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Start & Stop: a PhysiCell and PhysiBoSS 2.0 add-on for interactive simulation control.

Riccardo Smeriglio1, Roberta Bardini2, Alessandro Savino1

  • 1Department of Control and Computer Engineering, Politecnico di Torino, Corso Duca degli Abruzzi, 24, 10129, Turin, TO, Italy.

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Summary
This summary is machine-generated.

Computational biology simulations can now be interactively controlled. The new Start & Stop add-on for PhysiCell and PhysiBoSS 2.0 allows pausing, parameter adjustment, and resuming simulations, enhancing dynamic protocol exploration.

Keywords:
Computational biologyIn silicoModelingMulti-scaleSimulation

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Area of Science:

  • Computational biology
  • Systems biology
  • Bioinformatics

Background:

  • In silico simulators are crucial for understanding complex biological systems.
  • Hybrid multi-level simulators like PhysiCell and PhysiBoSS 2.0 offer deep insights but lack interactive parameter adjustment during simulation.
  • This limitation restricts dynamic protocol exploration for applications like biofabrication and drug testing.

Purpose of the Study:

  • To introduce the Start & Stop add-on for PhysiCell and PhysiBoSS 2.0.
  • To enable interactive parameter adjustments during ongoing simulations.
  • To enhance the flexibility and user interaction of multi-level biological simulators.

Main Methods:

  • Developed the Start & Stop add-on featuring multi-level state preservation and multi-modal stop control.
  • Integrated the add-on with PhysiCell and PhysiBoSS 2.0.
  • Validated the add-on using two established PhysiBoSS 2.0 use cases: TNF-stimulated 3T3 mouse fibroblasts and lung cancer cell invasion.

Main Results:

  • The Start & Stop add-on successfully enables pausing simulations based on time or cell conditions.
  • Users can adjust simulation parameters and resume from the exact halted state without altering original behavior.
  • Demonstrated preservation of simulator behavior and facilitated exploration of adaptive treatment strategies in validation use cases.

Conclusions:

  • The Start & Stop add-on significantly enhances the interactivity of PhysiCell and PhysiBoSS 2.0.
  • It bridges the gap between simulations and real-world in vitro scenarios, enabling more adaptive protocol development.
  • Expands the range of potential simulations and advances effective protocol design in computational biology.