SBMLeditor

SBMLeditor edits SBML files to create, modify, and validate Systems Biology Markup Language (SBML) models for computational representation of biological networks and pathways.

Key Features:

• Low-Level Editing: Provides programmatic access to construct and modify all components of SBML documents at the element level.
• Tree-Structured Interface (JCompneur): Represents SBML documents as an XML tree using JCompneur for structured navigation of SBML elements.
• Custom Dialogs: Supports tag-specific dialogs tailored to individual SBML elements and attributes for targeted editing operations.
• Validation and Consistency Checks (libSBML): Integrates libSBML to perform SBML syntactic validation and consistency checking against the SBML specification.
• Graphical Equation Editor (MathML): Includes a graphical editor for creation and editing of MathML mathematical expressions within SBML models.
• Integration with Systems Biology Workbench: Operates as a module that interfaces with the Systems Biology Workbench environment for use within larger workflows.

Scientific Applications:

• SBML model construction and modification: Enables creation and detailed editing of SBML-encoded biochemical network and pathway models.
• Model validation and standards compliance: Ensures SBML files conform to the SBML specification via libSBML validation and consistency checks.
• Mathematical expression authoring: Allows formulation and editing of model equations using MathML within SBML documents.
• Workflow integration: Integrates SBML model editing into Systems Biology Workbench–based computational workflows.

Methodology:

Implemented in Java, using JCompneur for XML tree visualization and libSBML for SBML validation and consistency checks.