Gene-O-Matic

 Downloads

• Gene-O-Matic.zip   9.2 MB   (All platforms, Java™ 1.4.2 or greater required)
• Mac OS X specific version available soon...

• eizelle-7e.xnet   28 KB   Caenorhabditis elegans blastomere fate specification (data from Platzer and Meinzer, 2004)
• wus-clv3.xnet   24 KB   Arabidobsis thaliana flower development (example for a network without predefined cell positions, data from Platzer, 2003)

 Installation

• Download and install the Java3D extensions (Windows/Linux, Mac OS X). You don't need this if you don't use the 3-dimensional view during the simulation.
  For Windows: You should use the DirectX version as it may be more stable than the OpenGL version.
  For Linux: You may need to install the Mesa OpenGl library, as "real" OpenGl may not work with the Java3D.
• Unpack the Gene-O-Matic.zip file. A directory Gene-O-Matic/ will be created.

 Usage

• Change to the Gene-O-Matic/ directory.
• For Linux and Mac OS X: use the command chmod +x Gene-O-Matic.sh to make the shell script executable if it isn't already.
• Run the Gene-O-Matic.sh (Linux or Mac OS X) or Gene-O-Matic.bat (Windows) script from a command line to start the program (if the java executable is not in the path, you need to modify the script so that the java command is found).

Further information on the usage of Gene-O-Matic is available via the help menu or the "?" buttons in the program.

This version of Gene-O-Matic is delivered without a "database network". You may add your own database by drawing a network with Gene-O-Matic and storing it in the data/worm/ directory under the name genes.xnet.