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This is a rewrite of a question that was perhaps-naively posed. I rephrase...

What file formats are ok/good/ideal/common/long-term-viable/archivable/useful for research papers?

And, also, there's the history-question:

What is the story of viable file-formats in the last 20+ years?

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    File formats for what? Data? Papers? Lab notebooks? This question to me sounds akin to asking, "I need to buy a storage container for my... stuff. Can you recommend me a common, archivable, useful one?" It completely depends on the purpose. – eykanal Jul 24 '12 at 1:17
  • Formats for writing, or for reading? – David Ketcheson Jul 24 '12 at 7:40
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    "This question is ambiguous, vague, incomplete, overly broad, or rhetorical and cannot be reasonably answered in its current form." - voting to close – EnergyNumbers Jul 24 '12 at 16:04
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    I work in a medical research department and its all .pdf – geminiCoder Jul 29 '12 at 16:13
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For mathematics, I think TeX/LaTeX is the way to go. This is the standard way to write papers in nearly all areas of math (perhaps not biomath, where collaborators necessitate Word), so there's little extra cost. One advantage of this approach is that it's easy to automate outputting in almost any format you want. Furthermore, as new formats develop, we will almost certainly develop tools to convert TeX source to these new formats. The arXiv is a great example of this model.

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Many people know what I'll say here, but I thought the re-format of the situation was appropriate...

For mathematics and "hard" sciences, PDF (portable document format) is absolutely standard now. Until a few years ago, PS (postscript) and DVI (device independent) formats were typical, but no more.

In mathematics, "Word" format was never common.

Currently, traditional (meaning various things) mathematics journals want a PDF file to send to referees. Everyone has software that can convert PostScript files to PDF, and so on. In fact, "OpenOffice", for example, can convert/export "Word" files to PDF.

So, in sciences, PDF, though "Word" may be forgivable.

The question of future readability of these or any other file formats is hugely non-trivial. (Similarly, kids-these-days, such as my almost-20 daughter, have great difficulty reading "cursive writing" of "old" people. :)

So: modulo issues that the original questioner can't afford to worry about, the current answer is "PDF, and tolerance for Word files, esp. from the humanities...".

The long-term answer about survivable file-formats... is troubling. :)

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Other things to consider (for the future) is the movement towards standard meta-data items contained with the research articles (e.g. structured abstracts, specific research repositories, meta-analyses), and supplemental material for reproducible analysis. These suggest to me the conversation should likely include more than one data file.

IMO we can be more imaginative than word or pdf files. For instance open access journals frequently have everything right there in html on the page. I even think this idea for a fast journal by Yihui Xie using markdown for revisions and compiling to html is a good idea.

This is forward thinking though. Realistic constraints force collaborations to work with WYSIWYG file formats and PDF for writing because such behavior has not permeated enough in many fields (although for exceptions in some fields that extensively write in Latex see Jeffe's comment below). That may change in the future though, especially if journals adapt submission standards that encourage such actions.

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    Obviously realistic constraints force collaborations to work with WYSIWYG file formats — Unless you're a mathematician, physicist, computer scientist, or somebody else who uses latex. – JeffE Jul 24 '12 at 2:16
  • @JeffE, sure and I didn't really intend that statement to be taken as deterministic about everyone in academia. I have updated to make this clear. That being said though, outside of those few fields which use latex extensively for writing documents that is certainly the exception. Also when you review a paper are you given the tex source? – Andy W Jul 24 '12 at 11:50
  • It's worth mentioning that you can do a lot with pdfs; check out some of the demos at the TeX showcase, including this interactive, randomly generated math quiz, this interactive periodic table, and this animated Lorenz Attractor. – eykanal Jul 24 '12 at 13:16
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    @AndyW: No, typically authors only submit PDFs for review (so referees necessarily only get PDFs). Many journals use the author's TeX source to prepare the camera-ready copy after the paper is accepted, but a few ask the author to do that, too. Also, I don't know anyone in my field who doesn't write LaTeX source directly, without using a wizzywig editor. – JeffE Jul 24 '12 at 13:37
  • @eykanal Thanks for sharing (I had never seen truly interactive in PDF before). Although I suspect the potential for interactivity in html is greater though. For one example, see some Elsevier journals related to spatial analysis now provide the ability to embed google maps in supplementary data. Wouldn't it be nice to have live applications in which you could pan and zoom graphics with tool tips for observations, or dynamic tables with publicly available data? I'm skeptical these things can be done in pdf (or only one file). – Andy W Jul 24 '12 at 13:49

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