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English Information

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Authors
# Name
1 Vincent Noël(vincent.noel@curie.fr)
2 Marco Ruscone(marco.ruscone@bsc.es)
3 Randy Heiland(heiland@iu.edu)
4 Arnau Montagud(arnau.montagud@csic.es)
5 Alfonso Valencia(alfonso.valencia@bsc.es)
6 Emmanuel Barillot(Emmanuel.Barillot@curie.fr)
7 Paul Macklin(macklinp@iu.edu)
8 Laurence Calzone(laurence.calzone@gmail.com)

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Reference
# Reference
1 Cappuccio, A., Tieri, P., and Castiglione, F. (2015). Multiscale modelling in immunology: a review. Briefings in Bioinformatics, 17(3):408–418.
2 CERN and OpenAIRE (2013). Zenodo.
3 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.
4 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.
5 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, Volume 188, Issue 17, 4711 - 4733.e37
6 Malik-Sheriff et al. (2019). Biomodels—15 years of sharing computational models in lifescience. Nucleic Acids Research, 48(D1):D407–D415.
7 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.
8 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.
9 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.
10 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.
11 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.
12 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.
13 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.
14 Wilkinson, M. D. et al. (2016). The fair guiding principles for scientific data management and stewardship. Scientific data, 3(1):1–9.