Qualitative Models

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

Data Structures
class	DefaultTerm_t
	qual The default result of a Transition_t. More...
class	FunctionTerm_t
	qual A function term. More...
class	Input_t
	qual The input to a QualitativeSpecies_t. More...
class	ListOfFunctionTerms_t
	qual A list of FunctionTerm_t objects. More...
class	ListOfInputs_t
	qual A list of Input_t objects. More...
class	ListOfOutputs_t
	qual A list of Output_t objects. More...
class	ListOfQualitativeSpecies_t
	qual A list of QualitativeSpecies_t objects. More...
class	ListOfTransitions_t
	qual A list of Transition_t objects. More...
class	Output_t
	qual The output from a QualitativeSpecies_t. More...
class	QualExtension_t
	qual Base extension class for the package. More...
class	QualitativeSpecies_t
	qual Extension of Species_t. More...
class	QualModelPlugin_t
	qual Extension of Model_t. More...
class	QualPkgNamespaces_t
	qual SBMLNamespaces_t extension for the package. More...
class	QualSBMLDocumentPlugin_t
	qual Extension of SBMLDocument_t. More...
class	QualValidator_t
	qual Entry point for package validation. More...
class	Transition_t
	qual A transition of a QualitativeSpecies_t. More...

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Data Structure Documentation

class QualExtension_t

class QualPkgNamespaces_t

class QualSBMLDocumentPlugin_t

class QualValidator_t