Supporting information for "BioDynaMo: a modular platform for high-performance agent-based simulation"

This repository contains all supporting material for the paper "BioDynaMo: a modular platform for high-performance agent-based simulation".

This paper was published in the Bioinformatics journal and is available at: https://doi.org/10.1093/bioinformatics/btab649

If you find this repository useful, please cite the following works:

Lukas Breitwieser et al., BioDynaMo: a modular platform for high-performance agent-based simulation, Bioinformatics, Volume 38, Issue 2, 15 January 2022, Pages 453–460, https://doi.org/10.1093/bioinformatics/btab649

@article{breitwieser_biodynamo_2022,
    author = {Breitwieser, Lukas and Hesam, Ahmad and de Montigny, Jean and Vavourakis, Vasileios and Iosif, Alexandros and Jennings, Jack and Kaiser, Marcus and Manca, Marco and Di Meglio, Alberto and Al-Ars, Zaid and Rademakers, Fons and Mutlu, Onur and Bauer, Roman},
    title = "{BioDynaMo: a modular platform for high-performance agent-based simulation}",
    journal = {Bioinformatics},
    volume = {38},
    number = {2},
    pages = {453-460},
    year = {2021},
    month = {09},
    issn = {1367-4803},
    doi = {10.1093/bioinformatics/btab649},
    url = {https://doi.org/10.1093/bioinformatics/btab649}
}

Lukas Breitwieser et al., High-Performance and Scalable Agent-Based Simulation with BioDynaMo. 2023, In Proceedings of the 28th ACM SIGPLAN Annual Symposium on Principles and Practice of Parallel Programming (Montreal, QC, Canada) (PPoPP ’23). Association for Computing Machinery, New York, NY, USA, 174–188. https://doi.org/10.1145/3572848.3577480 arXiv:2301.06984 [cs.DC]

This work received the Best Artifact Award at PPoPP '23.

@inproceedings{breitwieser_biodynamo_2023,
  author = {Breitwieser, Lukas and Hesam, Ahmad and Rademakers, Fons and Luna, Juan G\'{o}mez and Mutlu, Onur},
  title = {High-Performance and Scalable Agent-Based Simulation with BioDynaMo},
  year = {2023},
  isbn = {9798400700156},
  publisher = {Association for Computing Machinery},
  address = {New York, NY, USA},
  url = {https://doi.org/10.1145/3572848.3577480},
  doi = {10.1145/3572848.3577480},
  booktitle = {Proceedings of the 28th ACM SIGPLAN Annual Symposium on Principles and Practice of Parallel Programming},
  pages = {174–188},
  numpages = {15},
  keywords = {NUMA, HPC, performance evaluation, parallel computing, space-filling curve, high-performance simulation, performance optimization, agent-based modeling, memory layout optimization, memory allocation, scalability},
  location = {Montreal, QC, Canada},
  series = {PPoPP '23},
  archivePrefix = "arXiv",
  eprint        = "2301.06984",
  primaryClass  = "cs.DC"
}