The BioDynaMo Project

TL;DR

The BioDynaMo project develops a versatile simulation platform for biological research, addressing computational challenges and interdisciplinary collaboration to enable complex biological system modeling on hybrid cloud systems.

Contribution

This paper details the initial development challenges, methodologies, and lessons learned in creating a general biological simulation platform for research.

Findings

Identified key implementation challenges in early development stages.

Highlighted the importance of interdisciplinary collaboration.

Outlined strategies for deploying simulations on hybrid cloud systems.

Abstract

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 across different spatial and temporal scales. In order to facilitate research on such problems, the BioDynaMo project (\url{https://biodynamo.web.cern.ch/}) aims at a general platform for computer simulations for biological research. Since the scientific investigations require extensive computer resources, this platform should be executable on hybrid cloud computing systems, allowing for the efficient use of state-of-the-art computing technology. This paper describes challenges during the early stages of the software development process. In particular, we describe issues regarding the implementation and the highly interdisciplinary as well as international nature of the collaboration. Moreover, we explain the methodologies, the approach, and the lessons learnt by the team during these first stages.