Cytoscape WikiThe Cytoscape user manual exists as a Microsoft Word file in:
cytoscape\user_docs
To modify the manual, edit the document in Microsoft Word and check it back in to CVS. Someone (maybe it will be you!) will create a PDF from this Word document near release time for distribution.
We are considering moving to a more cross-platform and manageable solution to user documentation. One option is [http://docbook.org DocBook], however, as of late 2005 it appears that GUI DocBook editors, a requirement for us, are somewhat limited. If you are aware of other options, let us know.
Another possibility is to use HTML (for this one, there is a high number of editors) and use [http://htmldoc.org/ htmldoc] to convert to PDF. This has the advantage of letting users to consult the manual direct from the Cytoscape website.