Regex to change bracket citations into bibtex keys

Useful for converting in-text citations (from e.g. Word) into a LaTeX document.  Converts bracket notation into first 3 chars of first author’s last name (or 2 chars, if only 2 chars long), plus two-digit year: e.g. (Bobby 2009) becomes \citep{Bob09}.  See also my post on how to insert bibtex references into Word.

Search for:

\(([A-Za-z]{2,3})[A-Za-z -.]* (18|19|20)([0-9a-z]{2,3})\)

Replace with:

\\citep{\1\3}

Test citations:

(Bobby 2009)
(Bobby and Jonny 1909)
(Bobby et al. 1923)

(Maynard Smith 1989)
(Maynard Smith and Haigh 1974)
(Maynard Smith and Bobby-Jonny 1974)
(Maynard Smith and Maynard Smith 1974)
(Maynard Smith et al. 1993)

(Maisnier-Patin 1900)
(Maisnier-Patin and Bobby-Jonny 1956)
(Maisnier-Patin et al. 2002)

(Aa 1932)
(Aaa 1932)

Fluctuation test calculator: FALCOR copy/paste issue

FALCOR (Fluctuation AnaLysis CalculatOR) is a handy Java applet designed to estimate mutation rates from fluctuation test data.  A Java update prevents access to the clipboard to unsigned Java applets.  If you are having trouble copy/pasting your data into FALCOR, try modifying your java.policy file to include the line: permission java.awt.AWTPermission “accessClipboard” under where it says //”standard” properties that can be read by anyone.

// “standard” properties that can be read by anyone
permission java.awt.AWTPermission “accessClipboard”;

Save the file, exit and restart Java (or any programs using it, like Firefox or LibreOffice), and copy/paste should work again.  You may wish to consider removing the clipboard access after using FALCOR for security reasons.

Integrating .docx and BibTeX

I have nearly every paper I’ve ever read stored in a BibTeX database, so I wrote a BASH script to build a list of citations using BibTeX that could be easily copied into LibreOffice Writer.  I would prefer to write all my papers in LaTeX, but there are some disadvantages–poor adoption and inefficient track-changes methods–so I have to use LibreOffice Writer instead.  None of the available bibliography managers that integrate with LibreOffice seem particularly reliable to me, and I plan to convert my manuscripts back to LaTeX anyway when I put my thesis together.

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