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Using DokuWiki for PhD notes/citation management
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houshuang #1
Member since Apr 2011 · 11 posts
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Subject: Using DokuWiki for PhD notes/citation management
I am a PhD student in computer-supported collaborative learning at University of Toronto. I am very interested in Open Access to scholarly information, and especially "being an open scholar", meaning not only making the results of your research open, but the entire process. I was inspired by Cormac Lawler, who used a wiki (mediawiki) to keep notes during his PhD research on Wikiversity, including notes of discussions with his supervisor (which sometimes his supervisor would even edit!), etc, and wanted to do something similar.

One of my limitations was that I wanted something that I could edit offline (for use in conferences, on trains, etc), and still be able to easily share with people. That's when I thought of Dokuwiki, which I've used for some projects before. I simply run Dokuwiki locally on my Mac, and rsync once a day to my web server. I have two scripts, one which just rsyncs pages etc, and one which rsyncs the entire installation (for when I update plugins etc), works beautifully.

My wiki is here: http://reganmian.net/wiki

I have installed a ton of plugins, even written my own one, after much experimentation (I will try to release it, but right now it's very ideosyncratic to my setup). I've also written lot's of Ruby scripts that integrate Dokuwiki with Skim and Bibdesk, automatically generating wiki pages based on academic citations and Skim PDF highlights (even automatically important notes from Kindle!)... see for example: http://reganmian.net/wiki/GroupScribbles (try to mouse over citations, and view source), and then try to click on one of the linked citations.

Also, clicking on the page link after each clipping on article pages automatically opens the PDF in Skim on that page (on my system). And Sidewiki uses Javascript to load the raw clippings in one window, and opens editing of the "Key Ideas" in another window tiled (using frames, and print layout)

I will try to release all of my scripts etc, but again, given that they depend on so many programs, it's not going to be a "click here to install" process, you'll probably have to be a bit of a tinkerer to get it to work on your own system.

Anyway, super excited about Dokuwiki and the community around it, with documentation, plugins etc.

Stian
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lupo49 (Moderator) #2
Member since Jul 2009 · 1397 posts · Location: Warstein, Germany
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It's nice to see that DokuWiki fits so nice in your specialized environment. Also thank you for the intention to publish your own plugins. If you need some help while publishing it on dokuwiki.org, feel free to contact me (or one other member of the plugin/templates team).
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houshuang #3
Member since Apr 2011 · 11 posts
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Subject: Plugins
I have finished a screencast of how I use my system, together with lot's of technical documentation and links to the source here: http://reganmian.net/wiki/researchr:start ... I would be happy to publish the plugin, however right now it's extremely simple and all the heavy lifting is done by a Ruby script which batch processes my bibliography and generates a json file, which php then reads in and uses. (Partly because my bibtex file has more than 800 entries, and I think parsing the bibtex each time would take too long, and partly because I am much more comfortable in Ruby than in php :))... Given the specialized nature of the tool, and reliance on Ruby, I"m not sure how useful it would be to publish it here.

(I also have a similar script that renders academic citations on Wordpress blogs, using the same json file).
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lupo49 (Moderator) #4
Member since Jul 2009 · 1397 posts · Location: Warstein, Germany
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Yes, you're right. It's a bit too specialized and it's not a "real" plugin which can be easily installed by the plugin manager. But I think it's worth to mention it on this page http://www.dokuwiki.org/tips. You could create a link there which references to your wiki or create an own page on dokuwiki.org.
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