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I am a medical student approaching to the research world. Next month I am going to start a collaboration with a researcher that want me to learn how to create an article, to choose a specific journal, to look for materials, … It's been a while since I am (superficially) looking at tex world. In the last few days I downloaded an Elsevier template and tried to compile it, finding it relatively easy.

I now try to be more specific about my question. Do you guys know if medical researchers use tex to write articles? My concerns are related to the fact that there are a lot of different journals (science group, elsevier, nature, cell, …) and at the moment I don't know if you can for example compile the Elsevier template and at the end, when you choose a specified journal, easily switch to the journal's preferred style.

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my first question would be, what tool(s) are used by the researcher with whom you are collaborating? although i would have a strong preference for latex, the ability to share files with your collaborator is the most important consideration in a joint enterprise. continued file conversion can lead to unnoticed errors and other difficulties. –  barbara beeton Apr 27 '13 at 14:52

5 Answers 5

My particular view of utility of LaTeX in this case:

  1. To collaborate with others: In general, NO.

    Beside mathematicians and the like, and specially in biomedical research, unfortunately there are little chances to find LaTeX fans, although I think that it depend strongly of the academic environment (i.e., if your University have official thesis templates for LaTeX, maybe you can get lucky).

  2. To send to biomedical journals: Your mileage may vary.

    In many cases the editor in chief is a senior researcher (thus, apply point 1) with null interest about printing issues (that are left to a cheap printing house, where, well...see again point 1). This explain that guidelines usually ask for Word format or even commercial Pleistocene fossil formats (see mring's answer).

    Fortunately, among the exceptions there are important academic publishing companies as Elsevier or Kluwer with many of the best medical journals.

  3. To focus in the content while writing: YES

  4. To change easily the format: YES

    Both point 3 and 4 no need comments (are well explained in Mico's answer).

  5. To make reproducible research: YES. Invaluable

    As most experimental and observational studies include some statistics results or statistical graphs, the literate programing with R using Sweave or knitr is an advantage at many light years of write in Word translating by hand the results of SPSS or another program. In all honesty, there are also solutions to make reproducible research with R ouput in Word formats (.doc., .rtf or .odt, see Reproducible Research Task in CRAN) but I'm not aware of problems and easiness of this alternatives by respect the LaTeX way (edits about this issue are welcome).

That said, to focus on the contents and easily switch to the journal's preferred style requirements, you can consider some non LaTeX options:

  • Write in Lyx (good to focus in the content) and then export as needed to LaTeX, HTML, ODT.

    (...and yes, strictly LyX this is not a LaTeX option, because LyX is not [only] a LaTeX editor, but a document preparation system that export to LaTeX, DocBook (SGML,XML) and other formats.)

  • Write in plain text (nothing better to focus in the content) and then providing a basic structure (sections, list) and text format (italics in scientific names, etc.) with Markdown or reStructuredText. Any text editor is good for this, but at least for Linux users I suggest ReText (GUI with PDF preview with export options to HTML and ODT formats). The big advantage of lightweight markup languages is that with pandoc your can convert this text to LateX, RTF, Word, and many others formats.

Disclaimer: Format conversion is never cost free. You always "pay a toll" for file conversion according to the type of file formats, the complexity of the source document and the specific guidelines for the final document, but conversion of clean mardown to LateX or Word could be munch less problematic than direct export from .tex to .docx and .doc to .tex (often not a good idea).

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+10 (if I could). This is a really accurate answer. –  Alan Munn Aug 10 at 0:32

Interestingly enough, it seems that according to the Submission Guidelines of the Journal of the American Medical Association, under Manuscript File Formats, it states

For submission and review, acceptable manuscript file formats include Word and WordPerfect. Do not submit your manuscript in PDF format.

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there are a couple of journals which are forcing a bad typography :( –  Micha Apr 26 '13 at 19:30
I agree with you @Micha that this policy of JAMA doesn't seem like a good one. –  mring Apr 26 '13 at 19:33
@Micha I am not quite sure whether you are right here. Journals quite often do the type setting for their authors. Thus, they only want to have the 'content' in a -- for their internal processes -- suiting 'standardised' format. Often they use Adobe products (or similar WYSIWYG DTP software) to set. They just use copy & paste from the submitted doc/rtf files... So in this way the submission process is not directly related to the type setting / typographic process. To sum up, a tex or pdf file would make their live harder, that's why they don't want to have them for submissions. –  phx Aug 9 at 11:54

To be honest, I disagree with most of the answers that generally recommend LaTeX for your purpose. If your main aim is to publish scientific articles in some of the major journals of your field I would definitely have a look in their submission guidelines first. I know many journals in my field (psychology, educational science) that do not accept tex files at all. Nor do they accept PDF. They want to have doc or rtf or sometimes odt. The reason behind this is just their publishing process. Here a copy & paste from my comment above:

Thus, they only want to have the 'content' in a -- for their internal processes -- suiting 'standardised' format. Often they use Adobe products (or similar WYSIWYG DTP software) to set. They just use copy & paste from the submitted doc/rtf files... So in this way the submission process is not directly related to the type setting / typographic process. To sum up, a tex or pdf file would make their live harder, that's why they don't want to have them for submissions.

Another important aspect might be that most journals require you to submit the paper in a standardised (and ugly) formatting style (e.g., APA ...). So you do not need a tool that makes your paper to look nice because it does not have to look nice in the first place. Furthermore, many advantages of TeX (e.g., floating figures etc.) are not needed when the publisher typesets your paper or a certain formatting style is required. The APA style for instances wants you to put all figures at the end of the paper anyway. Nevertheless, I have to admit that TeX might make it easier to stick to the style they require when a certain style package already exists.

Furthermore, I completely agree with Fran concerning the collaboration issue: Unless most of your colleagues use TeX you will always be constrained to use the software they use (most often: standard office suits). In other words, the most often used tool by your colleagues will be the tool you want or have to use. (In my case I often cannot even use LibreOffice/OpenOffice because everybody else is using MS Word. Both are still not completely compatible and will probably never be.)

However, writing a paper takes time. There might be good reasons to use TeX for your own intermediate working papers. Fran wrote about reproducible research etc. As long as you do not have to collaborate on those intermediate versions TeX might be your best friend. However, make sure that you know how to convert your tex or pdf file in the format the journal requires (see e.g., pandoc).

tl;dr: Be clear what kind of formats the journals in your field accept for submissions. So you have to be aware that your type setting / word processing tool might be able to produce this format. If it doesn't it will cost you much time and much nerves at the end.

(Btw: That is also true for figures, many journals only accept png or tiff. However, that seldom should pose any problems since images are easily converted from one format into another. At least usually...)

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Regarding your main question, viz., is it a "good idea" to write scholarly pieces in the medical field using TeX/LaTeX rather than (say...) MS Word, I'd give a full-throated YES as my answer.

The main reason I'd give for saying the answer is YES is the separation of content and formatting of the content which is at the center of the LaTeX approach to typesetting. Say you've written an article and are considering submitting it to several journals for review and (hopefully...) publication. If these journals provide a LaTeX-based set of macros (either as an entire document class or as a style file) and if you've taken care during the writing of the paper not to put too many formatting-related directives in your paper, formatting your paper to the journals' specifications should be a snap.

You are definitely not alone if you're contemplating using LaTeX. Indeed, if you go to the websites of some of the leading journals (and even some of the not-so-leading journals...) in your field, you'll find that most of them provide well-designed LaTeX style files that address all formatting-related issues.

You'll also quickly find that separating content from formatting-related matters frees you up to focus on the content -- and that's where you would want to spend your time, right?

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I don't know about the medical world specifically, but the answer is almost certainly yes: LaTeX is an extremely high-quality system for typesetting anything, but particularly work that includes mathematical notation (as I imagine medical journals do).

Moreover, the ethos of writing in LaTeX is that you type what you mean: your content, and semantic (eg 'this should be emphasised, this is a heading) rather than typographical (eg 'this should be here, this should be written in a heavier type) information. That means that you can focus on writing, and whatever style is imposed (for whatever journal) will affect your whole document consistently.

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