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Large-scale parameter studies of cell-based models of tissue morphogenesis using CompuCell3D or VirtualLeaf.

Margriet M Palm¹, Roeland M H Merks

¹Centrum Wiskunde & Informatica (CWI), Science Park 123, 1098 XG, Amsterdam, The Netherlands.

Methods in Molecular Biology (Clifton, N.J.)

|September 24, 2014

Summary

This study introduces an automated protocol and scripts for large-scale parameter sweeps in cell-based models, enabling deeper insights into tissue formation. The method enhances understanding of how microscopic cell behaviors influence macroscopic tissue structures.

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Area of Science:

Computational biology
Biophysics
Tissue engineering

Background:

Cell-based models, like the Cellular Potts Model (CPM), are vital for studying tissue formation by simulating cell physical properties and collective behavior.
Current methods often rely on manual parameter tuning and visual evaluation, limiting comprehensive analysis of model dynamics.
Understanding the link between microscopic cellular processes and macroscopic tissue outcomes requires systematic exploration of model parameter spaces.

Purpose of the Study:

To develop and present a protocol and scripts for automating the setup, execution, and evaluation of large-scale parameter sweeps in cell-based models.
To facilitate the generation of morphospaces and gain deeper insights into how microscopic factors influence macroscopic tissue properties.
To demonstrate the protocol's applicability and versatility across different modeling frameworks.

Main Methods:

Development of a protocol for automated parameter sweep execution in cell-based modeling.
Creation of a script set to manage simulation setup, running, and evaluation.
Demonstration using a Cellular Potts Model of blood vessel formation in CompuCell3D and adaptation to the VirtualLeaf framework.

Main Results:

Successful implementation of an automated protocol for large-scale parameter sweeps in cell-based models.
Demonstrated efficiency and versatility of the protocol in analyzing complex biological systems.
Validation of the protocol's utility in a blood vessel formation model and its adaptability to other platforms.

Conclusions:

The automated protocol significantly enhances the ability to explore parameter spaces in cell-based models.
This approach provides a robust framework for understanding the relationship between cellular-level behaviors and emergent tissue-level properties.
The developed tools are valuable for researchers in computational biology and tissue engineering, enabling more systematic and comprehensive model analysis.