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BioDynaMo 1.0
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@LukasBreitwieser LukasBreitwieser released this 08 Apr 22:58
· 342 commits to master since this release
v1.0
4b1dfba

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
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