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I have written before on the issue of software tools to better aid scholarly research (also known as: writing your PhD), not just on this blog, but also on my technical blog let x=x. This post is spurred by a brief conversation I had this afternoon with postgrad classicists about organising their electronic information, and hopefully will tie together some of those threads.

TL;DR – scroll down to the conclusion.

A word of warning. I use an Apple Macintosh, I have done so for quite a few years and in fact I’ve just bought my 4th straight 15″ MacBook Pro and there are six Macs in the house at the moment. All software mentioned here runs on a Macintosh. Obviously some of it may be available for Windows or Linux users, or equivalents. However I don’t care. I’m discussing what works (and doesn’t) for me, and that means on a Mac.

Writing tools

Although this process is naturally later than research in a temporal sense, writing tools are so centrally important to the process of all researchers in any Humanities subject, that they have to be dealt with as a priority. You need to choose the writing tool that best suits what you need to do in the way you want to write it: research tools have to fit into that “flow” and if they don’t, you generally chuck them out rather than adapt your writing methods.

First, there is Microsoft Word. For some people. this is as far as it gets. Word is their world. I understand Word fairly well, but I also understand it’s limitations and it’s annoyances. I generally only use it when I have to.

For general research writing, I use a tool called Scrivener, from Literature and Latte. Its more tailored to people like scriptwriters or novelists, however, it’s an invaluable tool to organise your thinking. You can write small focussed chunks of text on a topic and theme, and then use things like the ‘cork board’ to organise those chunks (presented as index cards onto which you can write a summary of their contents) into something approaching a coherent argument. Then you can flip back to the ‘Scrivenings’ view, which shows you the full text of the selected items, to see what needs altering to make the argument flow properly.

Once you’re happy with your draft in Scrivener, you “compile” the document into a target format, like an .RTF document:

Compiling a document from Scrivner's cork board view

After this you can polish the document in the word processor of your choice.

I did use Apple Pages for the bulk of my M.A. Thesis. It’s a great tool. I did find it lacked a couple of features I use in Word — at the end I exported from Pages into Word format and did the final production to PDF from Word.

Probably for my PhD, at the production stage I will probably use some type of TeΧ tool, likeLaTeΧ. Suggestions welcome on this idea.

Research tools

Here’s where I gets trickier, I think. For my M.A. I tried to use Evernote to organise article PDFs I got from databases, but I found in the end, that Evernote was just not up to the mark in terms of scholarly research. It has a lot of other neat features that users like but I found it unsustainable in use, mainly because I had to search for documents in databases with my web browser and then import the PDF into Evernote, including typing out the title and author.

In the end I ditched Evernote for version 1 of a program called Papers. Version 2 is now out. Papers connects me to the academic databases (warning: has a built-in bio-science prejudice) – even using my university’s Ezproxy for free access to them – and then allows me to search the databases to my heart’s content. It then imports the PDF into your own database. So you build your research database over time, and as well as searching databases, you can search your own research collection, as below:

Searching for everyone who quotes Walsh inside my research database

It also has an iPad app that will automatically sync with the Mac program and put all the PDFs on your iPad so you can read them there. This is very, very handy. Reading PDFs off a screen is horrible. Before I got the iPad I had to print out all my articles – not good for the environment! On the iPad you can annotate the PDFs, but I don’t do this, I either take notes into a notebook the traditional way, or I type the notes into a special research document in Scrivener. But having the iPad set up on a stand next to my computer screen while I do this is a tremendous boon.

If you have PDF books, you can import them into Papers, although you may have to type-in the title and author data. Many PDFs that you download from databases have data in them in such a way that Papers can sometimes auto-determine this data for you, if you have the PDFs already on your disk, but book PDFs rarely do. Papers can also handle journal abbreviations.

If I get e-books (ePub) from my library I immediately strip the useless copy protection which prevents the document from being utilised in a sane manner, and then load them up on my iPad using Apple’s iBooks. You can annotate documents in iBooks. It also handles PDFs, but not as well as ePub. The only drawback with this method is that in iBooks you lose the “original page number” that you get in the Adobe DRM’d viewer. But I think this is a fault of the idea of citing a “page” number in a document that can reformat itself to conform with any desired display as necessary. Classicists already know the way to cite “continuously scrolling” documents! But alas, the necessary numbering system is never included in the ePub documents. So you are forced to refer back to the original to get the “proper” page reference (and this means another 24 hour borrowing of the ePub document from the “library” to get it. This stuff all proves me that proprietary DRM is anti-scholarship, as I’ve said before.

Alternatives in this area are Mendeley and Zotero. I signed up to a Mendeley account but I’ve not really used it as I stuck with Papers. Zotero claims that “It lives right where you do your work—in the web browser itself”, the only fly in that ointment is I don’t actually do much of my work in a web browser. I mean, wikipedia is still not an acceptable source, right? Plus with Papers I don’t have to search JSTOR and then go to Project Muse and enter the same search in there too. I can just search once right in Papers and make sure I’ve got both JSTOR and Project Muse and any other relevant databases selected. I can also review the articles before deciding to import them or not right in the one program.

Citation managers

I have also used Endnote (my University gives me a free licence) to manage my modern citations and their bibliography. However, the problem for Classicists with Endnote, and this goes for all citation managers, is that they assume you have only one referencing style. In other words, when you have to manage your ancient sources separately, and possibly cite them differently, as you generally do in Classics, a citation manager can get in the way, enormously. Also I find that many people can’t cope with the complexity of making a custom citation and bibliographical style especially if the one they need isn’t available as a default in their citation manager of choice. Although I could, being a professional computer programmer, and an anal-retentive taxonomic organiser, so much of this stuff doesn’t scare me as much, but I can’t bring myself to recommend it to anyone.

Papers 2 added citation features, which brings a great integration to your research database and your citations and bibliography. However they are fairly primitive at the moment, and geared towards science users and therefore not useful to Humanities scholars (especially Classicists without our multiple citation formats). I’m kind-of ambivalent about this. For me, Papers’ number one feature is research article search and database management, so I hope they don’t screw that over to compete with specialised citation managers like Endnote. I can cope managing this stuff manually, for the moment.

What I do use with Papers, though, is it’s ability to just “drag and drop” entries from it into an open document and it will paste the entry as in a Bibliographic entry. This is just plain text so it can be adjusted as required. I then tend to manually manage my citations (we currently use a hybrid system of MLA format in footnotes, not inline MLA).

Dragging and dropping a Bibliographic entry from Papers into Scrivener


I tend to live in Scrivener and Papers. I write mostly with Scrivener. I sync my article PDFs in Papers for the Mac across to iOS Papers on my iPad so I can read them on-the-go and without printing them all out. I read ePub in iBooks, and I don’t use electronic annotations very much – preferring to use a notepad and pencil, or just type my notes straight into the “Research” section in my Scrivener document. Citation managers I avoid, but I do love the drag-and-drop bibliographic entry function in Papers.

Comments, clarifications, suggestions, flames, all welcome.