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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. 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.
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Two options for DocBook editing with GUI editor:

 * XMLEditor is specific for XML:
  * http://www.happy-monkey.net/docbook/gui-editor.html
  * http://www.xmlmind.com/xmleditor/
 * [http://openoffice.org/ OpenOffice] can work with DocBook:
  * http://wiki.docbook.org/topic/OpenOffice
  * http://xml.openoffice.org/xmerge/docbook/UserGuide.html
  * [http://openoffice.org/ OpenOffice 2.0 (RC1)] has support for saving in docbook format directly:

attachment:ooo-docbook.png

An advantage of using OpenOffice is that it can open the current manual in MS-Word format (see the picture above). As many of Cytoscape developers are Mac users, OpenOffice is also not a problem as it runs on MacOSX too. It is also ported to Linux, FreeBSD, Solaris and Windows, so portability is not too much a problem here :-) . The source code is also available, so it can be ported to other platforms too.

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.
 * ["/Learn about DocBook"]
 * ["/DocBook GUI editor"]

The 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.

How_to_update_the_Cytoscape_manual (last edited 2009-02-12 01:03:38 by localhost)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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