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.
The code for the hybrid model simulation, the calibration and validation steps can be found in the repository of HyMetaGrowthXTreat.
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.
The 3D cell culture data associated with this study can be found in the FigShare repository.
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.
For information on the usage of the code have a look at the README file.
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