CYTOSIM 1.0

Francois Nedelec. EMBL, Cell biology and Biophysics.
( April 2002 )
Cytosim

Introduction

Cytosim is a simulation inspired by the cytoskeleton, the ensemble of fibers and proteins found 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 classical mechanics, for example 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 development, and this is only the first version...your feedback is precious.

This page explains how to download, and use the simulation on a PC running Windows32 (NT, 2000, XT), or on a macintosh running Mac OS X. The program should work on these computers, but if it does not, it would be nice if you can give me some feed-back.

Installation

To run a simulation, you will need three files, and Java 2:
  1. A file data.in (1KB) that specifies the parameters of the simulation.
  2. The simulation itself, for windows : cytosim (300KB), for mac OS X : cytosim_mac (1.3MB).
  3. jplay (60KB), which draws simulated systems.
  4. A Java 2 Runtime Environement to run jplay. It might be already installed on your system (this is the case on mac OS X). Otherwise, it can be downloaded from sun, ibm and others...(if you do not understand this, seek help from your system administrator).

Download:

The gzip-compressed tar archive contains everything you need: The archives will probably unzip automatically, creating a folder cytosim containing all the files needed. If not, you can unzip them manually with a program like stuffit expander. If that still does not work, you should create a folder called C:\cytosim, and download cytosim (300KB), jplay.jar (60KB) and data.in into this folder.

Basic Instructions

After installing a java2 runtime environment, you will then need to:
  1. open a command line window (Windows: start/cmd, on Mac OS X: utility/terminal)
  2. set the current directory to the folder cytosim (cd C:\cytosim),
  3. enter ./cytosim to start the simulation (enter ./cytosim_mac on a mac),
  4. Cytosim is not interactive, it uses data.in for its input. You should wait until it ends, at which point cytosim should have produced two files : result.out and data.out.
  5. type java -jar jplay.jar to start the graphical player. It will open a window and display the first simulation state stored in result.out. You should read jplay.help to learn how to use its main features... On mac OS X, you can start the jplay just by double-clicking on the file jplay.jar.
To run another simulation, you will need to edit the file data.in, saving it as a text file, and repeat from step 5. Cytosim only understand 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 will 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

Cytosim accepts some very limited command line options (try cytosim -h). The format used in the result.out files is described here. jplay include a "help" menus describing its main fonctions, the instructions are also here. jplay is in development, and your feedback will be very usefull,

Source code

The source code (C++) of version 1.0 is available to the academic community under a material transfer agreement , please inquire by Email.

Thanks!