Cytosim is a cytoskeleton simulation engine
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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/Doxyfile

This will generate an html folder in the root directory.

You can now open html/index.html in a browser.

Installation and compilation

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. For more information, please check src/doc/compile.dox.

After installing Apple's Xcode, enter these commands to compile:

git clone
cd cytosim


Once 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:

We hope cytosim can be useful for your research.

Sincerely yours, The Developers of Cytosim