Verification and reproducible curation of the BioModels repository

Area of Science:

• Computational Biology
• Systems Biology
• Bioinformatics

Background:

• The BioModels Repository houses over 1000 curated mechanistic models, primarily in Systems Biology Markup Language (SBML).
• SBML formally specifies models but lacks computational experimental conditions, hindering result reproducibility.
• Simulation Experiment Description Markup Language (SED-ML) standardizes experimental specifications for model simulations.

Purpose of the Study:

• To enhance the reproducibility and reusability of curated mechanistic models in the BioModels database.
• To update, correct, and generate Simulation Experiment Description Markup Language (SED-ML) files for 1055 models.
• To verify simulation results across multiple biosimulation engines using SED-ML.

Main Methods:

• Updated and corrected existing SED-ML files for over 450 BioModels entries.
• Generated new SED-ML files for remaining BioModels entries.
• Employed a wrapper architecture for SED-ML interpretation and cross-engine verification with five ODE-based biosimulation engines.

Main Results:

• Successfully updated/corrected/generated SED-ML files for 1055 curated mechanistic models.
• Verified simulation consistency across multiple ODE-based biosimulation engines.
• Identified and addressed issues in existing SED-ML files and simulation engines.

Conclusions:

• Improved SED-ML files significantly enhance the reproducibility and credibility of BioModels.
• Enhanced model reproducibility increases their utility for new investigations and multiscale modeling.
• Standardized simulation experiments facilitate cross-platform verification and model re-use.