Path2Models

Path2Models generates mathematical models from biochemical pathway resources as a specialized branch of the BioModels Database to provide standardized, SBML-encoded models and SBGN maps for systems biology simulation and analysis.

Key Features:

• Automated Model Generation: Path2Models uses a suite of freely available software tools to automatically generate mathematical models from pathway representations sourced from KEGG, BioCarta, MetaCyc, and SABIO-RK.
• Model Types: It produces kinetic, logical, and constraint-based models depending on the source data.
• Extensive Coverage: The project has generated models for over 2,600 organisms.
• Standardized Encoding: All models are encoded in the Systems Biology Markup Language (SBML).
• Comprehensive Model Details: Each model includes lists of participants, their interactions, relevant mathematical constructs, and initial parameter values.
• Graphical Representation: Most models are also provided as graphical representations using the Systems Biology Graphical Notation (SBGN).

Scientific Applications:

• Model Development: Provide initial starting models to accelerate development of mathematical models in systems biology.
• Simulation and Analysis: Support simulation and computational analysis of biochemical pathways using SBML-encoded models.
• Model Curation and Parameterization: Enable further curation and parameterization of models for organism- or context-specific studies.
• Comparative Pathway Studies: Facilitate cross-species and cross-database comparisons by supplying models covering over 2,600 organisms.

Methodology:

Automatic extraction of pathway representations from KEGG, BioCarta, MetaCyc, and SABIO-RK followed by generation of mathematical models using a suite of freely available software tools, with models encoded in SBML and many provided as SBGN maps.