PhysiCell Studio: a graphical tool to make agent-based modeling more accessible
Randy Heiland1, Daniel Bergman2,3, Blair Lyons4
1Department of Intelligent Systems Engineering, Indiana University. Bloomington, IN USA.
Biorxiv : the Preprint Server for Biology
|November 14, 2023
Summary
Creating complex multicellular models is simplified with PhysiCell Studio. This open-source tool offers a graphical interface for defining cell behaviors and microenvironment parameters, enhancing model sharing and reproducibility.
Area of Science:
- Computational biology
- Multicellular systems modeling
Background:
- Defining multicellular models involves numerous parameters, posing challenges for sharing and reproducibility.
- PhysiCell is an open-source, physics-based simulation framework utilizing XML for model definition.
- Manual XML editing for model modification can be cumbersome for users.
Conclusions:
- PhysiCell Studio significantly lowers the barrier to entry for using the PhysiCell simulation framework.
- It promotes easier model creation, sharing, and contributes to improved reproducibility in multicellular modeling.
- As open-source software, PhysiCell Studio encourages community contributions and further development.
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