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CYTOSIM 2.0

Nedelec Laboratory EMBL, Cell biology and Biophysics.
Main Contributors: Francois Nedelec, Dietrich Foethke, Cleopatra Kozlowski, Rose Loughlin
( Nov 2007 )
Previous versions: (1.7) (1.0)

Note: to use cytosim in conjunction with our published work, download the appropriate package from our publication page.

Introduction

Cytosim is a simulation inspired by the cytoskeleton, the ensemble of fibers and associated proteins found inside of eukaryotic cells. Its mathematical foundations are described in the New Journal of Physics "Collective Langevin Dynamics of Flexible Cytoskeletal Fibers". It is based on Brownian dynamics, the diffusion of molecules, their encounters leading to transient binding and the calculation of all forces present in the fibers and molecular complexes. Cytosim is under active development, and we are always happy to get your feedback.

This page explains how to use cytosim 2.0 on Windows32 (NT, 2000, XT) and Mac OSX (10.2.4 and above).

Installation

Download cytosim's package:
  1. For mac OS-X: cytosim20.dmg (900 KB)
  2. For Windows 32: cytosim20.zip (4 MB)
They include a simulation engine cytosim, three example parameter files and double-clickable scripts.
Copy all files to a new folder on your local disc.

Running the simulation

  1. Open a window where you can type unix-style commands (Terminal in Mac OS X, or 'cmd' in Windows).
  2. Go ('cd') to the directory where 'cytosim' and the parameter files have been copied.
  3. The command 'cytosim -l self1.cym' should open a window and start a new simulation using the parameters in 'self1.cym'.
The package includes 3 configuration files:

Self-organization (self1.cym):

Self-centering (holy.cym):

Gliding spiral (spiral.cym):
Self-Organization Self-Centering Gliding-Spiral
Click the pictures for Quicktime movies

For each of these examples, a script '.bat' or '.command' starts the simulation if you double-click it.
Cytosim has some basic built-in help, try: cytosim -h, cytosim -k. You can also obtain some on-screen info by pressing 'h' when the program is running.

Running your own simulation

You can your own simulation with cytosim -l after creating a parameter file config.cym. The tutorial is a step by step introduction to the most important parameters. It explain you how to create a valid config.cym. The option cytosim -p provides a short list of parameters, but most of them are not documented (yet) in the tutorial.
Cytosim only reads plain text, and we suggest you edit the parameter files with a simple text editor (e.g. TextEdit but not MS-Word).


Heidelberg, december 6th, 2007