cytosim 0.0.21

Cytosim: Langevin dynamics of active polymer networks

Cytosim

Cytosim is an open-source cytoskeleton simulation suite designed to handle large systems of flexible filaments with associated proteins such as molecular motors. It is a versatile base that has been used to study actin and microtubule systems in 1D, 2D and 3D. It is built around a cross-platform C++ core engine running on UNIX, Mac OSX, GNU/Linux and Linux-environments within Windows. The code is modular and extensible, making Cytosim a convenient base that can be customized to meet particular tasks. Some of the most common tasks encountered during a simulation project are implemented in Python.

Cytosim has been used for about 100 research articles from the Nedelec and other groups.

Cytosim is a suite of command-line tools with simulation and display capabilities. The simulation is specified in a configuration file, defining objects with their parameters and a suite of operations, such as advancing time, saving frames or generating reports. Here is a basic example, with parameters specified in units of seconds, micrometers and pico-Newtons.

set simul system
{
    time_step = 0.005
    viscosity = 0.02
}

set space cell
{
    shape = sphere
}

set fiber microtubule
{
    rigidity = 20
    segmentation = 0.5
    confine = inside, 200, cell
}
    
new cell
{
    radius = 5
}

new 5 microtubule
{
    length = 11
}

run 5000 system
{
    nb_frames = 10
}

Documentation

Link to documentation

The Brownian dynamics approach was described in:
Collective Langevin Dynamics of Flexible Cytoskeletal Fibers

The documentation source files use Markdown and are best viewed with MacDown (Mac OSX only) or Typora (Cross platform)

Installation

Cytosim is distributed as source code and must be compiled before use. On Mac OS X and Linux this should be uncomplicated even if you are not familiar with program development. Compiling natively on Windows would require changes to the code, but Cytosim should compile with the Windows Subsystem for Linux.

To download the source code, enter these commands in a terminal window:

git clone https://gitlab.com/f-nedelec/cytosim
cd cytosim

To compile using make, try:

make

If this fails, parameters of makefile.inc need to be updated manually. Altermatively, it is possible to use cmake to configure make automatically:

mkdir build
cd build
cmake ..
make

For troubleshooting, please check the compile instructions. Once cytosim is running on your machine, proceed with the tutorials, the page on running simulations, and the examples contained in the folder cym. Inspect in particular the short configuration files (e.g. fiber.cym, self.cym).

Contributors

The project was started in 1995, and received its name in 1999. We hope cytosim can be useful for your research. Sincerely yours, The Developers of Cytosim:

• Francois J. Nedelec 1995-
• Dietrich Foethke 2003-2007
• Cleopatra Kozlowski 2003-2007
• Elizabeth Loughlin 2006-2010
• Ludovic Brun 2008-2010
• Beat Rupp 2008-2011
• Jonathan Ward 2008-2014
• Antonio Politi 2010-2012
• Andre-Claude Clapson 2011-2013
• Jamie-Li Rickman 2014-2019
• Serge Dmitrieff 2013-
• Julio Belmonte 2014-
• Gaelle Letort 2014-
• Manuel Lera-Ramirez 2017-2022
• Maud Formanek 2020-2021

Contact

Email: [e-mail]