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---
id: cobrapy
version: 0.22.0
specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_COBRApy/279d477cf29eecfa9df3f606f43d7ed81acb5d17/biosimulators.json
specificationsPatch…
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---
id: cbmpy
version: 0.7.25
specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_CBMPy/828d797ec4e448503de231fdab3e0e26e58d577b/biosimulators.json
specificationsPatch:
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To go through the list:
Explicit embedded Runge-Kutta \(2, 3\) => No term yet
Explicit 4th order \(classical\) Runge-Kutta => Already KISAO\_0000032
Explicit embedded Runge-Kutta-Fehlberg …
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Some algorithms depend on a linear solver, and some implementations let the users pick this type of linear solver \(e.g. IDA, which provides direct solvers along with solvers based on Krylov Subspace …
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name: convex optimization
definition: Optimization of a convex function over a convex set
subClassOf: KISAO_0000472
Reported by: jonrkarr
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name: force physical correctness
definition: Indicates whether to force physical correctness
subClassOf: KISAO_0000243
isImplementedIn: COPASI
Reported by: jonrkarr
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name: reactions
definition: Reactions to compute the variablity of
subClassOf: KISAO_0000201
algorithm: FVA
isImplementedIn: COBRApy
Reported by: jonrkarr
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name: pFBA factor
definition: Maximum permissible sum of absolute fluxes
subClassOf: KISAO_0000201
algorithm: FVA
isImplementedIn: COBRApy
Reported by: jonrkarr
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name: loopless
definition: Whether to return only loopless flux solutions
subClassOf: KISAO_0000201
algorithm: FVA
isImplementedIn: COBRApy
Reported by: jonrkarr
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name: stop condition
definition: A condition upon which a simulation should terminate.
subClassOf: KISAO_0000201
isImplementedIn: BioNetGen
Reported by: jonrkarr