SBMLDiagrams

SBMLDiagrams provides programmatic functions to add, retrieve, and render layout and rendering information for Systems Biology Markup Language (SBML) models using the SBML Layout and Render package to produce biochemical pathway diagrams.

Key Features:

• SBML Layout and Render integration: Leverages the SBML Layout and Render package extension to store and describe layout and rendering metadata within SBML models.
• Python API: Exposes programmatic functions to add, retrieve, and modify layout and render information in SBML files.
• Rendering backend: Uses skia-python to perform diagram rendering.
• Export formats: Supports exporting rendered diagrams to common formats such as PNG and PDF.

Scientific Applications:

• Modeling and simulation: Visualizes biochemical models as pathway diagrams to support interpretation of system dynamics.
• Data sharing: Produces standard image outputs (PNG, PDF) for inclusion in publications and exchange between researchers.
• Education: Generates visual representations of biochemical pathways for teaching systems biology concepts.

Methodology:

Implements SBML Layout and Render package metadata manipulation via a Python API and performs rendering using skia-python with export to PNG and PDF.