO_0000661"
2314
+ LOGICAL_MODEL_TRAP_SPACE_IDENTIFICATION_METHOD = "KISAO_0000661"
2315
+
2316
+ # Klarner ASP logical model trap space identification method
2317
+ KISAO_0000662 = "KISAO_0000662"
2318
+ KLARNER_ASP_LOGICAL_MODEL_TRAP_SPACE_IDENTIFICATION_METHOD = "KISAO_0000662"
2319
+
2320
+ # BDD logical model trap space identification method
2321
+ KISAO_0000663 = "KISAO_0000663"
2322
+ BDD_LOGICAL_MODEL_TRAP_SPACE_IDENTIFICATION_METHOD = "KISAO_0000663"
2323
+
2324
+ # Second order backward implicit product Euler scheme
2325
+ KISAO_0000664 = "KISAO_0000664"
2326
+ SECOND_ORDER_BACKWARD_IMPLICIT_PRODUCT_EULER_SCHEME = "KISAO_0000664"
2327
+
2328
+ # maximum number of iterations for root finding
2329
+ KISAO_0000665 = "KISAO_0000665"
2330
+ MAXIMUM_NUMBER_OF_ITERATIONS_FOR_ROOT_FINDING = "KISAO_0000665"
2331
+
2332
+ # Jacobian epsilon
2333
+ KISAO_0000666 = "KISAO_0000666"
2334
+ JACOBIAN_EPSILON = "KISAO_0000666"
2335
+
2336
+ # memory size
2337
+ KISAO_0000667 = "KISAO_0000667"
2338
+ MEMORY_SIZE = "KISAO_0000667"
2339
+
2340
+ # Numerical Recipes in C 'stiff' Rosenbrock method
2341
+ KISAO_0000668 = "KISAO_0000668"
2342
+ NUMERICAL_RECIPES_IN_C__STIFF__ROSENBROCK_METHOD = "KISAO_0000668"
2343
+
2344
+ # Resource Balance Analysis
2345
+ KISAO_0000669 = "KISAO_0000669"
2346
+ RESOURCE_BALANCE_ANALYSIS = "KISAO_0000669"
2347
+
2348
+ # use multiple steps
2349
+ KISAO_0000670 = "KISAO_0000670"
2350
+ USE_MULTIPLE_STEPS = "KISAO_0000670"
2351
+
2352
+ # use stiff method
2353
+ KISAO_0000671 = "KISAO_0000671"
2354
+ USE_STIFF_METHOD = "KISAO_0000671"
2355
+
2356
+ # Numerical Recipes in C 'quality-controlled Runge-Kutta' method
2357
+ KISAO_0000672 = "KISAO_0000672"
2358
+ NUMERICAL_RECIPES_IN_C__QUALITY_CONTROLLED_RUNGE_KUTTA__METHOD = "KISAO_0000672"
2359
+
2360
+ # skip reactions that produce negative species amounts
2361
+ KISAO_0000673 = "KISAO_0000673"
2362
+ SKIP_REACTIONS_THAT_PRODUCE_NEGATIVE_SPECIES_AMOUNTS = "KISAO_0000673"
2363
+
2364
+ # presimulate
2365
+ KISAO_0000674 = "KISAO_0000674"
2366
+ PRESIMULATE = "KISAO_0000674"
2367
+
2368
+ # Broyden method
2369
+ KISAO_0000675 = "KISAO_0000675"
2370
+ BROYDEN_METHOD = "KISAO_0000675"
2371
+
2372
+ # degree of linearity
2373
+ KISAO_0000676 = "KISAO_0000676"
2374
+ DEGREE_OF_LINEARITY = "KISAO_0000676"
2375
+
2376
+ # maximum number of steps for presimulation
2377
+ KISAO_0000677 = "KISAO_0000677"
2378
+ MAXIMUM_NUMBER_OF_STEPS_FOR_PRESIMULATION = "KISAO_0000677"
2379
+
2380
+ # maximum number of steps for approximation
2381
+ KISAO_0000678 = "KISAO_0000678"
2382
+ MAXIMUM_NUMBER_OF_STEPS_FOR_APPROXIMATION = "KISAO_0000678"
2383
+
2384
+ # maximum time for approximation
2385
+ KISAO_0000679 = "KISAO_0000679"
2386
+ MAXIMUM_TIME_FOR_APPROXIMATION = "KISAO_0000679"
2387
+
2388
+ # duration
2389
+ KISAO_0000680 = "KISAO_0000680"
2390
+ DURATION = "KISAO_0000680"
2391
+
2392
+ # maximum time
2393
+ KISAO_0000681 = "KISAO_0000681"
2394
+ MAXIMUM_TIME = "KISAO_0000681"
2395
+
2396
+ # allow approximation
2397
+ KISAO_0000682 = "KISAO_0000682"
2398
+ ALLOW_APPROXIMATION = "KISAO_0000682"
2399
+
2400
+ # relative tolerance for approximation
2401
+ KISAO_0000683 = "KISAO_0000683"
2402
+ RELATIVE_TOLERANCE_FOR_APPROXIMATION = "KISAO_0000683"
2403
+
2404
+ # number of steps per output
2405
+ KISAO_0000684 = "KISAO_0000684"
2406
+ NUMBER_OF_STEPS_PER_OUTPUT = "KISAO_0000684"
2407
+
2408
+ # biological state optimization method
2409
+ KISAO_0000685 = "KISAO_0000685"
2410
+ BIOLOGICAL_STATE_OPTIMIZATION_METHOD = "KISAO_0000685"
2411
+
2412
+ # Enzyme Cost Minimization
2413
+ KISAO_0000686 = "KISAO_0000686"
2414
+ ENZYME_COST_MINIMIZATION = "KISAO_0000686"
2415
+
2416
+ # Max-min Driving Force method
2417
+ KISAO_0000687 = "KISAO_0000687"
2418
+ MAX_MIN_DRIVING_FORCE_METHOD = "KISAO_0000687"
2419
+
2420
+ # type of system described
2421
+ KISAO_0000688 = "KISAO_0000688"
2422
+ TYPE_OF_SYSTEM_DESCRIBED = "KISAO_0000688"
2423
+
2424
+ # mathematical system
2425
+ KISAO_0000689 = "KISAO_0000689"
2426
+ MATHEMATICAL_SYSTEM = "KISAO_0000689"
2427
+
2428
+ # biological system
2429
+ KISAO_0000690 = "KISAO_0000690"
2430
+ BIOLOGICAL_SYSTEM = "KISAO_0000690"
2431
+
2432
+ # metabolic system
2433
+ KISAO_0000691 = "KISAO_0000691"
2434
+ METABOLIC_SYSTEM = "KISAO_0000691"
2435
+
2436
+ # cellular system
2437
+ KISAO_0000692 = "KISAO_0000692"
2438
+ CELLULAR_SYSTEM = "KISAO_0000692"
2439
+
2440
+ # biochemical system
2441
+ KISAO_0000693 = "KISAO_0000693"
2442
+ BIOCHEMICAL_SYSTEM = "KISAO_0000693"
2443
+
2444
+ # ODE solver
2445
+ KISAO_0000694 = "KISAO_0000694"
2446
+ ODE_SOLVER = "KISAO_0000694"
2447
+
2448
+ # parameters for
2449
+ KISAO_0000695 = "KISAO_0000695"
2450
+ PARAMETERS_FOR = "KISAO_0000695"
2451
+
2452
+ # steady state root-finding problem
2453
+ KISAO_0000696 = "KISAO_0000696"
2454
+ STEADY_STATE_ROOT_FINDING_PROBLEM = "KISAO_0000696"
2455
+
2456
+ # SDE solver
2457
+ KISAO_0000697 = "KISAO_0000697"
2458
+ SDE_SOLVER = "KISAO_0000697"
2459
+
2460
+ # particle coordinates
2461
+ KISAO_0000698 = "KISAO_0000698"
2462
+ PARTICLE_COORDINATES = "KISAO_0000698"
2463
+
2464
+ # DAE Solver
2465
+ KISAO_0000699 = "KISAO_0000699"
2466
+ DAE_SOLVER = "KISAO_0000699"
2467
+
2468
+ # systems property
2469
+ KISAO_0000800 = "KISAO_0000800"
2470
+ SYSTEMS_PROPERTY = "KISAO_0000800"
2471
+
2472
+ # concentration control coefficient matrix (unscaled)
2473
+ KISAO_0000801 = "KISAO_0000801"
2474
+ CONCENTRATION_CONTROL_COEFFICIENT_MATRIX__UNSCALED_ = "KISAO_0000801"
2475
+
2476
+ # control coefficient (scaled)
2477
+ KISAO_0000802 = "KISAO_0000802"
2478
+ CONTROL_COEFFICIENT__SCALED_ = "KISAO_0000802"
2479
+
2480
+ # control coefficient (unscaled)
2481
+ KISAO_0000803 = "KISAO_0000803"
2482
+ CONTROL_COEFFICIENT__UNSCALED_ = "KISAO_0000803"
2483
+
2484
+ # elasticity matrix (unscaled)
2485
+ KISAO_0000804 = "KISAO_0000804"
2486
+ ELASTICITY_MATRIX__UNSCALED_ = "KISAO_0000804"
2487
+
2488
+ # elasticity coefficient (unscaled)
2489
+ KISAO_0000805 = "KISAO_0000805"
2490
+ ELASTICITY_COEFFICIENT__UNSCALED_ = "KISAO_0000805"
2491
+
2492
+ # elasticity matrix (scaled)
2493
+ KISAO_0000806 = "KISAO_0000806"
2494
+ ELASTICITY_MATRIX__SCALED_ = "KISAO_0000806"
2495
+
2496
+ # elasticity coefficient (scaled)
2497
+ KISAO_0000807 = "KISAO_0000807"
2498
+ ELASTICITY_COEFFICIENT__SCALED_ = "KISAO_0000807"
2499
+
2500
+ # reduced stoichiometry matrix
2501
+ KISAO_0000808 = "KISAO_0000808"
2502
+ REDUCED_STOICHIOMETRY_MATRIX = "KISAO_0000808"
2503
+
2504
+ # reduced Jacobian matrix
2505
+ KISAO_0000809 = "KISAO_0000809"
2506
+ REDUCED_JACOBIAN_MATRIX = "KISAO_0000809"
2507
+
2508
+ # reduced eigenvalue matrix
2509
+ KISAO_0000810 = "KISAO_0000810"
2510
+ REDUCED_EIGENVALUE_MATRIX = "KISAO_0000810"
2511
+
2512
+ # stoichiometry matrix
2513
+ KISAO_0000811 = "KISAO_0000811"
2514
+ STOICHIOMETRY_MATRIX = "KISAO_0000811"
2515
+
2516
+ # Jacobian matrix
2517
+ KISAO_0000812 = "KISAO_0000812"
2518
+ JACOBIAN_MATRIX = "KISAO_0000812"
2519
+
2520
+ # Eigenvalue matrix
2521
+ KISAO_0000813 = "KISAO_0000813"
2522
+ EIGENVALUE_MATRIX = "KISAO_0000813"
2523
+
2524
+ # flux control coefficient matrix (unscaled)
2525
+ KISAO_0000814 = "KISAO_0000814"
2526
+ FLUX_CONTROL_COEFFICIENT_MATRIX__UNSCALED_ = "KISAO_0000814"
2527
+
2528
+ # flux control coefficient matrix (scaled)
2529
+ KISAO_0000815 = "KISAO_0000815"
2530
+ FLUX_CONTROL_COEFFICIENT_MATRIX__SCALED_ = "KISAO_0000815"
2531
+
2532
+ # link matrix
2533
+ KISAO_0000816 = "KISAO_0000816"
2534
+ LINK_MATRIX = "KISAO_0000816"
2535
+
2536
+ # kernel matrix
2537
+ KISAO_0000817 = "KISAO_0000817"
2538
+ KERNEL_MATRIX = "KISAO_0000817"
2539
+
2540
+ # L0 matrix
2541
+ KISAO_0000818 = "KISAO_0000818"
2542
+ L0_MATRIX = "KISAO_0000818"
2543
+
2544
+ # Nr matrix
2545
+ KISAO_0000819 = "KISAO_0000819"
2546
+ NR_MATRIX = "KISAO_0000819"
2547
+
2548
+ # model and simulation property characteristic
2549
+ KISAO_0000820 = "KISAO_0000820"
2550
+ MODEL_AND_SIMULATION_PROPERTY_CHARACTERISTIC = "KISAO_0000820"
2551
+
2552
+ # intensive property
2553
+ KISAO_0000821 = "KISAO_0000821"
2554
+ INTENSIVE_PROPERTY = "KISAO_0000821"
2555
+
2556
+ # extensive property
2557
+ KISAO_0000822 = "KISAO_0000822"
2558
+ EXTENSIVE_PROPERTY = "KISAO_0000822"
2559
+
2560
+ # aggregation function
2561
+ KISAO_0000824 = "KISAO_0000824"
2562
+ AGGREGATION_FUNCTION = "KISAO_0000824"
2563
+
2564
+ # mean ignoring NaN
2565
+ KISAO_0000825 = "KISAO_0000825"
2566
+ MEAN_IGNORING_NAN = "KISAO_0000825"
2567
+
2568
+ # standard deviation ignoring NaN
2569
+ KISAO_0000826 = "KISAO_0000826"
2570
+ STANDARD_DEVIATION_IGNORING_NAN = "KISAO_0000826"
2571
+
2572
+ # standard error ignoring NaN
2573
+ KISAO_0000827 = "KISAO_0000827"
2574
+ STANDARD_ERROR_IGNORING_NAN = "KISAO_0000827"
2575
+
2576
+ # maximum ignoring NaN
2577
+ KISAO_0000828 = "KISAO_0000828"
2578
+ MAXIMUM_IGNORING_NAN = "KISAO_0000828"
2579
+
2580
+ # minimum ignoring NaN
2581
+ KISAO_0000829 = "KISAO_0000829"
2582
+ MINIMUM_IGNORING_NAN = "KISAO_0000829"
2583
+
2584
+ # maximum
2585
+ KISAO_0000830 = "KISAO_0000830"
2586
+ MAXIMUM = "KISAO_0000830"
2587
+
2588
+ # model and simulation property
2589
+ KISAO_0000831 = "KISAO_0000831"
2590
+ MODEL_AND_SIMULATION_PROPERTY = "KISAO_0000831"
2591
+
2592
+ # time
2593
+ KISAO_0000832 = "KISAO_0000832"
2594
+ TIME = "KISAO_0000832"
2595
+
2596
+ # rate of change
2597
+ KISAO_0000834 = "KISAO_0000834"
2598
+ RATE_OF_CHANGE = "KISAO_0000834"
2599
+
2600
+ # concentration control coefficient matrix (scaled)
2601
+ KISAO_0000835 = "KISAO_0000835"
2602
+ CONCENTRATION_CONTROL_COEFFICIENT_MATRIX__SCALED_ = "KISAO_0000835"
2603
+
2604
+ # amount
2605
+ KISAO_0000836 = "KISAO_0000836"
2606
+ AMOUNT = "KISAO_0000836"
2607
+
2608
+ # particle number
2609
+ KISAO_0000837 = "KISAO_0000837"
2610
+ PARTICLE_NUMBER = "KISAO_0000837"
2611
+
2612
+ # concentration
2613
+ KISAO_0000838 = "KISAO_0000838"
2614
+ CONCENTRATION = "KISAO_0000838"
2615
+
2616
+ # temperature
2617
+ KISAO_0000839 = "KISAO_0000839"
2618
+ TEMPERATURE = "KISAO_0000839"
2619
+
2620
+ # minimum
2621
+ KISAO_0000840 = "KISAO_0000840"
2622
+ MINIMUM = "KISAO_0000840"
2623
+
2624
+ # mean
2625
+ KISAO_0000841 = "KISAO_0000841"
2626
+ MEAN = "KISAO_0000841"
2627
+
2628
+ # standard deviation
2629
+ KISAO_0000842 = "KISAO_0000842"
2630
+ STANDARD_DEVIATION = "KISAO_0000842"
2631
+
2632
+ # standard error
2633
+ KISAO_0000843 = "KISAO_0000843"
2634
+ STANDARD_ERROR = "KISAO_0000843"
2635
+
2636
+ # sum ignoring NaN
2637
+ KISAO_0000844 = "KISAO_0000844"
2638
+ SUM_IGNORING_NAN = "KISAO_0000844"
2639
+
2640
+ # sum
2641
+ KISAO_0000845 = "KISAO_0000845"
2642
+ SUM = "KISAO_0000845"
2643
+
2644
+ # product ignoring NaN
2645
+ KISAO_0000846 = "KISAO_0000846"
2646
+ PRODUCT_IGNORING_NAN = "KISAO_0000846"
2647
+
2648
+ # product
2649
+ KISAO_0000847 = "KISAO_0000847"
2650
+ PRODUCT = "KISAO_0000847"
2651
+
2652
+ # cumulative sum ignoring NaN
2653
+ KISAO_0000848 = "KISAO_0000848"
2654
+ CUMULATIVE_SUM_IGNORING_NAN = "KISAO_0000848"
2655
+
2656
+ # cumulative sum
2657
+ KISAO_0000849 = "KISAO_0000849"
2658
+ CUMULATIVE_SUM = "KISAO_0000849"
2659
+
2660
+ # cumulative product ignoring NaN
2661
+ KISAO_0000850 = "KISAO_0000850"
2662
+ CUMULATIVE_PRODUCT_IGNORING_NAN = "KISAO_0000850"
2663
+
2664
+ # cumulative product
2665
+ KISAO_0000851 = "KISAO_0000851"
2666
+ CUMULATIVE_PRODUCT = "KISAO_0000851"
2667
+
2668
+ # count ignoring NaN
2669
+ KISAO_0000852 = "KISAO_0000852"
2670
+ COUNT_IGNORING_NAN = "KISAO_0000852"
2671
+
2672
+ # count
2673
+ KISAO_0000853 = "KISAO_0000853"
2674
+ COUNT = "KISAO_0000853"
2675
+
2676
+ # length ignoring NaN
2677
+ KISAO_0000854 = "KISAO_0000854"
2678
+ LENGTH_IGNORING_NAN = "KISAO_0000854"
2679
+
2680
+ # length
2681
+ KISAO_0000855 = "KISAO_0000855"
2682
+ LENGTH = "KISAO_0000855"
2683
+
2684
+ # median ignoring NaN
2685
+ KISAO_0000856 = "KISAO_0000856"
2686
+ MEDIAN_IGNORING_NAN = "KISAO_0000856"
2687
+
2688
+ # median
2689
+ KISAO_0000857 = "KISAO_0000857"
2690
+ MEDIAN = "KISAO_0000857"
2691
+
2692
+ # variance ignoring NaN
2693
+ KISAO_0000858 = "KISAO_0000858"
2694
+ VARIANCE_IGNORING_NAN = "KISAO_0000858"
2695
+
2696
+ # variance
2697
+ KISAO_0000859 = "KISAO_0000859"
2698
+ VARIANCE = "KISAO_0000859"
2699
+
2700
+ @staticmethod
2701
+ def get_name(kisao: "KISAO") -> Optional[str]:
2702
+ """Get name for term.
2703
+
2704
+ :returns: None if term does not exist in ontology.
2705
+ """
2706
+ return _terms.get(kisao.value, None)
2707
+
2708
+ @classmethod
2709
+ def validate(cls, kisao: "KISAOType") -> "KISAO":
2710
+ """Validate and normalize kisao."""
2711
+ term: "KISAO"
2712
+ if isinstance(kisao, str):
2713
+ if not kisao.startswith("KISAO"):
2714
+ raise ValueError(kisao + " is not a KISAO id.")
2715
+ if kisao.startswith("KISAO:"):
2716
+ kisao = kisao.replace(":", "_")
2717
+
2718
+ term = getattr(cls, kisao)
2719
+
2720
+ elif isinstance(kisao, "KISAO"):
2721
+ term = kisao
2722
+ else:
2723
+ raise ValueError
2724
+
2725
+ return term
2726
+
2727
+
2728
+ __all__ = [
2729
+ "KISAO",
2730
+ "KISAOType",
2731
+ ]