BioDynaMo

Project Goal

The project’s goal is to develop a platform that empowers scientists to effortlessly generate, execute, and visualize agent-based  simulations. Utilizing cutting-edge computing technologies, the BioDynaMo platform will facilitate simulations of unprecedented scale and complexity. This capability opens avenues for addressing intricate scientific research inquiries with greater ease.

Background

In the life sciences community, computer simulation is gaining prominence for modeling intricate biological systems. While numerous specialized tools exist, creating a highperformance, versatile platform represents a significant advancement. CERN leverages its extensive expertise in large-scale computing, supported by funding through the Gentner stipend, ETH Zurich, and the CERN budget for knowledge transfer to medical applications, to collaborate on this unique platform development. The project aims to provide a comprehensive solution for simulating diverse biological scenarios.

 

Biodynamo Project 1
 Simulation of a vascular tumor growth under treatment. Credit: Tobias Duswald et al., https://doi. org/10.1016/j.cma.2023.116566. Used under CC BY 4.0 DEED

Progress

At the beginning of 2023, our work on performance optimizations was published at the PPoPP conference, the premier forum for leading work on all aspects of parallel programming. We show that with our optimizations BioDynaMo is more than 1000x faster than Cortx3D and NetLogo, while also achieving an impressive 9x greater efficiency than Biocellion (https://doi.org/10.1145/3572848.3577480).These enhancements empower our users to simulate larger models, explore model parameters, and accelerate model development. We are deeply honored to receive the Best Artifact Award, recognizing our work’s exceptional quality and impact.

Further, our team published research in Computer Methods in Applied Mechanics and Engineering (CMAME) focusing on the complexities of cancer progression. We introduced a computational model simulating vascular tumor growth and responses to drug treatments in a 3D context. The project’s goal is to develop a platform that empowers scientists to effortlessly generate, execute, and visualize agentbased simulations. The study investigated a therapy involving Doxorubicin and Trastuzumab. Published in CMAME, this work demonstrated BioDynaMo’s capabilities by simulating vascular tumor growth with a volume of 400 mm3 using a total of 92.4 million agents.

Next Steps

Our plan is to make significant strides in enhancing the overall usability of our platform, with a dedicated focus on refining user experience and robustness. We will actively extend our documentation to ensure clarity and accessibility. Furthermore, we will continue our commitment to advancing various use cases in biology and beyond, continuously exploring innovative solutions and contributing to the broader scientific community.

 

Project Coordinator: Lukas Breitwieser

Technical Team: Lukas Breitwieser, Tobias Duswald

Collaboration Liaisons: Roman Bauer (University of Surrey), Vasileios Vavourakis (University of Cyprus)

In partnership with: University of Surrey, University of Cyprus

Discover more about BioDynaMo on biodynamo.org

 

Biodynamo Project 2
Best Artifact Award ceremony at PPoPP’23 in Montreal, Canada.