CYTOSIM 1.7

Francois Nedelec and Dietrich Foethke, EMBL, Cell biology and Biophysics.
( June 2003 )
Cytosim

Introduction

Cytosim is a simulation inspired by the cytoskeleton, the ensemble of fibers and proteins structuring the inside of eukaryotic cells. The model on which the simulation is built has been described in "Computer Simulations Reveal Motor Properties Generating Stable Anti-Parallel Microtubule Interactions", published in the Journal of Cell Biology Nb. 158(6) pp. 1005-1015, September 2002. It is based on Langevin 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, your feedback is precious.

This page explains how to use cytosim 1.7 on Windows32 (NT, 2000, XT) and Mac OSX (10.2.4 and above). If you experience problems, please contact us.

Installation

Click on one of the link below to download cytosim:
  1. For mac OSX: cytosim17Mac.dmg (800 KB).
  2. For Windows: cytosim17PC.tar (2 MB)
The files should open automatically. If not, double click on it, or use your favorite expander. A directory 'cytosim' will be created, containing a text file data.in specifying the parameter values, play, the simulation engine, plus some other necessary files.

Running the simulation

  1. Open a window where you can type line commands (e.g. Terminal in Mac OS X, or 'cmd' in Windows).
  2. Change the current diretory to the 'cytosim' directory where play and data.in are located.
  3. Typing 'play -l' should start a new simulation on your screen.
Please, read the file README.txt in the downloaded directory for more specific instructions. Try also the different options of play: play -h, play -k, play -p.
To run another simulation, you will need to edit the file data.in, saving it as a text file, and restart play. Cytosim only understands plain text files, so if you edit data.in with e.g. MS-Word, dont forget to save it as a text file! The tutorial below should make clear the jargon used in data.in.

Tutorial

The tutorial is a step by step introduction into the model. It will explain you how to create your own file data.in, and the meaning of the different parameters of the simulation. Do not miss it!

Advanced Instructions

The format used in the result.out files is described here. play uses OpenGL for rendering, and can read 'result.out' files produced by cytosim 1.0.