BioDynaMo version 1.0 was released on April 9, 2021.
The following people have contributed to this first major version (ordered by number of contributions):
- Lukas Breitwieser
- Ahmad Hesam
- Fons Rademakers
- Konstantinos Kanellis
- Jean de Montigny
- Roman Bauer
- Giovanni De Toni
- Jack Jennings
- Dorukhan Arslan
- Nam Nguyen
- Johannes Franz
- Lukasz Stempniewicz
- Robert Harakaly
- Sadyksaj
- Tobias Duswald
- Victor Drobny
Main features
- A general API to implement and customize agent-based models
- A fully parallelized, high-performance simulation engine
- Ability to offload computations to GPUs of all major vendors
- Large-scale model support. BioDynaMo can simulate billions of agents on a single server.
- Predefined building blocks for simulations in neuroscience, oncology, and epidemiology
- Support for spherical and cylindrical agent geometries
- Diffusion methods: Euler, Runge-Kutta
- Multi-scale simulation support
- Visualization in ParaView
- Parameter configuration: JSON, C++ interpreter script, command line, or in-code
- Automatic backup and restore functionality using ROOT
- BioDynaMo Notebooks for rapid web-based prototyping
For a more detailed description of BioDynaMo's features and capabilities, please have a look at the following publication:
BioDynaMo: a general platform for scalable agent-based simulation 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 bioRxiv 2020.06.08.139949; doi: https://doi.org/10.1101/2020.06.08.139949
Demos
BioDynaMo v1.0 comes with the following demos:
- Cell division
- Diffusion
- Soma clustering
- Tumor concept
- Epidemiology
- Gene regulation
- Parameters
- Multiple simulations
- Makefile project
Supported Platforms
- Ubuntu 18.04, 20.04
- CentOS 7
- macOS 10.15 and macOS 11.1