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libSBML Python API
5.18.0
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libSBML Python API
5.18.0
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The libSBML “fbc” extension implements support for the SBML Level 3 Flux Balance Constraints package. It can be used in SBML Level 3 Version 1 and Version 2 documents.
Constraint based modeling is a widely accepted methodology used to analyze and study biological networks on both a small and whole organism (genome) scale. Typically these models are underdetermined and constraint based methods (e.g. linear, quadratic optimization) are used to optimize specific model properties. This is assumed to occur under a defined set of constraints (e.g. stoichiometric, metabolic) and bounds (e.g. thermodynamic, experimental and environmental) on the values that the solution fluxes can obtain.
Perhaps the most well known (and widely used) analysis method is Flux Balance Analysis (FBA), which is performed on Genome Scale Reconstructions. When using FBA, a target flux is optimized (e.g., to maximize a flux to biomass or minimize ATP production) while other fluxes can be bounded to simulate a selected growth environment or specific metabolic state.
As constraint based models are generally underdetermined, i.e., few or none of the kinetic rate equations and related parameters are known, it is crucial that a model definition includes the ability to define optimization parameters such as objective functions, flux bounds and constraints. This is not well-supported in SBML Level 3 Core. The question of how to best encode constraint-based models in SBML is not new. However, advances in the methods used to construct genome scale constraint-based models and the wider adoption of constraint based modeling in biotechnological/medical applications have led to a rapid increase in both the number of models being constructed and the tools used to analyze them.
Faced with such growth, both in number and diversity, the need for a standardized data format for the definition, exchange and annotation of constraint based models has become critical. As the core model components (e.g., species, reactions, stoichiometry) can already be efficiently described in SBML, the Flux Balance Constraints (FBC) package is designed to extend SBML Level 3 Core by adding the elements necessary to encode current and future constraint-based models.
In version 2 of this package, the ability to encode gene products and gene product references was added, and the encoding of flux bounds was modified to reference parameters, instead of holding directly-encoded values.
This API documentation for libSBML does not provide a complete explanation of the SBML Level 3 Flux Balance Constraints (“fbc”) package. If you are developing software that uses “fbc”, you are strongly urged to read the actual specification for the package. A link to the specification document current is provided below, along with a link to the page of known issues (if any).
| Specification (in PDF format) | Known issues |
|---|---|
 Flux Balance Constraints package, Version 1 Release 1
|
 Errata page
|
|
Flux Balance Constraints package, Version 2 Release 1
|
Errata page
|
Classes | |
| class | libsbml.Association |
| fbc
Annotation helper class for “fbc” Version 1. More... | |
| class | libsbml.CobraToFbcConverter |
| fbc
COBRA to SBML Level 3 “fbc” converter. More... | |
| class | libsbml.FbcAnd |
| fbc
An “and” relationship for gene products More... | |
| class | libsbml.FbcAssociation |
| fbc
Base class for FbcAnd, FbcOr, and GeneProductRef More... | |
| class | libsbml.FbcExtension |
| fbc
Base extension class for the “fbc” package. More... | |
| class | libsbml.FbcModelPlugin |
| fbc
Extension of Model. More... | |
| class | libsbml.FbcOr |
| fbc
An “or” relationship for gene products More... | |
| class | libsbml.FbcPkgNamespaces |
| fbc
SBMLNamespaces extension for the package. More... | |
| class | libsbml.FbcReactionPlugin |
| fbc
Extension of Reaction by the “fbc” package. More... | |
| class | libsbml.FbcSBMLDocumentPlugin |
| fbc
Extension of SBMLDocument for the “fbc” package. More... | |
| class | libsbml.FbcSpeciesPlugin |
| fbc
Extension of Species. More... | |
| class | libsbml.FbcToCobraConverter |
| fbc
SBML Level 3 “fbc” to COBRA converter. More... | |
| class | libsbml.FbcV1ToV2Converter |
| fbc
Convert “fbc” Version 1 models to Version 2 More... | |
| class | libsbml.FbcV2ToV1Converter |
| fbc
Convert “fbc” Version 2 models to Version 1 More... | |
| class | libsbml.FluxBound |
| fbc
Max or min value for a reaction flux. More... | |
| class | libsbml.FluxObjective |
| fbc
An objective function for a flux. More... | |
| class | libsbml.GeneAssociation |
| fbc
Annotation helper class for “fbc” Version 1. More... | |
| class | libsbml.GeneProduct |
| fbc
Association of a gene product with a Reaction More... | |
| class | libsbml.GeneProductAssociation |
| fbc
Association between gene products and reactions More... | |
| class | libsbml.GeneProductRef |
| fbc
Reference to a gene product of a reaction More... | |
| class | libsbml.ListOfFbcAssociations |
| fbc
A list of FbcAssociation objects. More... | |
| class | libsbml.ListOfFluxBounds |
| fbc
A list of FluxBound objects. More... | |
| class | libsbml.ListOfFluxObjectives |
| fbc
A list of FluxObjective objects. More... | |
| class | libsbml.ListOfGeneAssociations |
| fbc
A list of GeneAssociation objects. More... | |
| class | libsbml.ListOfGeneProducts |
| fbc
A list of GeneProduct objects. More... | |
| class | libsbml.ListOfObjectives |
| fbc
A list of Objective objects. More... | |
| class | libsbml.Objective |
| fbc
An objective function. More... | |
The libSBML “fbc” extension implements support for the SBML Level 3 Flux Balance Constraints package. It can be used in SBML Level 3 Version 1 and Version 2 documents.
Constraint based modeling is a widely accepted methodology used to analyze and study biological networks on both a small and whole organism (genome) scale. Typically these models are underdetermined and constraint based methods (e.g. linear, quadratic optimization) are used to optimize specific model properties. This is assumed to occur under a defined set of constraints (e.g. stoichiometric, metabolic) and bounds (e.g. thermodynamic, experimental and environmental) on the values that the solution fluxes can obtain.
Perhaps the most well known (and widely used) analysis method is Flux Balance Analysis (FBA), which is performed on Genome Scale Reconstructions. When using FBA, a target flux is optimized (e.g., to maximize a flux to biomass or minimize ATP production) while other fluxes can be bounded to simulate a selected growth environment or specific metabolic state.
As constraint based models are generally underdetermined, i.e., few or none of the kinetic rate equations and related parameters are known, it is crucial that a model definition includes the ability to define optimization parameters such as objective functions, flux bounds and constraints. This is not well-supported in SBML Level 3 Core. The question of how to best encode constraint-based models in SBML is not new. However, advances in the methods used to construct genome scale constraint-based models and the wider adoption of constraint based modeling in biotechnological/medical applications have led to a rapid increase in both the number of models being constructed and the tools used to analyze them.
Faced with such growth, both in number and diversity, the need for a standardized data format for the definition, exchange and annotation of constraint based models has become critical. As the core model components (e.g., species, reactions, stoichiometry) can already be efficiently described in SBML, the Flux Balance Constraints (FBC) package is designed to extend SBML Level 3 Core by adding the elements necessary to encode current and future constraint-based models.
In version 2 of this package, the ability to encode gene products and gene product references was added, and the encoding of flux bounds was modified to reference parameters, instead of holding directly-encoded values.
This API documentation for libSBML does not provide a complete explanation of the SBML Level 3 Flux Balance Constraints (“fbc”) package. If you are developing software that uses “fbc”, you are strongly urged to read the actual specification for the package. A link to the specification document current is provided below, along with a link to the page of known issues (if any).
| Specification (in PDF format) | Known issues |
|---|---|
|
Flux Balance Constraints package, Version 1 Release 1
|
Errata page
|
|
Flux Balance Constraints package, Version 2 Release 1
|
Errata page
|
