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LaTeX is a powerful document typesetting system that I recommend for any large technical or academic work. LaTeX does have a significant learning curve, and works in a very different way to the modern WYSIWYG word processor, but the investment in learning this excellent system will pay dividends again and again. There are numerous front-ends that make learning the system even easier.

I store my entire research bibliography in bibtex format, a text-based open format, readable by many different bibliography management programs. I currently use Jabref, but there are many others.

A decent reference manager is essential when creating academic works. I would hesitate to do manual reference management for even the smallest projects. The benefits are:

• All references can be stored in one place
• References can be automatically downloaded from literature databases (e.g., Pubmed) minimising transcription errors.
• Many packages allow one to store other information and files along with a reference, such as the full-text PDF or a link to the full-text article.
• Dynamic reformatting of bibliography citation styles (e.g., switch to Harvard style), and bibliography style (depending on journal requirements – e.g., maximum three authors, year, journal name, volume, page numbers). Do not underestimate the workload involved in doing this manually!

LaTeX, BibTeX, Natbib and custom bibliography styles

I have 664 article references held in my central research bibliography database and use Jabref to manage them. I have manually typed in only three or four, as it is usually possible to download citations straight from Pubmed. I reference these articles from a number of different LaTeX documents including my thesis and several ancilliary papers being prepared for publication. I use the natbib package to provide more sophisticated control over citation formatting.

To understand how different this is to using Microsoft Word, I should show an example of simple LaTeX formatting along with a citation:


A useless fact\cite{Smith:2007}.


The \cite{} construct tells LaTeX to insert a citation. Depending on the citation style in use at the time, it may insert [1], (1), /1/, ¹, (Smith et al. 1975). Citation styles include numeric, author-year and authors, with a choice of bracket types.

You can do more complex things if you choose the right options:

Some other useless facts\cite{Smith:2007, Bob:1967, Evans:2004, Griffiths:1945}.


can create a citation such as [1, 3-5].

If you choose to not use natbib, then there are many more built-in bibliographic style files, and you may find one “off the shelf”. Some more technically inclined journals may even provide style files, although I haven’t see this in the medical literature!

My preference is to use natbib and a custom bibliography style file. In this way, I get fine control over both citation and bibliography style formats, and both can be changed very easily, with minimal or no changes to my LaTeX document.

Generating custom bibliography styles
To generate custom bibliography styles compatible with natbib, also read makebst package documentation. This allows one to create arbitrary bibliography styles, and should support any style requested by the most demanding of medical journals! They are many built-in bibliography styles with LaTeX, but medical journals tend to have different requirements, and I normally end up creating a style file to suit the journal. I suspect this isn’t the case in the computing or scientific communities, but medical and the life-sciences uses different defaults and different standards to most of the included style files.

For this run-through, I’m going to create a style file that uses numeric citations, in order of citation( not alphabetical order), with a list of authors (surname then initials), then the article title (in italics), then journal name, the year, then volume number, optionally the issue number in brackets, and finally the page number.

1. Getting started
   1. Run makebst.makebst is a tex program that generates style files. To run it, use
      
latex /opt/local/share/texmf-dist/tex/latex/custom-bib/makebst.tex

      You will need to use the correct path to the file itself, which will depend on your operating system and TeX installation.
   2. Type ‘Y’ to get more information
   3. Accept the default master file (merlin.mbs)
   4. Output file – name it something memorable – I type wibble.bst
   5. Type a comment – I type An example style file
   6. Say Y to verbose comments
   7. Name of language definition file – agree with default
   8. Include files for journal names? – no
   9. Internal language support – agree with default
2. Choosing style
   1. Choose numeric mode
   2. Choose normal LaTeX output
   3. Language field? no
   4. Annotations? no
   5. Ordering of references? Citation order – option c
   6. Order on “von” part? Sort on von part – although N/A for us
   7. Author names? Surname plus pure initials (option x)
   8. Editor names? Reversed as in authors’ – option r
   9. Position of “Junior” – comes last
   10. Author name punctuation – separate by commas
   11. Adjacent references with repeated names – always present
   12. Number of authors – all authors
   13. Typeface for authors – normal font
   14. Date position – date part of journal spec – option j
   15. Date format – plain month and year – default option
   16. Suppress month – yes – option x
   17. Date punctuation – semi-colon – option s
   18. Blank after date – no space – option x
   19. Date font – normal format
   20. Title font – italic
   21. Title capitalisation – title style (I ensure all bibtex entries are correctly capitalised manually by using {})
   22. Article title present – Yes
   23. Journal names – dotless names – option x
   24. Journal name font – plain
   25. Thesis title – like books
   26. Tech report – like article
   27. Tech report num – plain
   28. Journal volume font – plain
   29. Journal volume – vol(num) – default
   30. Volume punctuation – volume with colon – default
   31. Year in journal specification – as given by date specification
   32. Page numbers – start and stop numbers
   33. Large page numbers – no separators
   34. Word “page” in articles – no – numbers only – default
   35. Position of pages – default
   36. Word volume – number only -default
   37. Allow number without series – default
   38. Position of number and series – default
   39. Volume and series for books – option s
   40. Position of volume and series – default
   41. Journal name punctuation – space – option x
   42. Book title italic? Yes
   43. Pages in books plain – default
   44. Total pages printed – no
   45. Publisher,Address – default
   46. Publisher in paratheses – default no
   47. Publisher position – default
   48. ISBN – no
   49. ISSN – no
   50. DOI – no
   51. Editor after names – default
   52. Editor in collections – default
   53. Punctuation between blocks – default
   54. Punctuation after authors – default
   55. Punctuation after “in” – default
   56. “In” with journal names – default – no
   57. Final punctuation – period at end
   58. Abbreviate “pages” – omit – option x
   59. Abbreviate “editors” – yes – option a
   60. Other abbreviations – yes
   61. Abbreviation for edition – a
   62. Months with dots – option x (although not applicable as hidden)
   63. Editions as in database – default
   64. Stored journal names – default (not applicable)
   65. Ampersand – use word and – default
   66. Comma before “and” – no comma
   67. No “and” in reference list – No – option x
   68. Font of “et al” – plain
   69. RevTeX data fields – none (default)
   70. E-print data field – none (default)
   71. URL – none
   72. Reference component – none
   73. Emphasis – default
   74. Compatibility with plain TeX – default

After all that (most of the options we set to their default), we get:


Finished!!
Batch job written to file `acnr.dbj'
Shall I now run this batch job? (NO)


Choose YES, and your STY file is created!

You will notice that many of the options are actually not applicable. For example, you can choose not to have “AND” placed into the author list if there are only two authors, but it still asks you about using an ampersand or plain text. In these situations, it is normally possible to just select the default.

Copy it into your TeX distribution tree. I should be installing this into “texmf-local”, but for historic reasons, I keep all my custom style files within the texmf-dist directory. You need to run texhash to update TeX’s directory cache so BibTeX can find your new file.


sudo mkdir /opt/local/share/texmf-dist/bibtex/bst/mybst
sudo cp wibble.bst /opt/local/share/texmf-dist/bibtex/bst/mybst/
sudo texhash


And finally change the bibliography style setting in your LaTeX document:


\bibliographystyle{wibble}


Further reading: Wikibooks’ LaTeX bibliography management, Making style files with custom bib.