Summer Project Goals:

1) Develop basic simulations of cell growth, cell sorting, collective and individual cell migration, contact inhibition etc. that will allow us to compare Vertex Dynamics Model (in CHASTE) and Cellular Potts Model (in CompuCell3D).

2) Create re-usable code (mixture of CPP, Python and MATLAB) to collect data from mesh-based simulations, parse it and plot it. The data should include the following (and possibly more):

3) Build on top of CHASTE framework to make it accessible to everyone. This involves developing new classes to set up custom meshes, non-trivial tissue boundaries, adding new elementary mesh restructuring moves, attaching an ode solver to each cell, etc. The goal is to make development using CHASTE as easy and efficient as writing Python code for CompuCell3D.
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