libSBML C++ API
5.11.0
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The libSBML “fbc” extension implements support for the SBML Level 3 Flux Balance Constraints package.
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.
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 |
---|---|
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Classes | |
class | Association |
fbc
Proposed representation of gene associations. More... | |
class | CobraToFbcConverter |
fbc
COBRA to SBML Level 3 'fbc' converter. More... | |
class | FbcExtension |
fbc
Base extension class for the package. More... | |
class | FbcModelPlugin |
fbc
Extension of Model. More... | |
class | FbcPkgNamespaces |
fbc
SBMLNamespaces extension for the package. More... | |
class | FbcSBMLDocumentPlugin |
fbc
Extension of SBMLDocument. More... | |
class | FbcSpeciesPlugin |
fbc
Extension of Species. More... | |
class | FbcToCobraConverter |
fbc
SBML Level 3 'fbc' to COBRA converter. More... | |
class | FbcValidator |
fbc
Entry point for package validation. More... | |
class | FluxBound |
fbc
Max or min value for a reaction flux. More... | |
class | FluxObjective |
fbc
An objective function for a flux. More... | |
class | GeneAssociation |
fbc
Proposed annotation for gene associations. More... | |
class | ListOfFluxBounds |
fbc
A list of FluxBound objects. More... | |
class | ListOfFluxObjectives |
fbc
A list of FluxObjectives. More... | |
class | ListOfGeneAssociations |
fbc
A list of GeneAssociation objects. More... | |
class | ListOfObjectives |
fbc
A list of Objective objects. More... | |
class | Objective |
fbc
An objective function. More... | |
The libSBML “fbc” extension implements support for the SBML Level 3 Flux Balance Constraints package.
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.
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 |
---|---|
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