Package org.episteme.natural.biology.loaders.sbml

package org.episteme.natural.biology.loaders.sbml

Systems Biology Markup Language (SBML) loader for Episteme.

This package provides classes for parsing SBML files, the standard format for exchanging computational models in systems biology. It uses the JSBML library and supports SBML Level 3 Core and the FBC (Flux Balance Constraints) extension.

Key Classes:

• SBMLReader - Main parser class
• SBMLModel - Model with stoichiometry matrix
• SBMLReaction - Biochemical reaction
• SBMLSpecies - Metabolite/species

Usage Example:

SBMLReader reader = new SBMLReader();
SBMLModel model = reader.read(new File("ecoli_core.xml"));
RealDoubleMatrix S = model.getStoichiometryMatrix();

Since:

1.0

Author:

Silvere Martin-Michiellot, Gemini AI (Google DeepMind)

See Also:

• SBML.org

Related Packages

Package	Description
org.episteme.natural.biology.loaders
org.episteme.natural.biology.loaders.biopax	BioPAX loader for biological pathways and networks.
org.episteme.natural.biology.loaders.itis	Biological taxonomy, genetics, and physiological modeling.
org.episteme.natural.biology.loaders.neuroml	NeuroML loader for computational neuroscience models.
org.episteme.natural.biology.loaders.pdbml	PDBML loader for Protein Data Bank macromolecular structures.
org.episteme.natural.biology.loaders.phyloxml	PhyloXML loader for phylogenetic tree data.

Class	Description
SBMLBridge	Bridge for converting SBML DTOs to core Episteme domain objects.
SBMLCompartment	Represents a compartment in an SBML model.
SBMLException	Exception thrown when SBML parsing fails.
SBMLGeneProduct	Represents a gene product from the FBC extension.
SBMLModel	Represents an SBML model for systems biology.
SBMLParameter	Represents a global parameter in an SBML model.
SBMLReaction	Represents a reaction in an SBML model.
SBMLReader	Systems Biology Markup Language (SBML) Reader.
SBMLSpecies	Represents a species (metabolite) in an SBML model.