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:
Kinetic model instances
Kinetic model instances.
Accepted table names: KineticModelInstances, KineticModelInstance.
| Name | Type | Description | Aliases | Required |
|---|---|---|---|---|
idModelInstance |
AlphaNumeric (50) |
Unique identification code of the kinetic model instance. |
idModelInstance, Id, Code |
Yes |
idModelDefinition |
KineticModelType |
Identifier of the kinetic model definition for which this is an instance. |
idModelDefinition, ModelDefinition |
Yes |
Species |
AlphaNumeric (50) |
The species on which the experiment was performed. |
System, TestSystem, Species |
Yes |
Substances |
AlphaNumeric (150) |
Code or comma separated list of the codes of the substances. Unique identification code of substance, Default: valid for all substances. Should be omitted for parameters in the class Physiological |
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. |
Name |
No |
Description |
AlphaNumeric (200) |
Additional description of the kinetic model instance. |
Description |
No |
Kinetic model instance parameters
Kinetic model parameters
Accepted table names: 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) |
Name of the parameter in the kinetic model. |
Yes |
|
Description |
AlphaNumeric (200) |
Description of or reference for the parameter values in the kinetic model. |
No |
|
Value |
Numeric |
Mean. |
MEAN, mean |
Yes |
DistributionType |
ProbabilityDistribution | Distribution. |
DistributionType, Distribution |
No |
CvVariability |
Numeric |
Variability. |
No |
|
CvUncertainty |
Numeric |
Uncertainty. |
No |