Cytosim is a cytoskeleton simulation engine written in C++ working on Mac OS, GNU/Linux and Windows (with Cygwin).
The objects in the simulation and their parameters are defined within a single text file config.cym:
set simul example
{
time_step = 0.005
viscosity = 0.02
}
set space cell
{
shape = sphere
dimensions = 5
}
new space cell
set fiber microtubule
{
rigidity = 20
segmentation = 0.5
confine = inside, 200, cell
}
new fiber microtubule
{
length = 11
}
run 5000 simul example
{
nb_frames = 10
}
The documentation can be generated by doxygen:
doxygen src/doc/DoxyfileThis will generate an html folder in the root directory.
You can now open html/index.html in a browser.
In the documentation, you will find a module describing how to compile Cytosim. On Mac OS X and Linux this should be straightforward if you are familiar with compilation in general. On Windows, we suggest that you compile within Cygwin. More more information, please check src/doc/compile.dox.
Here is the steps to compile it in GNU/Linux:
git clone https://github.com/nedelec/cytosim.git
cd cytosim
makeOnce cytosim is running on your machine, check the tutorials, the page on "Running Simulations", and the examples contained in the folder "cym". We recommend starting with the shortest configuration files (e.g. fiber.cym). Finally, do not hesitate to contact us if you have difficulties: cytosim@cytosim.org
We hope cytosim can be useful for your research.
Sincerely yours, The Developers of Cytosim