I still remember in the 1980’s how impressed we physicists were when we discovered Tex. The program was written by Donald Knuth. The macro package Tex is so good and complete that all new developments are mere front ends and user interfaces to Tex, of which Latex and AmsTex packages are the most popular. Newer distributions deal with newer hardware, new fonts and better font management, and pdf creation, but the fundament is still Tex.

Those scientists, like chemists and biologists, that use an occasional mathematical formula can do without Tex. All kinds of handy add-ins allow incorporating math formula’s in standard office documents. However, if your paper has many math formula’s the Tex-way is the only solution. In the rest I will limit myself to LaTex.

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Every scientist has to cope with the problem of managing references (or citations, or notes, or literature, or whatever you call it.)  When writing his second paper he discovers that he has to type a number of references that he already typed in when preparing his first paper. This repetitive action calls for a repository of references. In an ideal world many group members submit their references to this repository and after some time a very efficient storage medium has been created.

Pitfalls
Alas. The real world is never like this. And for many reasons. Typos in entries will live for ever, or will give rise to duplicate entries. Incomplete entries will downgrade the usefulness of the database. Inconsistent use of case (uppercase, lowercase, title case) is causing a mess. Different spelling of names will lead to duplicate entries, or to angry readers when they see their name misspelled in a list of references in an article in a high-impact journal. Many programs (or ‘wizards’) that import references cannot deal with extended characters (leave alone Unicode).  Names with diacritics (like umlauts) are dealt with either inconsistently or wrongly.  Partitioning of names into initials, first names and last names is full of traps and many import filters fall in those traps. In this respect the following error in the book Latex by Leslies Lamport (an excellent book and excellent macro package, of course) is typical: on page 141 (Chapter on “The Bibliography Database”) Lamport discusses “von Beethoven, Ludwig”. The name of course is Ludwig van Beethoven, as the name is of Flemish origin. And indeed “Van” is not his middle name.

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