The libSBML “qual” extension implements support for the SBML Level 3 Qualitative Models package. It can be used in SBML Level 3 Version 1 and Version 2 documents.

Introduction

Quantitative methods for modeling biological networks require an in-depth knowledge of the biochemical reactions and their stoichiometric and kinetic parameters. In many practical cases, this knowledge is missing. This has led to the development of several qualitative modeling methods using information such as gene expression data coming from functional genomic experiments.

The qualitative models contemplated in this SBML Level 3 package for Qualitative Models are essentially based on the definition of regulatory or influence graphs. The components of these models differ from the species and reactions used in current SBML models. For example, qualitative models typically associate discrete levels of activities with entity pools; the processes involving them cannot be described as reactions per se but rather as transitions between states. These systems can be viewed as reactive systems, whose dynamics are represented by means of state transition graphs (or other Kripke structures representing, in the form of a graph, which nodes are the reachable states and in which the edges are the state transitions). In this context, logical regulatory networks (Boolean or multi-valued) and standard Petri nets are the two formalisms mostly used in biology that give rise to such behaviors. Published models using these approaches cover, far from exhaustively, gene regulatory networks, signalling pathways and metabolic pathways.

Despite differences from traditional SBML models, it is desirable to bring these classes of models under a common format scheme. The purpose of this Qualitative Models package for SBML Level 3 is to support encoding qualitative models in SBML.

Authors

The primary authors of the SBML Level 3; Qualitative Models specification are Claudine Chaouiya, Sarah M. Keating, Duncan Berenguier, Aurélien Naldi, Denis Thieffry, Martijn P. van Iersel and Tomás̮Helikar.

The specification for this SBML package

This API documentation for libSBML does not provide a complete explanation of the SBML Level 3 Qualitative Models (“qual”) package. If you are developing software that uses “qual”, 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 for SBML Level 3 Qualitative Models, current at the time of this libSBML release (5.18.0). Note: an Internet connection is required to access these documents.
Specification (in PDF format)	Known issues
Qualitative Models package, Version 1 Release 1	Errata page

More...

Classes
class	libsbmlcs.DefaultTerm
	qual The default result of a Transition. More...

class	libsbmlcs.FunctionTerm
	qual A function term. More...

class	libsbmlcs.Input
	qual The input to a QualitativeSpecies. More...

class	libsbmlcs.ListOfFunctionTerms
	qual A list of FunctionTerm objects. More...

class	libsbmlcs.ListOfInputs
	qual A list of Input objects. More...

class	libsbmlcs.ListOfOutputs
	qual A list of Output objects. More...

class	libsbmlcs.ListOfQualitativeSpecies
	qual A list of QualitativeSpecies objects. More...

class	libsbmlcs.ListOfTransitions
	qual A list of Transition objects. More...

class	libsbmlcs.Output
	qual The output from a QualitativeSpecies. More...

class	libsbmlcs.QualExtension
	qual Base extension class for the package. More...

class	libsbmlcs.QualitativeSpecies
	qual Extension of Species. More...

class	libsbmlcs.QualModelPlugin
	qual Extension of Model. More...

class	libsbmlcs.Transition
	qual A transition of a QualitativeSpecies. More...

Detailed Description

The libSBML “qual” extension implements support for the SBML Level 3 Qualitative Models package. It can be used in SBML Level 3 Version 1 and Version 2 documents.

Introduction

Quantitative methods for modeling biological networks require an in-depth knowledge of the biochemical reactions and their stoichiometric and kinetic parameters. In many practical cases, this knowledge is missing. This has led to the development of several qualitative modeling methods using information such as gene expression data coming from functional genomic experiments.

The qualitative models contemplated in this SBML Level 3 package for Qualitative Models are essentially based on the definition of regulatory or influence graphs. The components of these models differ from the species and reactions used in current SBML models. For example, qualitative models typically associate discrete levels of activities with entity pools; the processes involving them cannot be described as reactions per se but rather as transitions between states. These systems can be viewed as reactive systems, whose dynamics are represented by means of state transition graphs (or other Kripke structures representing, in the form of a graph, which nodes are the reachable states and in which the edges are the state transitions). In this context, logical regulatory networks (Boolean or multi-valued) and standard Petri nets are the two formalisms mostly used in biology that give rise to such behaviors. Published models using these approaches cover, far from exhaustively, gene regulatory networks, signalling pathways and metabolic pathways.

Despite differences from traditional SBML models, it is desirable to bring these classes of models under a common format scheme. The purpose of this Qualitative Models package for SBML Level 3 is to support encoding qualitative models in SBML.

Authors

The primary authors of the SBML Level 3; Qualitative Models specification are Claudine Chaouiya, Sarah M. Keating, Duncan Berenguier, Aurélien Naldi, Denis Thieffry, Martijn P. van Iersel and Tomás̮Helikar.

The specification for this SBML package

This API documentation for libSBML does not provide a complete explanation of the SBML Level 3 Qualitative Models (“qual”) package. If you are developing software that uses “qual”, 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 for SBML Level 3 Qualitative Models, current at the time of this libSBML release (5.18.0). Note: an Internet connection is required to access these documents.
Specification (in PDF format)	Known issues
Qualitative Models package, Version 1 Release 1	Errata page

Introduction

Authors

The specification for this SBML package

Classes

Detailed Description

Introduction

Authors

The specification for this SBML package