Researchr

• BibDesk
• Skim
• DokuWiki
• Kindle

• Ruby
• Keyboard Maestro
• Appscript
• Chrome
• Pashua
• Calibre
• Bibtex-ruby and Citeproc-ruby

• Looking up Google Scholar directly from BibDesk
• Importing citations from Firefox/Zotero with Zot2bib plugin
• Using Keyboard Maestro macro to search Google Scholar and grab metadata

• Script to automatically import and autolink the last downloaded file
• Script to search Google Scholar from within BibDesk and automatically download

• BibDesk
  • can export ref page to DokuWiki
• Ruby batch script that generates
  • json database for php scripts
  • Wikipage of full bibliography
  • individual authors' bibliographies

• Skim (opens directly from BibDesk)
• Kindle
  • export to Kindle, through USB or e-mail, with metadata

• Automatically export all clippings from Skim to wiki
• Automatically import notes from Kindle upon mount

• auto-generated pages
  • ref: namespace holds bibliography (generated upon import of clippings, or from BibDesk), as well as bibtex (hidden) and buttons to open PDF, open citation, or show sidewiki, uses plugin to “include”:
    • clip: clippings from Skim
    • skimg: images from Skim
    • kindle: clippings from Kindle
• notes: hold key ideas

• Automatically open a given reference from BibDesk, or Skim
• Sidewiki opens notes: and clip: in adjoining windows for easy editing of key notes based on clippings
• dokuwiki-sbs opens any page adjacent to the current page
• dokuwiki-clip takes selected text, and inserts it at the bottom of the selected wiki page, with reference to where it came from

Citekeys are the central organizing principle of the system. They are automatically generated by Skim using the pattern “first author's last name” + year + “first word of more than three letters in the title”. However, I manually edit it

• to remove punctation from citekey, especially trailing :
• to make last name complete, turning a citekey for De Jong from de2003knowledge to dejong2003knowledge

BibDesk is the canonical repository of citekeys. Ideally citekeys are changed before files are imported (otherwise, take care to move file to corresponding filename). BibDesk moves all files to Documents/Bibdesk, with the filename citekey.pdf. A custom plugin automatically renders citekey in both Dokuwiki and Wordpress as a correct citation (using a database pre-processed by bibtex.rb). All relevant DokuWiki pages are also named namespace:citekey. The citekey is inserted into the title of Kindle books to be able to import these correctly. Citekeys are also used in the writing of academic papers, which can be automatically converted to the desired citation style (usually APA), and at the same time, autolink to relevant webpages, etc.