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General-purpose word-processing programs are OK for academic writing. But I feel the experience can be much improved with some specialized software that takes better care of the special needs of academic writers, such as version control, collaboration, reference generation, in-text citation etc.

Is there any such software (either web-based or desktop-based) created specifically for academic writers?

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    I am not sure this question is a good fit for our site. It seems like a poll question where there are going to be lots of answers with each one arguing for a piece of software.
    – StrongBad
    Mar 31, 2015 at 9:47
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    Your question is too broad and vague to be answerable with concrete advice. I recommend reading the question guidelines of Software Recommendations Stack Exchange. You've given a user story — academic writing — but that could be clarified: papers, presentations and books are pretty different things. In terms of requirements, what kind of typesetting do you need? The need for diagrams, equations, multiple scripts, etc. greatly affects what software is suitable.
    – Gilles 'SO- stop being evil'
    Mar 31, 2015 at 10:12
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    P.S. I do NOT encourage migration to SR.SE: your question would be closed as too vague, and academics are better suited to answering this question.
    – Gilles 'SO- stop being evil'
    Mar 31, 2015 at 10:13
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    Why not using Latex in MikTEx (Windows) and Texmaker (linux) and a outside version control gui tool (Tortoise SVN) or RabbitVCS (Linux) integrated into explorer (Windows) or thunar / nautilus (Linux)
    – Alexandros
    Mar 31, 2015 at 10:44
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    @ba_ul LaTeX in the way to go. To have an easy start, try overleaf.com or sharelatex.com. Or authorea.com.
    – Piotr Migdal
    Mar 31, 2015 at 22:06

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First of all, academic writing is all about the mind putting words on paper, you are really looking for tools to help you with the technical side of putting together the material. Looking at your list of examples, I do not see much that is not already implemented in Word (probably being the most common writing tool in academia). A second that contains everything except a solid version control (revision tool) is (La)TeX (which is also free). But, if version control is required you can use GitHub, as I know many LaTeX authors do.

On a more personal side, the difficulty in writing science is not about getting the technical aspects right, it may be tedious and boring but is easily done. What matters is the text and how to be precise and concise and no software will help you there. Version control is sometimes a good tool but really, is it necessary to see everything one has written and deleted? Isn't the present text what really matters and what one has to consider for improvements? It is easy to get bogged down with the wrong details so getting tools to sort those out is never wrong but I do not necessarily see how a special purpose academic writing tool will help much more than with the technicalities than existing tools do.

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    I love the spirit of this answer, but I think you are poking a straw man with respect to version control. The major benefit of a vcs for academics isn't seeing all the old versions, but efficiently merging distributed changes to a single document. My last conference paper was only 6 pages with 3 co-authors and I wasted an entire afternoon merging edits because I had unwisely distributed a Word document simultaneously.
    – Tim
    Mar 31, 2015 at 9:47
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    I would like to add that GitHub is only a Git repository host. You can perfectly use version control using Git without GitHub. The two should not be confused.
    – mimipc
    Mar 31, 2015 at 11:20
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    Advice I've seen for programmers, which I'd imagine applies equally to academics (and other writers), is that version control lets you give yourself "permission" to throw stuff away, rather than leaving it commented out, bracketed, or suchlike. This means that it's not there to distract you when you write new stuff.
    – TRiG
    Mar 31, 2015 at 13:55
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    @TRiG : Exactly. Git allows you to throw everything away, write something else, and revert your changes if you think the first version was better. The key here is that it keeps all the changes you want it to keep. When you work with other people simultaneously, merges are also possible. This is an excellent way to collaborate and keep track of all the work done on a project.
    – mimipc
    Mar 31, 2015 at 14:07
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    Once you delete something, it's almost certainly going to stay deleted. But there's a possibility that you might want it. So you hang onto it. And your code gets cluttered with comments. Git gives you the freedom to actually get rid of the stuff. And you can go back for it if you need to, which is almost never. So it makes the code (and your brain) clearer and cleaner.
    – TRiG
    Mar 31, 2015 at 14:09
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I am personally a big fan of using Scrivener. It was originally designed for writing novels and organising all the research and drafts but also works well for writing research papers. Scrivener can also be set up to export to latex and to work with a backup folder containing .txt files (to enable version control trough ex Github).

I use Mendeley to store my papers and handle references as it is quite a hassle to keep organised.

Here is a link on how to set up scrivener with latex: http://harrisonsweeney.com/posts/scrivener-multimarkdown-and-latex.html

Edit: I should also mention writing in plain Latex.

Latex is a markup language designed for writing printable text (as opposed to web text), all the formatting is done by typing commands. This means that it can be written in any text editor and that there are generally no buttons to click for formatting (such as in word). Latex is used a lot in the exact science as it is a standard in rendering equations. The drawback is that it has a learning curve.

I'd say that Scrivener is the way to go if you are looking for a tool that aids you in organising and structuring your writing process. However if you require extensive rendering of equations and/or prefer the more direct control of latex go for that. Although any text editor would work for latex finding the one which works best for you is an entire question in itself.

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    May I ask: Are you associated with Scrivener?
    – Nobody
    Mar 31, 2015 at 9:57
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    Nope, not at all. I actually routinely switch around between several tools. I actually switched back to writing in plain latex (using the sublime text editor with the excellent latexing pluging) when I wrote my master's thesis and have used evernote to keep my notes as that is what the rest of the lab is using. I just switched back to Scrivener as I don't like organizing my notes in evernote. That being said, the latexing+sublime combo is superior in writing raw latex.
    – Adriaan
    Mar 31, 2015 at 10:44
  • Scrivener is good. I checked it out a few months ago and was impressed by a few features. But I didn't migrate to the program mostly because of its lack of integration with reference management programs. At the end of the day, it's designed for fiction writers, whose needs and workflows are different from academic writers.
    – ba_ul
    Mar 31, 2015 at 16:26
  • Using a good editor for latex that auto completes commands, enables easy insertion of common commands (or more complex macros), outlines of your code, shortcuts to see the compiled document, etc etc definitely improves the experience over a plain text editor. Sure no sane person wants to have to click a button to format text, but a shortcut to avoid writing \texttt{} all the time? Yes thank you.
    – Voo
    Mar 31, 2015 at 20:37
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You have plug-ins and storage methods to take care of this.

Software such as Endnote offers a plug-in to 'cite while you write' (as they call it). Microsoft Word has a referencing system itself, but I have no experience with it.

Using the revision options in Microsoft Word you can track all changes made to the document (giving you more advanced features then normal versioning). However you can also set up your computer to copy changed files to a backup location, storing multiple versions there.

I do not necessarily disagree with your suggestion that general-purpose word processors are not really suited for academics, however the questions that you have can be addressed using general-purpose word processors.

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  • What advanced features does word's versioning offer that you can't just as easily get with git and some diffs? Not discounting that there are some things that I missed, but when I checked word the last time it definitely seemed more primitive.
    – Voo
    Mar 31, 2015 at 20:42
  • I am approaching the problem the other way around OP claims there is no version control in standard Word Processors. Microsoft Word (and maybe others as well) offer Track Changes. This is more advanced then keeping a copy from every saved version (which is what versioning basicly is), as you can easily see what was changed.
    – Maarten van Wesel
    Mar 31, 2015 at 21:07
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    So just a misunderstanding about what "versioning" referred to, ok!
    – Voo
    Mar 31, 2015 at 21:18
  • I'd be worried about long term accessibility with software such as Word and Endnote, especially the latter would be rather expensive for an individual outside of organisational/institutional access.
    – DetlevCM
    Jul 20, 2017 at 13:38
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OP:

Is there any such software (either web-based or desktop-based) created specifically for academic writers?

Yes: Nota Bene is a software package that was purpose-built for "academic writing", and that in the context of the humanities. I used it heavily in the 90s, but needed to move on when development didn't keep pace with my Unicode requirements. It's fascinating software: essentially a suite of tools comprising a writing environment, textual/note database environment, and bibliographic database, all seamlessly integrated. It really is a powerful package.

But the further answer in all likelihood depends on what area the writing is for: "academic writing" is simply too broad. "Humanties", "social sciences", "[hard] sciences" would give a better spread of suggestions. The possibilities also depend on personal work habits: what makes for a congenial writing environment varies according to personal habits and taste.

TeX provides one good example: rare for most in the humanities, but common for mathematics and linguistics.

On the other hand, some of my colleagues are now doing all their writing in Markdown, and that has its own appeal, as well as limitations and challenges.

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  • Yes, this is the kind of software I'm talking about. This one, unfortunately, looks dated.
    – ba_ul
    Apr 1, 2015 at 4:37
  • @ba-ul It looks a little Windows 3.11, doesn't it. If you can get past the cosmetics, it really does what it claims to do. For me, however, it's no longer worth the expense. I know some who use it (top international scholars in their fields - I could name names!), and love it, though.
    – Dɑvïd
    Apr 1, 2015 at 6:39
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I haven't found anything that was perfect yet, but I have found the combination of Circus Ponies Notebook (for content outlines) and Scrivener (for stress free writing) really workable. This posting covers a lot of it.

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    Wow. Excellent article. Also, I'm so glad I found out about your blog and ebook through this.
    – ba_ul
    Apr 1, 2015 at 4:51
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OVERLEAF

Overleaf it is a collaborative web service for writing and publishing academic writings based on LaTeX and is especially design for this purpose. I think nowadays is the most used software for publishing in academics. The website describes its mission very clearly:

Overleaf is a collaborative writing and publishing system that makes the whole process of producing academic papers much quicker for both authors and publishers.

Overleaf is a free service that lets you create, edit and share your scientific ideas easily online using LaTeX, a comprehensive and powerful tool for scientific writing.

Writelatex Limited, the company behind Overleaf, was founded by John Hammersley and John Lees-Miller, two mathematicians who worked together on the pioneering Ultra PRT Project and who were inspired by their own experiences in academia to create a better solution for collaborative scientific writing.

Overleaf is supported by Digital Science. Digital Science is a technology company serving the needs of scientific research. Their mission is to provide software that makes research simpler, so there’s more time for discovery.

From Tex to Overleaf: a not so short history

I think is important to have a look at the history of the technologies that are used by overleaf to see that they are designed by academics and used by academics. The history is basically an encapsulation of powerful complex technologies in a more user-friendly platform.

TeX is the core technology it was designed by Donald Knuth who was a professor at Stanford University this is an excerpt from this site:

As it turned out, TeX was still a lot closer to a research project than to an industrial strength product, but there were certain attractive features:

it was intended to be used directly by authors (and their secretaries) who are the ones who really know what they are writing about; it came from an academic source, and was intended to be available for no monetary fee

LaTeX was set of macro to make TeX more accessible it was actually created at SRI International (SRI) an American nonprofit research institute by Leslie Lamport here an excerpt form an interview:

When Don was creating TEX80(?), the second version of TEX, the popular macro package at the time was one written by Max Diaz I've forgotten its name. I was in the process of starting to write a book, and I found Diaz's macros inadequate. So, I needed to write a set of macros for the book. I gured that, with a little extra eort, I could make a macro package that could be used by other people as well. That was the origin of LATEX.

Then it comes Overleaf so all these technologies are now on a server with ready-to-use templates from the most popular publishing companies and conferences.

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In terms of the mess you can get into with multiple versions, multiple authors, that @Tim mentioned -- I like Draftable for Word.

I like to have a shared dropbox folder with collaborators so we all have access to all the previous versions.

A feature of Word that I like is the outline view. It makes it easier to do restructuring on a large scale.

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