PSICS - the Parallel Stochastic Ion Channel Simulator
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Under development
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A wide variety of external tools are available that can be used to define the inputs and process the output of PSICS. This section lists tools that can be useful in this context but is by no means an exhaustive list.

Model specifications - creating XML files

Emacs + XML Lite

Emacs provides a number of ways for editing XML files, of which xml-lite mode is a good choice for the small files needed by PSICS. It handles tag matching and indentation without the complexity of requireing a schema or DTD.

Smultron (Mac OSX)

Availabel free from, "Smultron is a free text editor for Mac OS X Leopard 10.5 which is both easy to use and powerful. It is designed to not confuse newcomers nor disappoint advanced users.".


There are numerous XML editing plugins for Eclipse, an interactive development environment designed for software developers but that can be used writing many other types of content, including PSICS models. The default XML editor provides syntax checking and formatting.

Simple visualization

The two programs dview.jar and ccviz.jar are linked from the downloads page and provide a quick way to view the outputs of PSICS. They can be useful for checking the results before using more sophisticated tools.


Model specification files can include optional "ViewConfig" blocks that are used by PSICS to generate plots for the default summary pages. These can also be loaded in a stand-alone viewer, DView, which is part of Catacomb. The viewer supports panning and zooming to examine details of the results. Like PSICS it is an executable jar file. It be run with
java -jar dview.jar viewfile.xml


Another stand-alone Catacomb component, CCViz can read and display the discretized cell structure that is generated whenever a PSICS model is run.

Analysis and visualization

TBD - info about reading output in IGOR Pro, Matlab, Yorick etc.

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