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Papers written for conferences and journals are today mainly available as PDFs. There are several usability issues with the PDF format, one of which is that it is not especially well suited for the modern way of reading on screens. Unlike e-book formats such as epub or mobi, it doesn't adapt to a for the user desired text size, and is especially broken for e-ink readers that cannot rely on zooming and swiftly moving around as you scan for referenced figures and tables.

Thus, I would like to contribute to the death of the PDF to the best of my ability. All my scientific writing is already done in either Markdown or LaTeX which can then be exported using Pandoc to several different formats, but this only works as long as you don't try to use anything beyond the most basic of features in LaTeX. I guess I could in this manner upload all of my papers to a blog for general consumption, but I'm not sure this is the most appropriate way. One problem is that I won't actually use a lot of the power the web brings, e.g. direct links to cited sources, without requiring extra effort in the conversion step.

I am sure I'm not the first one thinking about this. Are there already people doing this, and if so how? Is there an ongoing discussion about the future of academic publishing in the age of the modern web?

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    @GEdgar No reference, other than personal experience and years of using Google Scholar. If you think otherwise I'm happy to edit my question. – Jimmy C Jul 5 '15 at 18:30
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    @GEdgar Sure, books are generally different. I was mainly thinking of (conference and journal) papers. Will update the question. – Jimmy C Jul 5 '15 at 18:38
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    @GEdgar: if you look at e-books on Amazon, indeed the only format you'll find is the Kindle one. But if you look at the publisher websites you frequently find the PDF format too (and not the Kindle one). – Massimo Ortolano Jul 5 '15 at 18:50
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    Getting decent mathematics in HTML and EPUB is still a challenge. Before Mathjax took over a few years ago, basically the only option was embedding images. Now things look a bit better for the web; however, for E-books, as far as I know there are no good options. MathML never took off and has limited support. – Federico Poloni Jul 5 '15 at 21:50
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    @GEdgar: On this site, I think it's reasonable to interpret "publishing" as "academic publishing". – Nate Eldredge Jul 6 '15 at 3:45
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For journals, at least, many now publish online in HTML. This includes many large cross-field publications including well-known venues such as Nature and PLOS ONE, to name only a few of many. Your paper will generally be available in PDF as well, but the default that the journal steers people to is generally HTML.

An action you might then take would be to choose to submit only to journals with HTML publication of this sort.

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    I wonder how many people read the HTML version... If I just want to skim the paper, the HTML version is ok, but if I want to read it I really do prefer the PDF version. – Massimo Ortolano Jul 6 '15 at 7:09
  • @MassimoOrtolano Me too --- but I think OP may not like our attitude. – jakebeal Jul 6 '15 at 18:20
  • @jakebeal No I agree, I rarely read the HTML versions when they are available. Mainly because the layout usually is horrible for reading, and often feels more like an after-thought (which it is, the conversion tools are often below-standard). – Jimmy C Jul 6 '15 at 19:34
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    @JimmyC What exactly do you expect? There are people whose sole jobs are arranging and formatting scientific papers to look nice with one specific layout (usually PDF). If you want the user to have more format-free content, then you won't get typesetters' expertise, and your document won't naturally look good. In the end someone -- either a typesetter or the end user -- has to put in effort to make a good document. – user4512 Jul 6 '15 at 21:36
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    @ChrisWhite I wouldn't expect much today, but we really ought to start typesetting for screen first, not for paper first. PDF is not the answer for this. – Jimmy C Jul 7 '15 at 9:54
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Rob Beezer has been working on MathBook XML, which is an XML application specifically for making online scientific documents. The XML has various features you can't do in pdfs, like in-line interactive computations and "knowls." Rob's Linear Algebra book gives an example in action, and you can find others listed on the MathBook XML page. He has slides from a talk about MathBook XML that give you an overview of what it's about. One of the goals is to be able to easily convert to other formats such as latex and epub, which sounds just like what you want. I haven't personally used it, so I don't know what stage the conversions are at now or how various features are implemented, but according to the slides (from last fall), the are conversions to html, latex and Sage notebooks are still being improved, and the epub conversion is still to do.

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