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 simulation engine.

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. BioDynaMo features a modular and high-performance simulation engine. We demonstrate that BioDynaMo can be used to simulate use cases in: neuroscience, oncology and epidemiology. For each use case, we validate our findings with experimental data or an analytical solution. Our performance results show that BioDynaMo performs up to three orders of magnitude faster than the state-of-the-art baselines. This improvement makes it feasible to simulate each use case with one billion agents on a single server, showcasing the potential BioDynaMo has for computational biology research. AVAILABILITY AND IMPLEMENTATION: BioDynaMo is an open-source project under the Apache 2.0 license and is available at www.biodynamo.org. Instructions to reproduce the results are available in the supplementary information. SUPPLEMENTARY INFORMATION: Available at https://doi.org/10.5281/zenodo.5121618.

The parallel ROOT facility, PROOF, enables the interactive analysis of distributed data sets in a transparent way. It exploits the inherent parallelism in data sets of uncorrelated events via a multi-tier architecture that optimizes I/O and CPU utilization in heterogeneous clusters with distributed storage. On a grid, PROOF can use the available services to find out the location of data to analyze and the resources to use. Dedicated PROOF-enabled test-beds are now being deployed for testing by the LHC experiments. Being part of the ROOT framework PROOF inherits the benefits of a high performance object-oriented storage system and a wealth of statistical and visualization tools. The basic ideas and architecture underlying the PROOF project are described, together with the status of the project, focusing mostly on the issues of data access optimization, scheduling of user sessions and user interface