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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Office document or (La)Tex
Creating a pdf file
Additional requirements
Bookmark generation with MS Word
Save to PDF
Show your tree
Skip numbered entries
Different numbering of the same level
Thinning your pdf file
Fast web view
Bookmarks with Latex
Example pdf files
Recap

Adobe has blessed the digital world with a document format that is really platform independent. I am referring to the pdf (“portable document format“). As a result the leading format for scientific articles is the pdf file. Scientific journal editors require from prospective authors that they submit their manuscript as a pdf document. More and more grant organizations also request proposals to be sent in as a pdf file.


Office document or (La)Tex
The pdf standard has many advantages. Its major disadvantage is its limited editing possibility. As a result authors have to keep at least two files of a manuscript in sync: the “source” manuscript and the pdf version. Additional graphic material is either embedded in the source or is kept as separate files. The most popular formatter for generating the source is Microsoft’s Word, or a comparable office document formatter. Another source approach is to use a simple ascii file, containing script language directives that are to be interpreted or compiled. Of the latter class the Tex, LaTex, AmsTex family is the most popular. For some fortunate reason the Tex-family has escaped the fate of almost any open-source project: multiple distributions, bad documentation, incompatible versions, and a Windows-hostile developers community.

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Depending on your discipline you write your scientific papers with either MS Word or you prepare them with a more professional text formatter like LaTeX.

Besides scientific papers scientist produce all kinds of other documents. I often notice that those MS-Word prepared documents have an ugly ragged right side, or have a repugnant flood of white space. With a little more effort it is possible to produce text, even with MS Word, with a professional look. Two aspects are important: hyphenation and justification.

Hy-phen-ation
When I look at the documents the Dutch ministeries produce, I must come to the conclusion that hyphenation is either never heard off or it is forbidden. In the Dutch language a complication is that in a sequence of nouns the nouns are combined into one word. So the Dutch language has a number of very long words, like “regeringsvoornemen” or “onafhankelijksverklaringstekst”. Using long words in a text without hyphenation makes the text ugly and unclear.

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I discovered something a few days ago that made me ask the question: Am I mad, or are all web designers out of their minds? The sun was shining in my office and I just could not read the information on the web site of a major multinational company.

In my book I spent tens of pages on how to improve the slides of a presentation. I consider the most important guiding principle whether or not people in the audience can actually read the slides. For a number of reasons the legibility is poor in at least 25% of the scientific presentations I have been going to lately. The two most important causes are: (i) too small font sizes and (ii) bad contrast.

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When you are doing research, you tend to collect a lot of papers. I remember that at the end of m PhD, when I moved to another continent to do a postdoc, I dumped a huge box of photocopies in my parents’ basement. A few years ago, I had collected two cupboards full of photocopies. It was getting seriously out of hand. Then, of course, journals started putting everything online as PDFs and the same process started all over again but this time filling up hard disk folders instead. I used to have subject-based folders, which sort of worked until something fit within 2 or 3 or 4 of my subjects. Searching for some old paper you had read a few years back became more and more nightmarish. Then somebody showed me Papers.

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I used to go to the library. Every couple of weeks or so I would go and check the journals, browse through their tables of content (TOCs), and flip through the pages. You would find odd articles in areas there weren’t quite your own. Slowly over time journals got bigger and were published more frequently. Then they started emailing TOCs out, which seemed like a pretty good improvement as you could just read them on your computer. Gradually, I started to run out of time: the TOCs were just too long and there were too many of them. Virtual journals (such as the Virtual Journal of Ultrafast Science) offered some hope but they don’t cover all journals such as Elsevier journals, so you would still end up having to read a bunch of emailed TOCs.

For a couple of years, I tried an RSS reader. A free reader, such as NetNewsWire for the Mac or FeedDemon for Windows (http://www.newsgator.com/individuals/) can collect RSS feeds containing TOCs from you chosen journal. FeedDemon has to possibility of searching through your feeds. That worked pretty well until I switched to a Mac and found that NetNewsWire couldn’t search through feeds. By the time the TOCs were simply to huge to read them “raw”.

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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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