academic software

Hi everyone,
I am looking for some help on academic software (for idiots) and as this forum seemed the friendliest place, and least full of computer jargon and the word LaTex, I thought I’d ask here.
I have recently started working on my PhD thesis, (on classical Athens), after taking a couple of years off, and find myself surrounded by boxes of pdfs, photocopies of books, handwritten quotes and summaries etc and would like to find a programme on the computer to help me organise my data better. My college in the UK is very PC based, so no help there.
I have tried demos of various software (Scrivener, DevonThink, Tinderbox, Circus Ponies etc) but I am finding it difficult to work out which actually does what I need, particularly as I am not very computer literate! I was going to use Skim to annotate pdfs, Sente both for bibliographic management and to link quotes to various sources, and then write up in Mellul as it supports greek fonts, but I don’t feel this combination gives me the ability to sort and see patterns in my work.
I need to be able to:

  1. Take down quotes and summaries from secondary sources and sort them in various ways.
  2. Take lines and blocks of text from primary sources (eg Greek tragedies) with linked quotes and ideas from secondary commentaries and also play around with the primary text to find patterns and links, for example all the usages of a particular metaphor from different plays.
    I do not need any multi-media capabilities as I only use text, no images or graphs or equations or anything like that.
    I have looked at lots of forums and find myself bemused by how complicated everything sounds. If there is anyone out there who could help me find a path through this I would be very grateful, as I am getting to the point where I may just return to good old card indexing!
    Thanks :slight_smile:

wow, i never thought i’d find myself giving advice to a classical greek scholar.

for my money i’d go with devonthink. the power and its artificial intelligence way of associating information and documents looks and feels like black magic - you can organise and control mountains of (irregular) data easily. when you’re ready to start drafting proper, start working in scrivener, but i’m not sure how it handles the greek stuff. probably Keith could answer you better.

TBH I don’t think there is anything that will do exactly what you want. Probably the nearest would have been DevonThink but you’ve already rejected that. CP Notebook is useful for keeping notes of supervisions, but I never found it very useful for much else.

Something you could look at is ‘Scribe’ This is free so you don’t lose anything if it doesn’t fit. It’s a Filemaker application designed by historians, so you might find it useful.

Sorry I can’t help more. :smiley:

I’ve been trying to sort out my workflow for a couple of years. I’m now well into my PhD thesis but still finding my way.

At the moment I use DevonThinkPro to store quotes from books, articles, etc. Over the years I have developed a system which works for me, but which others, I’m sure, would either improve upon or avoid like the plague. In DTP I have an ‘Author’ folder into which I make subfolders for each author I wish to quote. These subfolders all then fall automatically into alphabetical order so that I can easily find what I’m looking for if I want to see if I’ve already made citations from a particular work. Into these individual authors’ folders I then add another subfolder for each work they have written from which I’m making citations, naming this folder starting with the year of publication followed by the title of the work (either book or article). Into these I put citations from that work as text files in RTF format. I name these text files by author’s name+year@page number. This system is basically as follows:

AUTHOR [folder]
- Bately, Janet [subfolder]
– 1978 The Anglo-Saxon Chronicle [subfolder]
— Bately1978@107 [text file]
— Bately1978@108 [text file]
— Bately1978@119 [text file]
– 1985 The Anglo-Saxon Chronicle - again [subfolder]
— Bately1985@90 [text file]
— Bately1985@94 [text file]
- Dumville, David [subfolder]
– 1985 The Annals of St Neots [subfolder]
— Dumville1985@xviii [text file]
-Wainwright, F. T. [subfolder]
– 1970 Scandinavian England
— Wainwright1970@215 [text file]
Etc., etc.

Over time my citations have built up to thousands. What I find great about DTP is the AI feature [the ‘See Also and Classify’ command under the DATA menu] which finds related material to whatever text you highlight, listing the files in a sidebar which you can click through. This has helped me enormously in finding associations which I have either forgotten or hadn’t made previously. In my system the related files then appear by author’s name, year of publication and page number, which I find useful. Also, DTP’s AI feature works best if the files are bite-sized rather than article-length.

When I want to start pulling things together, I turn to Scrivener. Subjects are organised by folders in the Binder into which I drag and drop files from DTP. Here I also add my own thoughts and related ideas. Most of my actual writing (academic, that is), however, I usually do in Mellel, working back and forth from Scrivener and on occasion DTP, with Bookends as my bibliographical database. I only use Bookends as a bibliography manager, however.

One other piece of software I’ve found quite useful is TextSoap for ‘cleaning up’ text from various sources, web pages, pdfs, etc.

Hope this helps.

Maybe you should have a look at WriteFlow.

The other day I read an article about this new writing software combined with bibliographic functions.

The concept seems rather interesting, I did not yet have time to try the application.

At this state the app seems to behave rather buggy, as the developers mention in their blog. So it’s too early to recommend it, but in the future might be what you are looking for.

Thanks to everyone who posted some advice - it’s very much appreciated! I am trying both writeflow and scribe.

Skallegrim - your ‘workflow’ example was really useful so thanks for that - I just wondered why you use both devonthink and scrivener? Do you think you could achieve the same ends using just one or the other?

Thanks :smiley:

One reason is the ‘Edit Scrivenings’ feature. Another is Scrivener’s exporting capabilities. A third is the way Scrivener handles footnotes.

DTP works well with gigabytes of information and its AI is a unique feature. I see the two programs as quite distinct.

In a word: no. DevonThink is an unsurpassed research repository, but is mediocre at best as a writing environment. Scrivener is an unsurpassed writing environment, but is no more than adequate as a research repository. Particularly for a project as large as a thesis, you need top-quality tools on both the writing and research sides.

There’s a similar thread over at the DevonTechnologies forum. Might be worth a look.


I use Zotero
Besides being free, it is exceptionally functional. Check it out.


I’ve just been playing with WriteFlow (thanks, Ursula!), which looks really excellent and close to what you’re looking for, gmg. I’m impressed with the program and concept, and with the speed with which its developers write back. I’m looking forward to using this alongside Scrivener; I know people love DevonThink, but as Katherine mentioned, it’s a “mediocre writing environment.” Also, it doesn’t play well with image-only PDF files, which covers most of the digitized original materials I work with.

Another program that comes to mind, when you describe working with text and finding/developing theme links, might be Tinderbox. I have not used it in-depth, mostly because it’s very expensive and its trial is too limited. Also, I just can’t get past its visual looks. It’s apparently very powerful, though.

For brainstorming ideas and themes, I tend to use mindmapping programs like Cmap (

Enjoy developing your dissertation and remember: “A good dissertation is a done dissertation.” (Didya hear that, Marianne? Hmmm?)

Some people like Papers:

I just finished a non-fiction book, 200 pages.

I found the combination DevonThink plus Scrivener best for my particular workflow which required a lot of research.

DevonThink, though it has a very unelegant (some say ugly) UI and often unfriendly support team, is unsurpassed for the accumulation of websites, quotations etc… When it comes to forging it all together, creating coherency, creating a “story”, Scrivener is just phantastic.


I found a couple of posts a while back at a website called studyhacks that might be useful to you.

The first post describes how to use a wiki to organize research. … arch-wiki/

The second post describes a workflow using excel: … -database/

If you go the wiki way, you can probably use Voodoopad.

Any further thoughts about WriteFlow? I was intrigued by this application when you first mentioned it. It seems to be missing some functionality, which the developer says will be coming along. Thanks!


Steve, I wanted to ask exactly the same question to henrietta, who wrote she tried to use WriteFlow.

As for me, I just bought Curio and still need time to integrate this application into my workflow. At this state I don’t want to use another app, who still seems to be in a very beta state. (Henrietta, am I right with this?) I’m a lousy beta-tester, I know, unable to detect why things are not working as they should and to make propositions how to improve this.

Like henrietta I found the developer very responsive. But for a beta the price is really to high for me at this moment, so I wouldn’t buy it anyway. I still like the concept and the look from what can be seen on their screenshots.

I had a look at WriteFlow after seeing it mentioned in this forum today (had never heard about it before), and while I really like the concept, I think there’s a long way to go for them before I would consider using it in my workflow.

The idea of having one integrated research application that you “live in” all the time is rather appealing, but it also ties you up a bit. From what I can see, their concept of bibliographic management could potentially knock the socks of the competition in terms of citation management and note taking. As far as I can see they only support the Harvard format (which makes it quite useless for me until they develop more formats), and the citation system only works within WriteFlow itself. In other words, it doesn’t seem like I would be able to use the citation management in tandem with Scrivener or Mellel.

Being tied in to the application with the citation manager, you have to do all of your writing within WriteFlow, and I don’t see anyway to outline and structure your text at a macro level. The way they approach text structuring at a detailed level (with the margin notes) is fascinating, but if they can’t help you structure a 100,000 word thesis, why should an academic choose to use tis software in the first place?

Finally, they seem to be very aware of a tight use of styles (which I really applaud), so that you don’t need to do any editing of any kind in a word processor after exporting your writing. Ideally, they should be able to set up your title page, do the TOC, bibliography and index, so that you could export a pdf, ready for publishing.

This is a lot of functionality, and some of it quite advanced. I fear that it will take years for the developers to catch up and make this brilliant software concept useful for a serious academic.

I tried WriteFlow too and while I have to agree with florestan that it needs quite a lot more work to fully replace another word processor, there are some neat features I didn’t find anywhere else.

I work with a lot of quotes and it has always been a hassle to manage them in a satisfactory way.

WriteFlow actually made me smile more than once with quite amazing solutions…

What I used for writing my dissertation: DT Pro to warehouse my research material, Mellel to write my dissertation. Mellel is ugly and clunky in many ways, but is quite powerful. It allowed me to utilize multiple footnote/endnote streams and its outliner made it extremely easy to move material around and see it all as a ‘gestalt.’ It’s been a few years since I completed my dissertation, so I’m not sure if other programs have improved their capabilities in these areas.