CSML2SBML: a novel tool for converting quantitative biological pathway models from CSML into SBML

Area of Science:

• Systems Biology
• Computational Biology
• Bioinformatics

Background:

• XML-based standards like Chemical Simulation Markup Language (CSML) and Systems Biology Markup Language (SBML) facilitate biological pathway modeling.
• Interoperability between different modeling formats is crucial for widespread adoption and analysis.

Purpose of the Study:

• To introduce CSML2SBML, a novel format converter for quantitative pathway models.
• To enable seamless translation of CSML-encoded models into the SBML standard.

Main Methods:

• Development of a format converter, CSML2SBML, based on CSML version 3.0 and SBML Level 2 Version 4.
• Testing the converter on pathway models from the CSML repository and the Macrophage Pathway Knowledgebase (MACPAK).
• Validation of converted SBML models using libSBML Consistency Check and simulation comparison with CellDesigner and Cell Illustrator.

Main Results:

• CSML2SBML successfully converted 11 out of 15 CSML models and 228 MACPAK models to SBML.
• Converted models maintained structural and kinetic information without loss.
• Simulations of converted SBML models reproduced the dynamics of the original CSML models.

Conclusions:

• CSML2SBML provides a reliable method for converting quantitative pathway models between CSML and SBML formats.
• The tool enhances interoperability, allowing for broader analysis and simulation using compliant software like CellDesigner.
• The successful conversion and validation pave the way for increased utilization of CSML models within the SBML ecosystem.