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Kinetic Modeling using BioPAX ontology.

Oliver Ruebenacker¹, Ion I Moraru, James C Schaff

¹Center for Cell Analysis and Modeling, University of Connecticut Health Center, Farmington, CT, 06030.

Proceedings. IEEE International Conference on Bioinformatics and Biomedicine

|September 24, 2010

Summary

This summary is machine-generated.

This study introduces a software system to convert Biological Pathways Exchange (BioPAX) data into kinetic models for simulation. It enhances the usability of pathway data for systems biology research.

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Area of Science:

Systems Biology
Computational Biology
Biochemical Pathway Analysis

Background:

Biochemical interaction data is available in Biological Pathways Exchange (BioPAX) format from curated databases.
The BioPAX format lacks information required for kinetic modeling and simulation.
The System Biology Markup Language (SBML) is the standard for kinetic modeling, but SBML models are scarce and difficult to reuse.

Purpose of the Study:

To develop a software system that facilitates the creation of kinetic models from BioPAX data.
To enable visualization, editing, and simulation of kinetic models using the Virtual Cell (VCell) platform.
To improve the conversion of BioPAX data to SBML format for broader compatibility with simulation tools.

Main Methods:

Developed a software system to process and convert BioPAX data.
Integrated BioPAX to SBML conversion capabilities.
Enabled kinetic model creation, visualization, editing, and simulation within the VCell environment.

Main Results:

Successfully created a system to leverage BioPAX data for kinetic modeling.
Facilitated the generation of kinetic models that can be simulated in VCell.
Improved the conversion process to SBML, enhancing model interoperability.

Conclusions:

The developed software system effectively bridges the gap between BioPAX pathway data and kinetic modeling requirements.
This facilitates the creation and simulation of kinetic models, advancing systems biology research.
Enhanced conversion to SBML improves the accessibility and reusability of biological models.