PBK model parametrisations data formats
- Data tables:
Kinetic model instances
Kinetic model instance parameters
PBK model parametrisations contain specifications for kinetic model definitions and their parameterisation for build in (C-code) and uploadable (SBML) kinetic models.
PBK model data format
The PBK model parametrisations data format specifies PBK model definitions and parameters.
Download empty dataset template:
PBK model instances
PBK model instances/parametrisations.
Accepted table names: PbkModelInstances, PbkModelParametrisations, KineticModelInstances, KineticModelInstance.
| Name | Type | Description | Aliases | Required |
|---|---|---|---|---|
idModelInstance |
AlphaNumeric (50) |
Unique identification code of the PBK model instance/parametrisation. |
idModelInstance, Id, Code |
Yes |
idModelDefinition |
KineticModelType |
Identifier of the PBK model definition of which this is an instance/parametrisation. |
idModelDefinition, ModelDefinition |
Yes |
Species |
AlphaNumeric (50) |
The species to which this instance/parametrisation applies. |
Species, System, TestSystem |
Yes |
Substances |
AlphaNumeric (150) |
Code or comma separated list of the codes of the substances. Only applies for substance-specific parameters. |
idSubstance, idSubstances, SubstanceId, SubstanceCode, SubstanceCodes, Substance, Substances |
No |
Reference |
AlphaNumeric (100) |
Reference or author. |
References |
No |
Name |
AlphaNumeric (100) |
Name of the kinetic model instance/parametrisation. |
Name |
No |
Description |
AlphaNumeric (200) |
Additional description of the model instance/parametrisation. |
Description |
No |
PBK model instance parameters
PBK model instance/parametrisation parameter values.
Accepted table names: PbkModelInstanceParameters, PbkModelInstanceParameterValues, KineticModelInstanceParameters, KineticModelInstanceParameter.
| Name | Type | Description | Aliases | Required |
|---|---|---|---|---|
idModelInstance |
AlphaNumeric (50) |
Unique identification code of the kinetic model instance to which this parameter belongs |
Id, Code |
Yes |
Parameter |
AlphaNumeric (50) |
Identifier of the parameter in the PBK model. |
Yes |
|
Description |
AlphaNumeric (200) |
Description of or reference for the parameter values in the model. |
No |
|
Value |
Numeric |
Nominal parameter value of the distribution. |
Mean |
Yes |
DistributionType |
ProbabilityDistribution | Parameter distribution type. |
DistributionType, Distribution |
No |
CvVariability |
Numeric |
Variability of the parameter expressed as a coefficient of variation (CV). |
No |
|
CvUncertainty |
Numeric |
Uncertainty of the parameter expressed as a coefficient of variation (CV). |
No |