OBSOLETE Cytosim

This is a deprecated version of Cytosim. Please use the more up-to-date code
hosted on Gitlab:

https://gitlab.com/f-nedelec/cytosim

Description

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
}

Documentation

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

Please, do not use this outdated version

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 https://github.com/nedelec/cytosim.git
cd cytosim
make

Usage

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: [email protected]

We hope cytosim can be useful for your research.

Sincerely yours, The Developers of Cytosim