Repository for calibration, simulation, and validity assessment of a Hybrid Discrete-Continuum model of cancer growth with applications in 3D cancer cell cultures (paper) in presence and absence of treatment.
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The code for the hybrid model simulation, the calibration and validation steps can be found in the repository of HyMetaGrowthXTreat.
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The code for the image processing and segmentation pipeline can be found in 3D-Preprocessing-Nuclei-Segmentation repository. Details on the image processing and segmentation pipeline can be found here.
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The 3D cell culture data associated with this study can be found in the FigShare repository.
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The RNA-sequencing data associated with this study can be found in the NCBI GEO database under the accession number: GSE223350. The code used for the differential gene expression analysis can be found in DiffGeneAnalysis directory.
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For information on the usage of the code have a look at the README file.
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A presentation related to the numerical methods and their implementation in GPU code can be found here.
For any question feel free to contact me at: nikolaos.dimitriou [at] mail.mcgill.ca
If you intend to use this code or data in your publications, please cite:
Dimitriou, N. M., Flores-Torres, S., Kyriakidou, M., Kinsella, J. M., & Mitsis, G. D. (2023). Cancer cell sedimentation in 3D cultures reveals active migration regulated by self-generated gradients and adhesion sites. BioRxiv. https://doi.org/10.1101/2023.02.15.528731