-
name: stop condition
definition: A condition upon which a simulation should terminate.
subClassOf: KISAO_0000201
isImplementedIn: BioNetGen
Reported by: jonrkarr
-
name: Error control strategy
definition: Error control strategy for sensitivity variables.
subClassOf: KISAO_0000242
algorithm: IDAS
isImplementedIn: Sundials
Reported by: jonrkarr
-
name: absolute tolerance for root finding
definition: absolute error tolerance for root finding
subClassOf: KISAO_0000242
isImplementedIn: COPASI
Reported by: jonrkarr
-
name: parallelism
definition: Number of parallel processes to use
subClassOf: KISAO_0000201
algorithm: FVA
algorithm: gFBA
isImplementedIn: COBRApy
Reported by: jonrkarr
-
A number of annotations in biomodels contain references to 'miriam:unknown', which are almost certainly simply errors. Here's a full list, just from 'grep':
BIOMD0000000498/BIOMD0000000498_urn.xml…
-
---
id: amici
version: 0.11.14
specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_AMICI/e15c02d6d178068d1ca6ed3f3a63ae4f598a0168/biosimulators.json
specificationsPatch:
…
-
name: optimization solver
definition: Optimization solver such as CPLEX, GLPK, or Gurobi
subClassOf: KISAO_0000201
isImplementedIn: COBRApy, CBMPy, RAVEN
Reported by: jonrkarr
-
---
id: amici
version: 0.11.11
specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_AMICI/e15c02d6d178068d1ca6ed3f3a63ae4f598a0168/biosimulators.json
specificationsPatch:
…
-
---
id: boolnet
version: 2.1.5
specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_BoolNet/a9ecbd0176a956437ba850dfc7adc8238918aad6/biosimulators.json
specificationsPatch:…
-
name: noise level
definition: standard deviation of the Gaussian noise which is added to each prediction
subClassOf: KISAO_0000201
isImplementedIn: BoolNet
Reported by: jonrkarr