Free software for biologists pt. 1 – writing tools

This is the first in a planned series of five posts, to cover (1) writing tools, (2) data management and analysis, (3) preparing figures, (4) writing presentations and (5) choosing a new operating system. They will eventually be collated here.

Document-writing tools

Microsoft Word remains the default word processing software for the majority of people. Its advantage is exactly that, which makes collaboration relatively straightforward. The track changes function is appreciated by many people, though I would argue it’s unnecessary and can lead to problems; see below for tips on collaborative writing.

If you’re going to be spending a large proportion of your life writing then Word is not the ideal solution, especially for scientists. On this point it’s worth making clear that `scientist’ is just another word for `writer’. We write constantly — papers, grant proposals, lecture notes, articles and books. Professional writers use other commercial software such as Scrivener; this however is just paying for something different. Microsoft Word has improved in recent years, but there are still problems. The main limitations are:

  • It’s terrible at handling large documents (e.g. theses, or anything more than a couple of pages). Do you really need to do all that scrolling?
  • Including equations or mathematical script is difficult and always looks poor quality.
  • Embedded images are reproduced at low resolution.
  • Files are unnecessarily large in size.
  • The .docx format is very unstable. Send it to a collaborator on another computer (even with Windows) and it will appear different, with mangled formatting.
  • The default appearance doesn’t look very professional, and improving it takes forever.
  • It keeps reformatting everything as you go along, particularly when you combine sections from different documents.

I didn’t realise how much time was spent fighting Word’s defaults until I tried other software. Escaping isn’t tricky, as this blog post reveals. Several options are available to the scientific writer, and will improve both the quality and the experience of writing.

LibreOffice Writer. Want something that looks exactly like Microsoft Word, does everything that Word does, but don’t fancy paying for it? Just download LibreOffice and you’ll find it works equally well (if not better). This is perhaps the best option if you have an out-of-date or bootlegged version of Word and can’t access updates. With LibreOffice you will be able to open, edit and share all of your existing Word documents, and even save them in .doc format. The native format is .odt (for open document text). This is recommended as a stable document format by the British Government, which tells you something. Your Word-using colleagues will be able to open them as well.

Markdown. This has grown in popularity with scientists as it’s easier to use than professional tools such as LaTeX (see below) but provides many of the document-formatting tasks that scientists need. You can even write Markdown scripts in Word, but why would you. Combining it with pandoc makes it even more powerful because you can convert a Markdown template into any other format to match the requirements of a journal (or your collaborators). This is much easier to do than with LaTeX, which requires some programming nous. A good, free Markdown editor is Retext.

LaTeX. The gold standard, as used by many professional writers and editors (it’s pronounced lay-tech; the final letter is a chi). All my handouts are prepared in LaTeX, as are my presentations, manuscripts, in fact pretty much everything I write apart from e-mails. The problem is that learning LaTeX takes time. Most word processor programs run on the principle of WYSIWYG (What You See Is What You Get), whereas in LaTeX you need to explicitly state the formatting as you go along.

There are a number of gateway programs which allow you to write in LaTeX but with a more familiar writing environment. These therefore ease the transition and can show you the potential. I know many people who swear by LyX. My preferred editor is Kile, though this will involve a steeper learning curve. A great help while writing in LaTeX is to be able to see what the document looks like as you write. I pair Kile with Okular, but there are many other options that are equally good.

As a health warning, before diving into the deep end, bear in mind that working in LaTeX will initially be much slower. It takes time to become competent, and there are annoying side issues that remain frustrating (installing new fonts, for example, is bizarrely complex). While the majority of journals and publishers accept LaTeX submissions, and most will provide a template to format your manuscripts, there are still a few who require .doc format. This is changing though due to demand on the part of authors.

Collaborative writing

In the old days, when you collaborated on writing a paper, it required dozens of e-mails to be sent round as each author added her comments. Version control became impossible as soon as there were multiple copies and it was easy to lose track. Some people persist in working this way despite the fact that there are loads of tools that make this unnecessary. By using an online collaborative-writing site, multiple authors can contribute simultaneously, and you can even chat to each other while you’re at it.

The best-known is of course Google Docs which has the virtue of a familiar interface. It’s not designed for scientific writing though, and unsurprisingly there are more specific tools out there. While I’ve not used it, Fidus Writer looks like a promising option with a familiar layout to Google Docs but more better suited to the demands of science writing.

The one I’ve used most often is Authorea, which has the major advantage that anyone can write in any style and on any platform. This means that one person can write the technical parts in LaTeX while another adds sections Markdown, or you can cut-and-paste text from a normal word processor. The final document can be exported in your format of choice. This solves the problem of having all your collaborators needing to use the same software. My favoured option (for LaTeX users only) is shareLaTeX, though writeLaTeX looks to be equally good.

I haven’t mentioned GitHub here, even though I know many people who use it to maintain version history in collaborative work. This is particularly true of programmers who need to trace changes in code as it’s being developed. The same functionality can be very helpful in writing manuscripts, but using GitHub is not easy to use and it’s rare in biology that you will find yourself working with a pool of collaborators who know what they’re doing.

As a final note, I discourage the use of tracked changes due to many bad experiences. The main issue is that once more than one person has commented on a document it gets completely mangled, and it can take a long time to reconstruct the flow of the text once all the contradictory changes have been accepted. Furthermore, if your reason for having a WYSIWYG processor is that you want to see how the final document will look, then tracked changes remove that benefit and make your document unreadable. Lastly, whenever I’ve been forced into using them (in one notable occasion by a journal editor) it has invariably introduced errors into the text. By using some of the software recommended here there should be no need for the track changes function at all.

References and citations

The old standard for reference management used to be Endnote, which is an expensive solution if you don’t have either an institutional license or a student discount. Much the same can be said of Papers, which I hear is excellent but have never used.

I strongly recommend Mendeley to all my students. Think of it as iTunes for papers. It’s free and integrates smoothly with all the word processing software above. Even better is the online functionality which means you can synchronise documents across all your devices, including a commenting function, and share with colleagues. So you can read a PDF on the train, make notes on it, then open your office computer and retrieve all the notes straight away before dropping the citation directly into your manuscript. There are many tutorials online and the few hours you spend learning to use it will be rewarded by much time saved. Apparently Zotero, which is also free, offers similar functionality, but I’ve not tried it.

Having said all that, I don’t use Mendeley. If you’re using LaTeX then citing references is done through BibTeX, and I prefer kBibTeX to manage my reference library as it integrates nicely with Kile. This is only a personal choice though, and Mendeley would achieve the same result.

 

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13 thoughts on “Free software for biologists pt. 1 – writing tools

  1. ScientistSeesSquirrel

    Markus – interesting and useful. But I’m curious: why is it important to you that a writing tool be open-source? I mean, that’s right in your title. I could understand a preference for _free_ writing tools, but a preference for open-source puzzles me. (All of them run on proprietary chipsets anyway, so it can’t be knowledge of the process, even if I could figure out why that would matter for word processing.) What am I missing?

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    1. Markus Eichhorn Post author

      I do try whenever possible to recommend FOSS (free open-source software) but in this case the ‘free’ part is the most important. The value of open-source tools is that someone will almost certainly have created additional resources aimed at scientists, whereas proprietary software is harder to tweak or modify, and usually set up for the general user.

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    1. Markus Eichhorn Post author

      Thanks Mike. @Martin_Ecology mentioned Overleaf on Twitter. Although they have a pricing plan, he says that the free package is pretty generous. I haven’t given it a go yet but will add it to the list.

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    1. Markus Eichhorn Post author

      Thanks Dylan, and it’s interesting to see where someone else’s trajectory has ended up. I also use Emacs, but only for coding and R. You’re one of a number of people who appear to live inside Emacs. I can see the appeal of having a single environment for everything, but sometimes bespoke tools are just… easier. It’s not a shift I can foresee myself making.

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  2. Pingback: Free software for biologists pt. 2 – data management and analysis | Trees In Space

  3. Pingback: Free software for biologists pt. 3 – preparing figures | Trees In Space

  4. Pingback: Free software for biologists pt. 5 –operating systems | Trees In Space

  5. Pingback: Free software for biologists pt. 4 – presentations | Trees In Space

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