Simulating Solid Tumors with a Microenvironment-Coupled Agent-Based Computational Model

[1] Starruß, J., de Back, W., Brusch, L., Deutsch, A. “Morpheus: a user-friendly modeling environment for multiscale and multicellular systems biology”, Bioinformatics 30, 9 (2014) 1331–1332.Search in Google Scholar

[2] Ghaffarizadeh, A., Heiland, R., Friedman, S. H., Mumenthaler, S. M., Macklin, P., “PhysiCell: an open source physics-based cell simulator for 3-D multicellular systems”, PLoS Comput. Biol. 14, 2 (2018).Search in Google Scholar

[3] Kang, S., Kahan, S., McDermott, J., Flann, N., Shmulevich, I., “Biocellion: accelerating computer simulation of multicellular biological system models”, Bioinformatics 30, 21 (2014) 3101–3108.Search in Google Scholar

[4] Drasdo, D., Höhme, S., “Individual-Based Approaches to Birth and Death in Avascular Tumors”, Mathematical and Computer Modelling 37, (2003) 1163–1175.10.1016/S0895-7177(03)00128-6Search in Google Scholar

[5] Drasdo, D., Hoehme, S., Block, M., “On the Role of Physics in the Growth and Pattern Formation of Multi-Cellular Systems: What can we Learn from Individual-Cell Based Models?”, Journal of Statistical Physics 128, 1 (2007) 287–345.Search in Google Scholar

[6] Walker, D. C., Southgate, J., Hill, G., Holcombe, M., Hosea, D. R., Wood, S. M., Mac Neil, S., Smallwood, R. H., “The epitheliome: agent-based modelling of the social behaviour of cells.”, BioSystems 76, (2004) 89–100.10.1016/j.biosystems.2004.05.02515351133Search in Google Scholar

[7] Cytowski, M., Szymanska, Z., “Large-Scale Parallel Simulations of 3D Cell Colony Dynamics”, Computing in Science & Engineering 16, 5 (2014) 86–95.10.1109/MCSE.2014.2Search in Google Scholar

[8] Cytowski, M., Szymanska, Z., Uminski, P., Andrejczuk, G., Raszkowski K., “Implementation of an Agent-Based Parallel Tissue Modelling Framework for the Intel MIC Architecture”, Scientific Programming 8721612, (2017).10.1155/2017/8721612Search in Google Scholar

[9] Waclaw, B., Bozic, I., Pittman, M. E., Hruban, R. H., Vogelstein, B., Nowak, M. A., “A spatial model predicts that dispersal and cell turnover limit intratumour heterogeneity”, Nature 525, 7568 (2015) 261–264.10.1038/nature14971478280026308893Search in Google Scholar

[10] Summers, H. D., Wills, J. W., Brown, M. R., Rees, P., “Poisson-Event-Based Analysis of Cell Proliferation”, Cytometry A. 87, 5 (2015) 385–392.10.1002/cyto.a.22620496494725572722Search in Google Scholar

[11] Yates, C. A., Ford, M. J., Mort, R. L., “A Multi-Stage Representation of Cell Proliferation as a Markov Process”, Bulletin of Mathematical Biology 79, 12 (2017) 2905–2928.Search in Google Scholar

[12] Ghaffarizadeh, A., Friedman, S. H., Macklin, P., “BioFVM: an efficient, parallelized diffusive transport solver for 3-D biological simulations”, Bioinformatics 32, 8 (2016) 1256–1258.Search in Google Scholar

[13] Ramachandran, P., Varoquaux, G., “Mayavi: 3D Visualization of Scientific Data”, IEEE Computing in Science & Engineering, 13, 2 (2011), 40–51.Search in Google Scholar

[14] Roberts, D. L., Selim, M. S., “Comparative study of six explicit and two implicit finite difference schemes for solving one-dimensional parabolic partial differential equations”, International Journal for Numerical Methods in Engineering 20 (1984) 817–844.10.1002/nme.1620200504Search in Google Scholar

[15] Mombach, J., Glazier, J., “Single cell motion in aggregates of embryonic cells”, Phys. Rev. Lett. 76, 3032 (1996).Search in Google Scholar

[16] Grimes, D. R., Kelly, C., Bloch, K., Partridge, M., “A method for estimating the oxygen consumption rate in multicellular tumour spheroids”, J. R. Soc. Interface 11, 20131124 (2014).10.1098/rsif.2013.1124389988124430128Search in Google Scholar

[17] Macklin, P., Edgerton, M. E., Thompson, A. M., Cristini, V., “Patient-calibrated agent-based modelling of ductal carcinoma in situ (DCIS): From microscopic measurements to macroscopic predictions of clinical progression”, Journal of Theoretical Biology 301 (2012) 122–140.Search in Google Scholar

[18] Kiss, D., Lovrics, A., “Performance analysis of a computational off-lattice tumor growth model”, Proceedings of the IEEE 30^th Jubilee Neumann Colloquium (2017).10.1109/NC.2017.8263270Search in Google Scholar