Cytoscape Wiki|
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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. | Cytoscape also uses [http://java.sun.com/products/javahelp/ JavaHelp] to manage help within the Cytoscape application. This is currently a mirror of the PDF manual. To update this content, edit the files in the following directory in CVS. The main content is in HTML format and the indexes are in XML format and are relatively easy to edit. Commercial GUIs are [http://java.sun.com/products/javahelp/industry.html available] for automating this. |
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| Two options for DocBook editing with GUI editor: |
{{{ cytoscape\help }}} |
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* 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: |
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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* ["/Learn about DocBook"] * ["/DocBook GUI editor"] |
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| 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. | 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. |
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| 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. | Yet another possibility is to use the wiki for all content editing and then write scripts that create a PDF and JavaHelp directly from the wiki. We could have an index page to all content and each 'chapter' would have its own wiki page. This would make updating the manual very easy, but we would have to develop scripts to convert the index and chapter pages to PDF and JavaHelp. |
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.
Cytoscape also uses [http://java.sun.com/products/javahelp/ JavaHelp] to manage help within the Cytoscape application. This is currently a mirror of the PDF manual. To update this content, edit the files in the following directory in CVS. The main content is in HTML format and the indexes are in XML format and are relatively easy to edit. Commercial GUIs are [http://java.sun.com/products/javahelp/industry.html available] for automating this.
cytoscape\help
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.
Yet another possibility is to use the wiki for all content editing and then write scripts that create a PDF and JavaHelp directly from the wiki. We could have an index page to all content and each 'chapter' would have its own wiki page. This would make updating the manual very easy, but we would have to develop scripts to convert the index and chapter pages to PDF and JavaHelp.