CARTopiaX

This repository provides an agent-based simulation of tumour-derived organoids and their interaction with CAR T-cell therapy.
Developed as part of Google Summer of Code 2025, the project is released under the Apache License 2.0.

The simulation integrates computational modeling and biological insights to explore tumour–immune dynamics and assess treatment outcomes under various scenarios.

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Table of Contents

1. Project Overview
2. Dependencies
3. Installation
4. Building the Simulation
5. Running the Simulation
6. Visualizing Results
7. Acknowledgments
8. License

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Project Overview

This project implements an agent-based model to simulate the behavior of tumour-derived organoids (lab-grown tumour models) and their response to CAR T-cell therapy.

With this simulation, researchers can:

• Recreate in vitro conditions for tumour growth.
• Introduce CAR T-cells and analyze their effectiveness in solid tumor microenvironments.
• Explore different treatment strategies and parameter variations.
• Evaluate outcomes such as tumour reduction, elimination, or relapse risk.

By adjusting biological and therapeutic parameters, the model enables in silico experimentation to complement laboratory research.

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Dependencies

• BioDynaMo (tested with version 1.05.132)
• CMake ≥ 3.13
• GCC or Clang with C++17 support
• GoogleTest (for unit testing)

Note: Ensure BioDynaMo is installed and sourced before running the simulation.

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Installation

Clone the repository:

git clone https://github.com/compiler-research/CARTopiaX.git
cd CARTopiaX

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Building the Simulation

Option 1:
Use BioDynaMo’s build system:

biodynamo build

Option 2:
Manual build:

mkdir build && cd build
cmake ..
make -j <number_of_processes>

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Running the Simulation

After building, run the simulation using one of the following methods:

Option 1:
With BioDynaMo:

biodynamo run

Option 2:
Directly from the build directory:

./build/CARTopiaX

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Results

Data about tumor growth and diffrent types of cell populations is output in ./output/final_data.csv

To visualize the results in paraview use:

paraview ./output/CARTopiaX/CARTopiaX.pvsm

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Acknowledgments

This project builds upon the BioDynaMo simulation framework.

Lukas Breitwieser, Ahmad Hesam, Jean de Montigny, Vasileios Vavourakis, Alexandros Iosif, Jack Jennings, Marcus Kaiser, Marco Manca, Alberto Di Meglio, Zaid Al-Ars, Fons Rademakers, Onur Mutlu, Roman Bauer.
BioDynaMo: a modular platform for high-performance agent-based simulation.
Bioinformatics, Volume 38, Issue 2, January 2022, Pages 453–460.
https://doi.org/10.1093/bioinformatics/btab649

Some of the mathematical models and solver implementations are based on the research of
Luciana Melina Luque and collaborators, as described in:

Luque, L.M., Carlevaro, C.M., Rodriguez-Lomba, E. et al.
In silico study of heterogeneous tumour-derived organoid response to CAR T-cell therapy.
Scientific Reports 14, 12307 (2024).
https://doi.org/10.1038/s41598-024-63125-5

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License

This project is licensed under the Apache License 2.0. See the LICENSE file for details.