Tissue Simulation Toolkit, v0.1.3
0.1.3
Welcome to the Tissue Simulation Toolkit, a library for two-dimensional simulations of Glazier and Graner's Cellular Potts model (Glazier and Graner, 1993).
The TST aims to provide a simple set of computational tools to get you started with the Cellular Potts Model (CPM), also called Glazier-Graner-Hogeweg (GGH) model.
The current version of the TST includes example programs for the following published simulations:
- Differential adhesion driven cell sorting (Glazier and Graner, 1993)
- Cell elongation dependent vasculogenesis (blood vessel growth) (Merks et al., 2006)
- Vasulogenesis and angiogenic sprouting driven by contact-inhibited chemotaxis (Merks and Glazier, 2006; Merks et al, PLoS Comp. Biol.)
The TST provides many recent extensions to the CPM, including
- Infinite number of PDE layers (forward Euler)
- Interaction of CPM cells and PDE (secretion, absorption)
- Chemotaxis
- Length and connectivity constraints
and visualization of:
- Cells, according to cell type or anything you wish
- Chemical fields, using color ramps and contour lines (level sets)
The TST has been compiled on Windows XP (minGW), and Linux and MacOSX systems (GNU C++). The following libraries are required:
Qt (version 4.3) libpng (url) and libz (url)
For Unix, we also have an X11-only version, although compilation is easiest with the qmake tool shipped with Qt (see http://www.trolltech.com)
With Qt, simply type:
qmake make
If you want to use a different "main" program (examples are given: vessel.cpp and sorting.cpp), just change "TARGET" in the file "CellularPotts2.pro".
A small Cellular Potts tutorial making use of the example programs sorting.cpp and vessel.cpp is provided by the document "exercises.pdf" included in the source package.
An automatically generated class documentation is included in html/index.html.
- Glazier, J. A. and Graner, F. 1993. Simulation of the differential adhesion driven rearrangement of biological cells. Phys. Rev. E 47, 2128-2145.
- Merks, R. M. H., Brodsky, S. V., Goligorsky, M. S., Newman, S. A. and Glazier, J. A., 2006. Cell elongation is key to in silico replication of in vitro vasculogenesis and subsequent remodelling. Dev. Biol. 289, 44-54.
- Merks, R. M. H. and Glazier, J. A., 2005. A cell-centered approach to developmental biology. Phys. A. 352, 113-130.
- Merks, R. M. H. and Glazier, J. A., 2006. Dynamic mechanisms of blood vessel growth. Nonlinearity 19, C1-C10.
- Merks, R. M. H., Perryn, E. D. and Glazier, J. A. Contact-inhibited chemotactic motility in de novo and sprouting blood vessel growth. PLoS Computational Biology
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