PSICS - the Parallel Stochastic Ion Channel Simulator
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Under development
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The current development version is psics-1.1.1.jar   (18-May-2011) .

The channel user interface is icing-0.8.1.jar (see below for 3D visualization).

These are executable jar (Java ARchive) files containing everything that is needed to run the programs on a system that has a suitable version of Java installed. Mac OSX comes with Java included so nothing more should be required for PSICS itself. For Windows and Linux you need to "get java" first from if it is not already installed. For further details, see the User guide.

The same jar files apply for Linux(x86), MacOSX and Windows XP/Vista. The PSICS jar file contains compiled executables for the computational core on each of these platforms.

3D images in ICING

ICING supports two ways of visualizing cells: a basic projection view that uses only standard java features, and a 3D view using Java 3D version 1.5 which will need to be installed separately.

Java 3D is available from with installation instructions in the README file at the top of that page.

For Mac OSX, better instructions are available from Martin Morissette at Sun. Note that Macs come with Java3D included but only version 1.3. This supports some, but not all, of the features icing needs, so it is still necesary to install the latest version even if it appears to work at first.

Running Icing

Although you can start Icing by double-clicking on the jar file, this is not much use for the 3D visualization. By default, it starts with restricted access to memory (64MB for Mac OSX) which is too little for any but the simplest cells. Instead, it should be started from the command line with something like
java -Xmx512M -jar icing-0.7.0.jar

The "-Xmx" part tells the java virtual machine how much memory it is allowed to use (in this case 512MB).

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