MML toolkit and work flow overview: Creating temporo-spatial heart models from CellML

Area of Science:

• Computational biology
• Systems biology
• Biophysics

Background:

• Biological modeling requires efficient development and solving tools.
• CellML is a standard for describing biological models.
• Integrating diverse CellML models into a unified framework presents challenges.

Purpose of the Study:

• To introduce the open-source Modeling Markup Language (MML) toolkit.
• To present a workflow for creating multi-scale cardiac tissue models using CellML.
• To demonstrate the interoperability and scalability of the MML framework.

Main Methods:

• Development of an open-source toolkit for the MML framework.
• Utilizing CellML models from repositories and other sources.
• Testing model interoperability with the MML framework.
• Implementing a workflow for cardiac tissue model development.
• Creating a model of atrial electrical activation.

Main Results:

• The MML framework and its open-source toolkit were successfully developed.
• A workflow for generating cardiac tissue models of varying scales was established.
• Interoperability of various CellML models with the MML framework was confirmed.
• The MML framework demonstrated its capability to deploy models across different geometric scales.
• A functional model of atrial electrical activation was successfully generated.

Conclusions:

• The MML framework provides an efficient paradigm for developing and solving biological models.
• The open-source toolkit enhances accessibility and usability for researchers.
• The framework supports the creation of multi-scale cardiac models and diverse geometric representations.
• MML shows promise for advancing computational biology and personalized medicine through detailed physiological modeling.