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.
It would be nice to have a more cross-platform and manageable solution to user documentation. Mike Smoot suggested DocBook, though as of late 2005, it appears not to have a GUI editor, which is definitely a requirement for us. If you are aware of other options, let us know.
Two options for DocBook editing with GUI editor:
OpenOffice can work with DocBook: http://wiki.docbook.org/topic/OpenOffice and
XMLEditor is specific for XML: http://www.happy-monkey.net/docbook/gui-editor.html and http://www.xmlmind.com/xmleditor/
I haven't tested OpenOffice with DocBook (because I never worked with DocBook 
) and just found XMLEditor using Google, so I haven't tested it either.