PSICS - the Parallel Stochastic Ion Channel Simulator
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Getting started

PSICS runs on Linux, MacOSX and Windows. It requires the Java Runtime Environment (JRE), version 1.5 or later.

For those familiar with java/unix: PSICS is distributed as an executable jar file and the model to run should be supplied as an argument. The output goes to a new folder with an index file summarizing the results. With "-st" and no model file it runs an internal test case.


If necessary, install the Java Runtime Environment. This is available free from To check the installed JRE it can be run with the -version argument from a unix shell or command prompt:
java -version
This should produce something like:

java version "1.5.0_10"
Java(TM) 2 Runtime Environment, Standard Edition (build 1.5.0_10-b03)
Java HotSpot(TM) Client VM (build 1.5.0_10-b03, mixed mode, sharing)

Versions beginning "1.5" and "1.6" are fine: PSICS will not work with 1.4 or earlier. If you have multiple versions of the JRE installed it may be necessary to specify the full path to the java executable. Under unix the path being used can be found by typing "which java". Depending where it is installed, the path to other JRE's could be something like /usr/local/jdk1.6.0/bin/java

PSICS itself comes as a single executable jar file with a name like "psics-0.3.0.jar" where the numbers indicate the version. Once you have downloaded the file, no further installation is required, although it can be convenient to move it to a memorable folder such as "psics" or "jars".

Running PSICS

Assuming the jar file is in the current directory, the command
java -jar psics-xxxx.jar
(where "xxx" is replaced by the actual version) should run PSICS. No command line arguments have been specified so it will print out the usage message and exit.

The command:
java -jar psics-xxx.jar -st
should run one of the built-in models. It will create a folder for the results under the current working directory called wcspikes and will will add a file called index.html summarizing the results of the calculation. It will also save the model specification that was used in the wcspikes folder.

If there is a model specification in the current directory with a main file called run1.xml then the command
java -Xmx1g -jar psics-xxx.jar run1.xml
will run that model. The results will go in a new folder called run1.

The flag "Xmx1g" is optional. By default, java restricts its memory usage to a number normally much lower than what is available on the machine. This can be a problem for large models and lead to an out of memory error. This form of the flag tells the Java virtual machine to use up to 1GB of memory. You can also use "m" for MB as in "Xmx512m".

If the jar file is not in the current directory then the full path to the file will be required. Unix users may find it convenient to set up an alias in the .bashrc file (or equivalent). For example, if the 1.5 JRE is installed in /usr/local/jdk5/ and the psics jar file is /usr/local/psics/psics-0.3.0.jar then the line
alias psics="/usr/local/jdk5/bin/java -jar /usr/local/psics/psics-0.3.0.jar"
added to the .bashrc file will enable PSICS to be run by simply typing

On Macs, the default location for Java is under /System/Library so the line for the .bashrc file could be something like:
alias psics="/System/Library/Frameworks/JavaVM.framework/Versions/1.5/Commands/java -jar /Users/xyz/PSICS/psics-0.7.0.jar"

Command line options

A full list of options is available by running PSICS with the -help argument.

When running PSICS on a file the control parameters are set within the file rather than being supplied on the command line so no additional arguments are required.

Command line arguments provide access to some of the peripheral functionality such as running internal tests or constructing text summaries of output data. In particular:
-sttells PSICS to run the internal short test. This can be useful for checking an installation: no other arguments are required. Other similar options are -lt for a longer series of tests and -v for the rallpack validation models.
-irebuilds an index page listing the models that have been run in the current directory. The page can be viewed from a web browser and provides a convenient way to access a set of models and their results.

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