Chaste - Cancer Heart And Soft Tissue Environment - main public repository.
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Updated
May 24, 2024 - C++
Chaste - Cancer Heart And Soft Tissue Environment - main public repository.
Spheroid models of morphogenesis for the GPU.
Matlab scripts to recreate figures of the JR Soc Interface article "Model reduction enables Turing instability analysis of large reaction-diffusion models"
Ontology of human developmental anatomy
"Scutoids are a geometrical solution to three-dimensional packing of epithelia" - https://www.nature.com/articles/s41467-018-05376-1.
vertex model implementation to simulate biological tissue in 3D
vertex model for simulating two-dimensional epithelial tissues
"Theoretical tool bridging cell polarities with development of robust morphologies" published in eLife (2018)
Files used to generate Michelle Franc Ragsac's Ph.D. Dissertation
deep-learning for metadata extraction from the C. elegans embryo
R package that uses rstan capabilities to sample using `HMC' and inference for developmental rate dynamics of species in ecology
Analysis scripts for the Ebbing et manuscript: "Spatially-resolved transcriptomics in C. elegans identifies sex-specific differences in gene expression patterns"
"A quantitative principle to understand 3D cellular connectivity in epithelial tubes" Gomez-Galvez et al
Goo is the Blender library for simulating biological cells, tissues and embryos in 3D.
Python code to model the syncytial development of a cricket in 3D. Additional Mathematica Code for rendering mesh2 objects in povray.
sEMTor is an online simulation for epithelial-mesenchymal transitions (EMT)
This repo contains code and presentations used for ad-hoc analyses regarding liver cell toxicology and development. It also contains analyses on human and mice immune cells.
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