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CYTOSIM

Nedelec Laboratory EMBL, Cell biology and Biophysics Unit.
( 2011 - 2017 )

Introduction

Cytosim is a simulation of the cytoskeleton under active development. Cytosim was designed to simulate large systems of fibers with associated proteins such as molecular motors. The Brownian dynamics approach was described in the New Journal of Physics: "Collective Langevin Dynamics of Flexible Cytoskeletal Fibers".

Filaments can be flexible, and other objects such as beads can be used and combined to build more complex structures.

Modularity

One particularly fascinating aspect of life is the contrast between the relative unityfound at the molecular scale, and the astonishing diversity of life forms, observable already at the cellular scale. A reduced set of cellular components and activities, tuned and combined differently, supports the high diversity of cellular shape and behaviors across all kingdoms of life. The number of combinations present in nature is colossal.
Modularity
Addressing this diversity has been the motivation behind the radical transformation of cytosim that took 5 years to complete. Previously, users could change parameters, but the system was defined in the source code of the program itself. The modernized version offers a powerful environment, in which the virtual cell is defined using a set of elementary instructions. It is now easy to combine elements of the predefined toolkit to build complex virtual systems containing composite objects (see figure). One can fully exploit the robust object-oriented design of the simulation engine, without having to learn C++. Users can select building blocks such as flexible filaments and the activities associated to them: nucleation, binding, motility, severing, etc. Multiple instances of these entities can be created, each with their own set of parameters, and can be combined into multifunctional objects. For example, it is possible to define two types of filaments (e.g., actin and microtubules), a molecular motor (e.g., myosin), a molecule binding near the ends of the filaments (Eb1) and to make an entity containing the two activities (Eb1≡Myosin). Finally, one defines a system by selecting the geometry of the cell and the quantity of objects within it.

A single configuration file provides access to all functionalities: The result is a modular, powerful and also more user-friendly simulation. We have extensively revised the code, and the changes are nearly complete. The documentation is minimal, but a lot of things are easy to do.

Source Code

Cytosim is an Open Source project hosted on github.

Download

Download our beta software for Mac OSX 10.6+: cytosim-beta.zip. This program is distributed in the hope that it will be useful, but withoug any warranty. It is provided 'as is' with absolutely no warranty of any kind, expressed or implied ... The package contains executables for 2D and 3D simulations, the current documentation and many sample configuration files. This package is updated irregularly, a version number is contained in bin/info.txt.
Please, report your experience by email to support -- hat -- cytosim.org.

Example of Configuration File

set simul example
{
    time_step = 0.005
    viscosity = 0.02
}

set space cell
{
    geometry = ( sphere 5 )
}

new space cell

set fiber microtubule
{
    rigidity = 20
    segmentation = 0.5
    confine = inside, 100
}

new 2 fiber microtubule
{
    length = 8
}

run 5000 simul *

Examples

Please, check our gallery of movies

Notes

Previous versions