PhysiBoSS-Models: A database for multiscale models
Resumo
PhysiBoSS é uma plataforma de código aberto que integra a modelagem baseada em agentes de populações celulares com redes Booleanas estocásticas intracelulares, permitindo simulações multiescalares de comportamentos biológicos complexos. Para promover o compartilhamento e o versionamento de modelos, apresentamos o banco de dados PhysiBoSS-Models: um repositório curado de modelos multiescalares construídos com o PhysiBoSS. Ao oferecer uma API Python simples, o PhysiBoSS-Models permite baixar e simular modelos preexistentes com facilidade por meio de ferramentas como o PhysiCell Studio. Ao fornecer acesso padronizado a modelos validados, o PhysiBoSS-Models facilita a reutilização, validação e comparação de desempenho, apoiando pesquisas em biologia.
Palavras-chave:
Modelos Multiescala, Banco de Dados
Referências
Cappuccio, A., Tieri, P., and Castiglione, F. (2015). Multiscale modelling in immunology: a review. Briefings in Bioinformatics, 17(3):408–418.
CERN and OpenAIRE (2013). Zenodo.
Ghaffarizadeh, A., Heiland, R., Friedman, S. H., Mumenthaler, S. M., and Macklin, P. (2018). Physicell: An open source physics-based cell simulator for 3-d multicellular systems. PLoS computational biology, 14(2):e1005991.
Heiland, R., Bergman, D., Lyons, B., Waldow, G., Cass, J., da Rocha, H. L., Ruscone, M., Noël, V., and Macklin, P. (2024). Physicell studio: a graphical tool to make agent-based modeling more accessible. Gigabyte, 2024:gigabyte128.
Johnson, J. A. I., Bergman, D. R., Rocha, H. L., Zhou, D. L., Cramer, E., Mclean, I. C., Dance, Y. W., et al. (2025). Human interpretable grammar encodes multicellular systems biology models to democratize virtual cell laboratories. Cell (in press).
Malik-Sheriff et al. (2019). Biomodels—15 years of sharing computational models in life science. Nucleic Acids Research, 48(D1):D407–D415.
Metzcar, J., Wang, Y., Heiland, R., and Macklin, P. (2019). A review of cell-based computational modeling in cancer biology. JCO Clinical Cancer Informatics, (3):1–13. PMID: 30715927.
Montagud, A., Ponce-de Leon, M., and Valencia, A. (2021). Systems biology at the giga-scale: Large multiscale models of complex, heterogeneous multicellular systems. Current Opinion in Systems Biology, 28:100385.
Ponce-de Leon, M., Montagud, A., Noël, V., et al. (2023). Physiboss 2.0: a sustainable integration of stochastic boolean and agent-based modelling frameworks. npj Systems Biology and Applications, 9(1):54.
Ruscone, M., Checcoli, A., Heiland, R., Barillot, E., Macklin, P., Calzone, L., and Noël, V. (2024). Building multiscale models with physiboss, an agent-based modeling tool. Briefings in Bioinformatics, 25(6):bbae509.
Ruscone, M., Montagud, A., Chavrier, P., Destaing, O., Bonnet, I., Zinovyev, A., Barillot, E., Noël, V., and Calzone, L. (2023). Multiscale model of the different modes of cancer cell invasion. Bioinformatics, 39(6):btad374.
Sauro, H. M., Agmon, E., Blinov, M. L., Gennari, J. H., Hellerstein, J., Heydarabadipour, A., Hunter, P., Jardine, B. E., May, E., Nickerson, D. P., et al. (2025). From fair to cure: guidelines for computational models of biological systems. ArXiv, pages arXiv–2502.
Stoll, G., Caron, B., Viara, E., Dugourd, A., Zinovyev, A., Naldi, A., Kroemer, G., Barillot, E., and Calzone, L. (2017). Maboss 2.0: an environment for stochastic boolean modeling. Bioinformatics, 33(14):2226–2228.
Wilkinson, M. D. et al. (2016). The fair guiding principles for scientific data management and stewardship. Scientific data, 3(1):1–9.
CERN and OpenAIRE (2013). Zenodo.
Ghaffarizadeh, A., Heiland, R., Friedman, S. H., Mumenthaler, S. M., and Macklin, P. (2018). Physicell: An open source physics-based cell simulator for 3-d multicellular systems. PLoS computational biology, 14(2):e1005991.
Heiland, R., Bergman, D., Lyons, B., Waldow, G., Cass, J., da Rocha, H. L., Ruscone, M., Noël, V., and Macklin, P. (2024). Physicell studio: a graphical tool to make agent-based modeling more accessible. Gigabyte, 2024:gigabyte128.
Johnson, J. A. I., Bergman, D. R., Rocha, H. L., Zhou, D. L., Cramer, E., Mclean, I. C., Dance, Y. W., et al. (2025). Human interpretable grammar encodes multicellular systems biology models to democratize virtual cell laboratories. Cell (in press).
Malik-Sheriff et al. (2019). Biomodels—15 years of sharing computational models in life science. Nucleic Acids Research, 48(D1):D407–D415.
Metzcar, J., Wang, Y., Heiland, R., and Macklin, P. (2019). A review of cell-based computational modeling in cancer biology. JCO Clinical Cancer Informatics, (3):1–13. PMID: 30715927.
Montagud, A., Ponce-de Leon, M., and Valencia, A. (2021). Systems biology at the giga-scale: Large multiscale models of complex, heterogeneous multicellular systems. Current Opinion in Systems Biology, 28:100385.
Ponce-de Leon, M., Montagud, A., Noël, V., et al. (2023). Physiboss 2.0: a sustainable integration of stochastic boolean and agent-based modelling frameworks. npj Systems Biology and Applications, 9(1):54.
Ruscone, M., Checcoli, A., Heiland, R., Barillot, E., Macklin, P., Calzone, L., and Noël, V. (2024). Building multiscale models with physiboss, an agent-based modeling tool. Briefings in Bioinformatics, 25(6):bbae509.
Ruscone, M., Montagud, A., Chavrier, P., Destaing, O., Bonnet, I., Zinovyev, A., Barillot, E., Noël, V., and Calzone, L. (2023). Multiscale model of the different modes of cancer cell invasion. Bioinformatics, 39(6):btad374.
Sauro, H. M., Agmon, E., Blinov, M. L., Gennari, J. H., Hellerstein, J., Heydarabadipour, A., Hunter, P., Jardine, B. E., May, E., Nickerson, D. P., et al. (2025). From fair to cure: guidelines for computational models of biological systems. ArXiv, pages arXiv–2502.
Stoll, G., Caron, B., Viara, E., Dugourd, A., Zinovyev, A., Naldi, A., Kroemer, G., Barillot, E., and Calzone, L. (2017). Maboss 2.0: an environment for stochastic boolean modeling. Bioinformatics, 33(14):2226–2228.
Wilkinson, M. D. et al. (2016). The fair guiding principles for scientific data management and stewardship. Scientific data, 3(1):1–9.
Publicado
29/09/2025
Como Citar
NOËL, Vincent; RUSCONE, Marco; HEILAND, Randy; MONTAGUD, Arnau; VALENCIA, Alfonso; BARILLOT, Emmanuel; MACKLIN, Paul; CALZONE, Laurence.
PhysiBoSS-Models: A database for multiscale models. In: SIMPÓSIO BRASILEIRO DE BIOINFORMÁTICA (BSB), 18. , 2025, Fortaleza/CE.
Anais [...].
Porto Alegre: Sociedade Brasileira de Computação,
2025
.
p. 240-245.
ISSN 2316-1248.
DOI: https://doi.org/10.5753/bsb.2025.15091.
