Bioinformatics Zen


// Wed December 24 2008

LaTeX (pronounced lay-tek) is a document creation system aimed at scientific and technical documents. LaTeX documents are written in plain text using markup to describe which parts should be sections tables or pictures. The LaTeX system parses the markup and formats the text to produce either dvi, postscript or pdf output. As LaTeX is entirely text based, the content can be tracked using a version control system. Plain text files mean that you can work on a document with your favourite editor, and can also be manipulated at the command line using Unix tools. The syntax of LaTeX markup will take an hour or two of practice to learn, but the advantage of creating documents from a marked up source is that the results are consistent and reproducible, which isn't always the case for graphical document editors.


The main reason for using LaTeX is that it allows you to work on the content of the document, not the formatting. If you were using a graphical editor you format the text as type, but with LaTeX you only have to add the markup to the document and LaTeX takes care of the rest. This can save a lot of time with large documents. The basic features of LaTeX include automatic generation of tables of contents, tables of figures and automatic numbering of sections tables and figures. BibTeX is the companion to LaTeX which adds simple organisation and addition of citations. Citations are added to documents using a simple "cite" command in the text, without the requirement for third party software. One of the benefits of creating documents using LaTeX is that the produced formatting is the result of best practices in typography and document presentation, which means LaTeX documents look better than the average.

Templates and Plugins

LaTeX is free software and available for most operating systems. There is a large LaTeX community which develops themes and modules that can be added to LaTeX documents. Many journals also provide LaTeX templates in which papers can be submitted. There are templates available for writing a thesis or dissertation, and there is likely a specific templates which follows your own institution guidelines. There are many useful third party plugins for adding extras to a document. For example beautiful formating of tables, grouping figures into subfigures, replacing text inside figures and even a framework for including R-code inside a LaTeX document.

Creating a LaTeX document

In this video I'm illustrating how to create a simple LaTeX document with text and headings. An overview of LaTeX document structure is outlined by Andrew Roberts


Creating figures in LaTeX

This screencast illustrates how to add a figure to a LaTeX document. The figure size is changed and a list of figures is added to the document. Andrew Roberts LaTeX site shows different examples of LaTeX figure settings.


Creating tables in LaTeX

This screencast illustrates adding a simple table to a LaTeX document. The table is then formatted to look more "professional" using the booktabs package. More information on tables in LaTeX can be found at Andrew Robert's website and on the Wikibooks website


Adding references in LaTeX

This screencast shows how to add dynamic references to the text in a document. This includes automatically adding references to tables and figures. The second half of the video illustrates how to add a bibliography to a LaTeX document, and how to cite articles in the text. More information about citations can be found on Andrew Robert's website.