libSBML C++ API  5.20.2
Classes
Flux Balance Constraints

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.

Introduction

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.

Authors

The primary authors of the SBML Level, 3 Flux Balance Constraints package are Brett G. Olivier and Frank T. Bergmann.

The specification for this SBML package

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). we apologise that our known issues pages are under reconstruction.

Specification for SBML Level 3 Flux Balance Constraints, current at the time of this libSBML release (5.20.2). Note: an Internet connection is required to access these documents.
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
More...

Classes

class  Association
 
class  CobraToFbcConverter
 
class  FbcAnd
 
class  FbcAssociation
 
class  FbcExtension
 
class  FbcModelPlugin
 
class  FbcOr
 
class  FbcPkgNamespaces
 
class  FbcReactionPlugin
 
class  FbcSBasePlugin
 
class  FbcSBMLDocumentPlugin
 
class  FbcSpeciesPlugin
 
class  FbcToCobraConverter
 
class  FbcV1ToV2Converter
 
class  FbcV2ToV1Converter
 
class  FbcValidator
 
class  FluxBound
 
class  FluxObjective
 
class  GeneAssociation
 
class  GeneProduct
 
class  GeneProductAssociation
 
class  GeneProductRef
 
class  KeyValuePair
 
class  ListOfFbcAssociations
 
class  ListOfFluxBounds
 
class  ListOfFluxObjectives
 
class  ListOfGeneAssociations
 
class  ListOfGeneProducts
 
class  ListOfKeyValuePairs
 
class  ListOfObjectives
 
class  ListOfUserDefinedConstraintComponents
 
class  ListOfUserDefinedConstraints
 
class  Objective
 
class  UserDefinedConstraint
 
class  UserDefinedConstraintComponent
 

Detailed Description

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.

Introduction

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.

Authors

The primary authors of the SBML Level, 3 Flux Balance Constraints package are Brett G. Olivier and Frank T. Bergmann.

The specification for this SBML package

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). we apologise that our known issues pages are under reconstruction.

Specification for SBML Level 3 Flux Balance Constraints, current at the time of this libSBML release (5.20.2). Note: an Internet connection is required to access these documents.
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