cytosim 1.0.5

Cytosim: Langevin dynamics of active polymer networks

Cytosim

Cytosim is an Open Source cytoskeleton simulation suite designed to model large systems of flexible filaments and their associated proteins, such as molecular motors. It has been extensively used to study actin and microtubule dynamics in 1D, 2D, and 3D.

Built around an optimized C++ core engine, Cytosim runs on UNIX, macOS, GNU/Linux, and within the Windows Subsystem for Linux (WSL). The modular and extensible design makes it highly adaptable, allowing customization for specific research needs. Additionally, a versatile set of Python programs streamlines the standard simulation workflow. It is also available as a python module.

Cytosim has been used in approximately 100 research articles from our and other research groups.

Cytosim offers command-line tools with simulation and display capabilities. Simulations are defined using a configuration file which specifies objects, their parameters, and a sequence of operations such as advancing time, saving frames, or generating reports. Below is a basic example, where parameters are expressed in 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
}

Installation

Cytosim uses the CPU and does not require any specific hardware. It can be installed via Anaconda, or can be compiled from source code before use.

To install it using Anaconda (requires no library installation) :

conda install -c conda-forge cytosim

To compile cytosim from source code :

• On Mac OS X: install Xcode, free on the App Store.
• Linux: install the GNU compiler or another standard compiler.
• Compiling natively on Windows would require changes to the code. For Windows 10 and later, please use the Windows Subsystem for Linux, and for older Windows versions, use Cygwin.

Required Libraries

• BLAS
• LAPACK
• Ncurses

• pthreads
• OpenGL
• GLUT or freeGLUT.

There are different ways to install these libraries.

Instructions

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. Altermatively, it is possible to use cmake to configure make automatically in a separate folder build:

mkdir build
cd build
cmake ..
make

Compilation will take a few minutes and should produce two executables: sim and play.
For troubleshooting, please check the compile instructions.

Testing

A batch simulation is started from the command line preferably in a separate folder, for example run0:

mkdir run0
cp cym/self.cym run0/config.cym
cd run0
../bin/sim

Within less than a minute, this should produce output files (objects.cmo and properties.cmp) in the subdirectory. These binary files can be read by play to produce a graphical display:

../bin/play

Alternatively, a live graphical simulation can be started also from the command line by specifying the path of a configuration file, for example:

bin/play cym/self.cym

This will open a window and display the simulated cytoskeleton directly, without writing any file. Once these tests passed and cytosim is running on your machine, proceed with the tutorials, the page on running simulations, and the examples contained in the folder cym.

Documentation

Link to documentation

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

A recent protocol demonstrating the use of Cytosim is: A Typical Workflow to Simulate Cytoskeletal Systems

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

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
• Gaelle Letort 2014-2022
• Maud Formanek 2020-2023
• Manuel Lera-Ramirez 2017-2024
• Serge Dmitrieff 2013-
• Julio Belmonte 2014-

History

Older versions of the project:

• Cytosim-2017
• Cytosim-2023

Contact

F.J. Nedelec