Nedelec Laboratory EMBL, Cell biology and Biophysics Unit.
( 2011 - 2017 )
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.
One particularly fascinating aspect of life is the contrast between the relative unity￼found 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.
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.
- parameters are grouped in logical units,
- these units correspond to entities in the simulation,
- an arbitrary number of definitions and objects can be created,
- definitions and commands can be mixed.
Cytosim is an Open Source project hosted on github.
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 *
Please, check our gallery of movies
- To use cytosim in conjunction with our published work, use the appropriate package from our publication page.
- The source code corresponding to any published article is available upon request.
- Compilation on Microsoft Windows is not supported, but it works well under UNIX and Linux.