Bibliography tools

Reference management is usually underrated but doing it properly is a massive timesaver in the long run plus it helps to establish a solid knowledge base when writing technical or scientific reports.

Most of my technical writing happens in LaTeX, with work-related writing in M$ Word/PPT, however, luckily Shell has a LaTeX-template for technical report writing (which I am maintaining together with a colleague).

BibDesk has been around for about 20 years as Mac-only application and I have been using it since it first appeared as my main reference management tool. It is a very robust program that plays well with Skim.

JabRef is a Java-based reference manager for all major OSs. It's main database format is BibTeX/BibLaTeX and hence it is geared primarily to a LaTeX-audience, although there are plug-ins for OpenOffice/Word. It is probably the only FOSS tool which lets you collaborate with others by using a shared database that uses MySQL/PostgreSQL.

Recently, JabRef's development has picked up pace and it also gained a few tricks to increase interoperability with BibDesk, understanding macOS's based-64 encoded file aliases in the form of the ``bdsk-url`` and ``bdsk-file``.

Zotero is a really nice GUI-based reference manager which I mostly use on Windows. Key plugins I am using are ZotFile and BetterBibTeX. These allow individual library export when collaborating with others in projects. With Zotero7, the filing has been integrated better in Zotero. In Preferences → General → Customize Filename Format, the renaming options can be set. Zotero's renaming patterns offers flexibility to adopt the renaming patters to personal preferences. As I am using BibDesk and JabRef as my default reference database managers, I am using the same renaming patterns there and in Zotero.

Zotero also lets you share bibliographies on the web with groups, requiring an account on the platform though.

Plug ins:

• ZotFile - no longer actively maintained and required for Zotero >= v7. Attanger and Zotmoov are replacement options.
• BetterBibTeX for maintaining compatibility with BibTeX/BibLaTeX.

Speeding up Zotero (found on the Zotero forum:

• Quit Zotero
• Open the Zotero database SQLite file using DB Browser for SQLite and chose Compact database. Maybe advisable to make a backup of the original file first, if you don't have that yet.
• Open Zotero again

Zotero & BibLaTeX – my previous setup was such that automagically generated BibTeX cite keys contained characters which failed compilation with biber. An easy workaround for this is in the Better BibTeX plugin for Zotero is to set the citation key generator pattern to [Auth:clean].[year]. I use Author.YYYY[a-z] as cite keys.

Sometimes it is convenient to use the command line to download a citation in BibTeX format, copy it to the clipboard and generate an entry in BibDesk.

curl -LH "Accept: text/bibliography; style=bibtex" https://doi.org/10.1038/nature13435 | pbcopy

This uses the https://doi2bib.org website, fetches the citation in BibTeX format and pipes it to the MacOS clipboard (pbcopy) - adapted from StackOverflow