Publications

cellular_raza has been published in the Journal of Open Source Software joss.theoj.org/papers/10.21105/joss.07723. You can use the following BibTex entry to cite it.

@article{Pleyer2025,
    doi = {10.21105/joss.07723},
    url = {https://doi.org/10.21105/joss.07723},
    year = {2025},
    publisher = {The Open Journal},
    volume = {10},
    number = {110},
    pages = {7723},
    author = {Jonas Pleyer and Christian Fleck},
    title = {cellular\_raza: Cellular Agent-based Modeling from a Clean Slate},
    journal = {Journal of Open Source Software}
}

2026

Gaindrik, P., Pleyer, J., Brunner, M., Pérez Rodríguez, F., & Fleck, C. (2026). “The pool model: A mechanistic ODE framework for bacterial consortia inFood science.” doi: doi.org/10.2139/ssrn.6616864

2025

Pleyer, J. and C. Fleck, (2025) “cellular_raza – Novel Flexibility in Design of Agent-Based Models in Cellular Systems” Proceedings of the 9th bwHPC Symposium 2023, 2nd October 2025, doi: doi.org/10.25521/maconf.2025.1027

Pleyer, J. and C. Fleck, (2025) “cellular_raza: Cellular Agent-based Modeling from a Clean Slate” Journal of Open Source Software, June 10th, 2025. doi: joss.theoj.org/papers/10.21105/joss.07723.

Pleyer, J. (2025). “cellular_raza: cellular agent-based modeling from a clean slate” At the Scientific Computing in Rust conference (Youtube, Slides).

M. Licheva et al., “Phase separation of initiation hubs on cargo is a trigger switch for selective autophagy,” Nature Cell Biology. Springer Science and Business Media LLC, Jan. 07, 2025. doi: 10.1038/s41556-024-01572-y.

2024

Toquinha Bergmann et al., (2024). Trichome Pattern Formation: Computational Exploration of the Robustness and mechanistic influences of the Turing Mechanism. At the “Self-Organization in Biology” Symposium, Freiburg.

Pleyer, J. (2024). cellular_raza - Think like a cell. At the Group Seminar of Jens Timmer.

2023

Pleyer, J. (2023). cellular_raza - Novel Flexibility in Design of Agent-Based Models in Cellular Systems. At the bwHPC Symposium 2023.

J. Pleyer and C. Fleck, “Agent-based models in cellular systems,” Frontiers in Physics, vol. 10. Frontiers Media SA, Jan. 04, 2023. doi: 10.3389/fphy.2022.968409.