Cell-based computational model for simulating stream emergence of neural crest. Published in PLOS Comp Biol: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007002 (DOI: 10.1371/journal.pcbi.1007002).
The code is based on the Tissue Simulation Toolkit first described in the publication: R M H Merks, & J A Glazier. (2005). A cell-centered approach to developmental biology. Physica A, 352(1), 113–130. doi:10.1016/j.physa.2004.12.028, for which the code is available here: https://sourceforge.net/projects/tst/
To compile, use:
cd prog
qmake
make
To run simulations:
cd prog
tst ../runs/par
Parameters for the simulations are specified in a parameter file par. An example is provided in runs/par.
Note: the code has only been tested under Linux.