Lukas Breitwieser

• ETH Zurich

Motivation Agent-based modeling is an indispensable tool for studying complex biological systems. However, existing simulation platforms do not always take full advantage of modern hardware and often have a field-specific software design. Results We present a novel simulation platform called BioDynaMo that alleviates both of these problems. BioDyn...

Agent-based modeling plays an essential role in gaining insights into biology, sociology, economics, and other fields. However, many existing agent-based simulation platforms are not suitable for large-scale studies due to the low performance of the underlying simulation engines. To overcome this limitation, we present a novel high-performance simu...

Agent-based modeling is indispensable for studying complex systems across many domains. However, existing simulation platforms exhibit two major issues: performance and modularity. Low performance prevents simulations with a large number of agents, increases development time, limits parameter exploration, and raises computing costs. Inflexible soft...

Understanding how genetically encoded rules drive and guide complex neuronal growth processes is essential to comprehending the brain’s architecture, and agent-based models (ABMs) offer a powerful simulation approach to further develop this understanding. However, accurately calibrating these models remains a challenge. Here, we present a novel app...

Calibration is a crucial step in developing agent-based models. Agent-based models are notorious for being difficult to calibrate as they can express various degrees of freedom when model parameters are unknown. Models that appear correctly calibrated to match macro-level observed data perform poorly when micro-level insights need to be inferred. A...

Understanding how genetically encoded rules drive and guide complex neuronal growth processes is essential to comprehending the brain's architecture, and agent-based models (ABMs) offer a powerful simulation approach to further develop this understanding. However, accurately calibrating these models remains a challenge. Here, we present a novel app...

Researchers in biology are faced with the tough challenge of developing high-performance computer simulations of their increasingly complex agent-based models. BioDynaMo is an open-source agent-based simulation platform that aims to alleviate researchers from the intricacies that go into the development of high-performance computing. Through a high...

Computer simulations have become a very powerful tool for scientific research. Given the vast complexity that comes with many open scientific questions, a purely analytical or experimental approach is often not viable. For example, biological systems comprise an extremely complex organization and heterogeneous interactions across different spatial...

Motivation Agent-based modeling is an indispensable tool for studying complex biological systems. However, existing simulators do not always take full advantage of modern hardware and often have a field-specific software design. Results We present a novel simulation platform called BioDynaMo that alleviates both of these problems. BioDynaMo featur...

This paper develops a three-dimensional in silico hybrid model of cancer, which describes the multi-variate phenotypic behaviour of tumour and host cells. The model encompasses the role of cell migration and adhesion, the influence of the extracellular matrix, the effects of oxygen and nutrient availability, and the signalling triggered by chemical...

A distributed middleware early prototype has been designed for the BioDynaMo project, which aims to be a general platform for computer simulations of biological tissue dynamics. The middleware’s functionality has been implemented keeping in mind the diversity of the performance and reliability characteristics of highperformance clusters and cloud e...

Computer simulations have become a very powerful tool for scientific research. Given the vast complexity that comes with many open scientific questions, a purely analytical or experimental approach is often not viable. For example, biological systems comprise an extremely complex organization and heterogeneous interactions across different spatial...

Computer simulations have become a very powerful tool for scientific research. In order to facilitate research in computational biology, the BioDynaMo project aims at a general platform for biological computer simulations, which should be executable on hybrid cloud computing systems. This paper describes challenges and lessons learnt during the ear...

This paper is a brief update on developments in the BioDynaMo project, a new platform for computer simulations for biological research. We will discuss the new capabilities of the simulator, important new concepts simulation methodology as well as its numerous applications to the computational biology and nanoscience communities.

Computer simulations have become a very powerful tool for scientific research. Given the vast complexity that comes with many open scientific questions, a purely analytical or experimental approach is often not viable. For example, biological systems (such as the human brain) comprise an extremely complex organization and heterogeneous interactions...

Computer simulations have become a very powerful tool for scientific research. Given the vast complexity that comes with many open scientific questions, a purely analytical or experimental approach is often not viable. For example, biological systems (such as the human brain) comprise an extremely complex organization and heterogeneous interactions...