LaTeX

Why use LaTeX?

 * On average LaTeX generated documents have a better layout than those made with word processors like Microsoft Word (e.g. ligatures, variable space, orphan lines, figure placement,..). See this typography comparison for details.


 * LaTeX's automatic typesetting routines save you time especially in the last stages of document preparation (cross-references, citations, figure and text placement). For example, there is a clever little routine that thinks about the best possible placement for all your figures in relation to the text.


 * It makes reuse of figures, tables and equations across papers, presentations and posters very easy. For some, this is the main motivation of using LaTeX.  .eps files scale well so you can just include the same figure in papers and posters and you don't have to (usually) worry about bizarre scaling effects.  Equations are even nicer.


 * LaTeX is free. Apart from saving you money this has the obvious advantage that you will not be locked into using a type of software. LaTeX offers many import and export features to interface with other pieces of software.


 * An addition to LaTeX called BibTeX makes referencing very easy. Again, BibTeX is free unlike Endnote which is a common software package for use with Microsoft Office. The BibTeX database software for OS X, BibDesk, is superior to Endnote in many ways. Also, there's an online tool for creating a BibTeX entry from a PubMed search query.


 * There's lots of free online information and help about how to do stuff in LaTeX.

See also Word vs. LaTeX for a comparison of the two typesetting programmes in life science.

Why not use LaTeX?

 * There is a learning curve associated with the language. For just the essential features this is around several hours. For in-depth knowledge and making your own document templates rather than using one of the many free, ready-made ones this could be days. This means if you are trying LaTeX for the first time, plan some extra time at the beginning. (Whether this really slows you down overall is debatable, since Word requires a lot of time from your side to prepare the layout, move figures, place references,..)


 * Most LaTeX editor do not show you immediately how the layout will be (it is not WYSIWYG - what you see is what you get). It splits the process into two: 1) content, 2) layout. This can even be advantageous at times to keep you from twiddling with the layout rather than write the text.
 * Lyx is a WYSIWYG-like editor for LaTeX. It offers you a basic typeset view before the compilation of the content file to the final typeset PDF.
 * preview-latex and AUCTeX for Emacs is excellent for looking at your figures inside Emacs (pretty much WYSIWYG).


 * LaTeX is not (yet?) widespread among life scientist and administration. Often in writing scientific literature, whether an internal report or thesis proposal to publishing a paper, you will be working with people that don't use LaTex. This is a main disadvantage when collaborative editing is required.

LaTeX on OpenWetWare
A formal disadvantage was that collaboration and editing tools among multiple users was lacking. But now there are tools on OWW to connect wiki technology with LaTeX. Both WikiTex and LatexDoc are installed on OWW. WikiTex allows embedding parts of TeX formatting like diagrams and things into wiki pages. LatexDoc allows collaborating on entire LaTeX documents on the wiki.

more documentation needed here

Some LaTeX related files:
 * Bibtex: collection of bibtex style files

Martin Jambon is working on an extension to convert bibtex entries into a format compatible with the biblio extension. You can try it here.

Austin Che wrote an extension to allow collaborative writing of latex docs on OpenWetWare.

Bill Flanagan wrote an extension to allow editing of mathematical formulas as part of documents within the text editor editor.

LaTeX software
TeXShop is a nice frontend for using LaTeX on MacOSX. Read through the site carefully for instructions on how to install both TeXShop and TeXLive-teTeX (the backend).

BibDesk is a nice frontend for managing your library of references (ie your BibTeX library). It even autofiles your library of PDFs which makes maintaining and searching your collection of papers much easier than before.

Beamer is a LaTeX class that allows you to create a beamer presentation. It can also be used to create slides. It behaves similarly to other packages like Prosper, but has the advantage that it works together directly with pdflatex, but also with dvips.