Academic workflows: when to use what, and how

Dellu (who has blog very similar to mine, but addressing Windows, check it out here) left me a very good question on my post about Circus Ponies Notebooks:

How do you develop your workflow between Scrivener, Papers , Sente and the iPad apps and Ponies Notebook? It seems that you are using a dozen tools to do your task and somehow confusing to develop a smooth workflow.

Dellu has hit the nail on the head here. I think the past year, since I switched to mac, has indeed been a search for that ‘smooth workflow’, and I’ve made a lot (a lot!…) of detours in that process. Some of the detours come from wanting to test out different apps before I decide between them, other detours are more about exploring how different apps can be used in conjunction with each other. Some of the apps I’m not using actively, I’ve still mentioned on this blog (such as Papers, PDF Expert, GoodReader or 7NotesHD), because I think they are high quality apps that others may benefit from.

I’m still not fully at the 100% ‘smooth workflow’ mark, but I think I am a lot closer now than I was, say, six months ago. So, in this post, I’ll outline my current workflow for typical academic tasks. I’ll start with the disclaimer that this is still somewhat of a work in progress. If anyone has suggestions for improvement, please leave your comments!

The data analysis process

Naturally, such processes vary widely depending on what kind of data you use, and which discipline you are in. I primarily work ethnographically, where I use qualitative observation and interview data, which are captured through video and audio recordings (and to a lesser extent, written field notes). I work with sociocultural perspectives when I analyse data, which means that I draw on e.g. interaction analysis or other methods that are compatible with a social practice perspective. Hence, what I describe below may not be relevant to those working in other traditions.

My first interaction with my data (apart from converting video files, which I’m still doing on a Windows computer at work) will usually be transcribing in Inqscribe. I’ll write more on Inqscribe in a future post, but in short, it’s the most user friendly and likeable app I’ve found for this task.

When I have transcribed the data, I will typically do a number of inductively informed readings using iAnnotate. I’ve written here about how I use this app to do some initial chunking and note taking of the data.

I then typically move to Curio. Here, I might create a mind map that helps me to trace different inductively identified themes across the data material, or I might create a table where I start some initial organisation of data based on broad theoretically informed categories. Exactly how this process looks like will depend on the analytical approach I’m taking for a given writing process, but in general I find that using mind maps, tables and index cards in curio are good tools for gaining that first overview over a large data corpus. Based on this chunking, I will then often turn to more descriptive accounts, which I usually type up in Pages and then import to Curio, which acts as my ‘hub’ for writing projects (more on this in a Curio dedicated, future post). I suspect part of this process could also be well served by HyperResearch, which is on my to do list for checking out (I used it briefly several years ago, on Windows).

On Windows, I’m a fan of Videograph, but I haven’t found the mac counterpart yet. If anyone knows it, then let me know!

The writing process

Brainstorming and outlining starts in a mind map application, and continues in a dedicated outliner app. I have a post nearly written up on mind mapping which I’ll be publishing here soon. On my mac, mind mapping happens in Curio, and on the iPad, it happens in iThoughtsHD.

Once I have refined the brainstorming a bit, I will typically move to a dedicated outlining app. Exactly when this happens is a bit hard to say, but it’s often at some point where I feel that what I’m writing up is a bit more of a ‘linear’ argument than it was during the brainstorming process. On my mac, I use OmniOutliner or Curio. Doing this in Curio is very convenient in the sense that you can just convert mind maps to outlines with a couple of clicks. However, when I move from ‘visual idea generation’ to more ‘linear idea organisation’, I often create a new outline anyway. Strictly speaking, I could stick to Curio and leave OmniOutliner out of my workflow. However, it’s such a great outlining tool that I am sticking to it (more on OmniOutliner in a separate, future post). At the moment, I’m not really bothered by having both apps in the mix, but if you want to cut down on apps, staying in Curio might be a good option.

Then, when I’m ready to actually start writing, I switch to Scrivener. There, I import any literature notes, outlines, mind maps, data extracts or journal articles that I’d like to be able to view side by side with my draft writing. I sync Scrivener with Elements on my iPad, so that my drafts are always with me (I always carry my iPad) even if my mac is left at the office.

One of my small head aches over the past year has been which tool to use as a citation manager in conjunction with Scrivener. There are different options, and I’ve tried Sente, Papers, and, now, EndNote. Long story short, at the moment I’m sticking with EndNote for cite while you write functionality. In spite of how old fashioned and clunky that app has become, it’s the only one that gives me peace of mind in terms of formatting of references and bibliography, and it’s relatively easy (at least for me, because I’ve used EndNote for years) to make minor edits to a style depending on which journal you are targeting. It’s extremely rare that I ever have to edit information coming in (when importing reference information into EndNote), or information going out (when using cite while you write). When using Papers and Sente, I experienced several times that formatting didn’t quite turn out right. I should say that some of this might be down to me not being sufficiently competent with Papers or Sente, as my knowledge of how to manipulate styles in those apps are nowhere near what I could do in EndNote. However, as I was posting on online forums about this, I saw that others had had similar experiences. I think a lot of this also comes down to which discipline you are in, to what extent the stock styles of an app cover your needs, and whether you are writing a monograph where you can stick to a style of your choice throughout, or whether you are working on a lot of writing projects in parallel where each has its own citation style due to editors’ requirements.

I then stay put in Scrivener for a while, as I’m developing my text. If I have to share it for comments or review, I export it to Word or PDF using the compile feature. Then, when I’m at a stage where I’m approaching the end of the writing process, I switch to Word. This is usually triggered by being in a phase where I’m exchanging the text frequently with colleagues, and/or it’s getting ready for submission for a journal. In both cases, I use Word, partially because I work in a Windows environment, and partially because most journals in my field ask for submissions in Word format.

The literature review process

My review process starts in Sente, which I use to mark up journal articles. This is typically done on the iPad. I prefer it to the mac due to the form factor and the option for stylus input. However, quite often I will use the mac side by side with the iPad, typing up notes and summaries in Circus Ponies Notebooks, as I’ve described here.

While CPN has a very nice feature for creating links between pages, I sometimes feel the need for a less linear way of working when I explore how particular concepts or theories have been dealt with in research literature, and then I switch to mind mapping. Later, I can import the mind map either to CPN as a PDF file, or to Scrivener as support for a particular writing project. Others have also told me they find outlining to be a good tool, for example using OmniOutliner to gain an bird’s eye view of longer time periods, if you are doing historical research.

CPN and Sente function as my general repositories for pdf management and review notes. When I want to draw on particular articles or review notes during a writing process, I import them to Scrivener.

So, this is what the ‘big three’ look like for me. My routines for project management are still in the making, but at the moment they include Curio, Evernote, and iThoughtsHD – I’ll be doing a future post on this when I’ve got things more settled. I’ve written about task management here (using OmniFocus and SmallTask), and hand writing on the iPad here (where I use Notability). When reviewing colleagues’ or students’ work, I will often use a combination of iAnnotate and Word. My note taking routines depend on purpose: CPN is my main repository for my academic work, but I find their iPad app a bit flimsy, so I will sometimes work on notes in Pages (or any other writing app that a) allows formatting and b) syncs seamlessly between iPad and mac) and then later integrate them into CPN. Evernote is used for more personal notes, as well as project management notes (e.g. conference management and seminar organisation). The latter is especially useful in conjunction with my mail client Postbox, which has very good Evernote integration.

So, I think that concludes my response to Dellu for now – suggestions for improving my work flow are very welcome!

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9 Responses to Academic workflows: when to use what, and how

  1. Dellu says:

    This is interesting article, I highly appreciate your fast and detailed response for my question. I was expecting a small paragraph, you did it quiet generously. Thank you for explain things with this depth.
    There is one fundamental difference between your workflow and mine: I finish my work in Latex, not in word. That puts the question of reference manager out of picture: I don´t look around any of these app you mentioned: as you said many of them are really mediocre (I remember,lack of a satisfactory reference manager software was one of the main reasons why I shift to Latex last year; I am glad I did!). But, I found the quoting and commenting system of Sente, as you explained it in the other post, quite elegant. So, I am specially fascinated by your integration of Circus Ponies Notebooks with Sente. I have both of the apps on my mac. I specially like two features from Ponies Notebook:

    1. Voice annotation (<–best for recording classroom lectures: the timing of the voice follows my bullet points; writing and voice recording going hand in hand: perfect!)
    2. Keywords (Multidex) <–There are only two note-taking softwares in the world, right now, that could tag ideas at a bullet point level (a paragraph or a phrase): they are MS OneNote and Ponies Notebook. I really love this feature, so crucial for researchers in humanities (I tag my ideas, key phrases, key authors that I don´t ever want to forget); tagging files is good, but less effective.
    A question for you here: does HyperResearch has such a feature (tagging a specific idea or a bullet point in your extended note)? I heard Nvivo is great at doing this kinds of things (your kind of things specially the video+audio workflow). But, Nvivo is windows only. I think I want to hear from you about tagging a specific idea, and relating that idea, using some magic tool, with other ideas. MInd-mapping could be the thing here (but, I personally find mind mapping useless: I am not a creative person; i couldn´t generate new ideas; i always develop my ideas by reading other´s works, for which, the note in Sente gives me the pleasure). I have also been thinking of Tinderbox for this purpose. But, God damn, so awfully complex application, and there is no good guide for it (I bought the developer´s book, but has no practical idea: pack with personal "philosophical" hodgepodge) .

    There is also a serious issue that disturbs me: the more tools I use the more I procrastinate.
    I am playing a lot with these tools. So, I am thinking to avoid Ponies NOtebook (and also Curio and OmniOutliner) from my workflow and stick to the Sente-Scrivener (+ the indispensable Devonthink) combination. Curio and OmniOutliner seem great tools, but, I think they are not really crucial to my workflow, which mainly is about reading PDFs and writing articles.

    -The first is regarding mind mapping. If you like to integrate mind mapping into your work environment, you might be interested in Docear. It is really promising app: specially the fact that it can extract annotations from PDFs, is quite great feature. It mainly targets the academic researchers using mind-mapping Docear might help you to kill both Curio and OmniOutliner (assuming you also want to minimize your tools).

    -The second is about Evernote: couldn´t you totally replace it with Devonthink? (I know you have devonthink; put all your personal stuff in one database in Devnothink).

    What do you think of me avoiding Ponies NOtebook? Do you think the flow between Sente, Scrivener and Ponies NOtebook is really smooth? (Sent-Scivener is straightforward, use a script to export to RTFD to import in Scrivener, or via Devonthink). But, I couldn´t see a place for Ponies Notebook in this flow. May be, I have use it for class room lectures only.

    I will be looking forward to hear from you!

    • macademise says:

      Hi Dellu,

      About HyperResearch and tagging: I don’t know, it’s such a long time since I’ve used it. I’m going to look into it again early next year and see if I want to use it more for my data analysis, as I’ve yet to find a mac app to replace the kind of features offered by Nvivo.

      About relating ideas: In CPN I work a lot with linking between pages, which I find useful for literature reviews. I also find mind mapping very useful, and with a good mind mapping app you can also import files, notes, images, and so on. However, I don’t think there’s a set answer to this, and what kind of work flow people end up with often comes (at least partially) down to personal preferences. You just need to see what works for you! Thanks for the Docear suggestion, I hadn’t heard of it before and will have a look.

      In my workflow, Evernote is quite different from DevonThink. A primary reason for this is the sync feature of Evernote, which makes it available and easily synced no all my platforms (my mac, iPad, windows and android phone). So, information that I need to have readily available wherever I am goes into Evernote. DevonThink serves me two purposes at the moment. One is a personal database, where I keep everything from scanned receipts to bank statements to licence codes for apps and so on. The other is a repository for a future writing project. I want to write a book that I don’t really have time to work on now, but every time I find resources that might be useful towards that project I stick them in DT – that includes research articles as well as web resources such as blogs, newspaper articles or organisational web sites. However, that’s just a tiny bit of what DT can do for you – again, it’s a lot down to personal preferences and how you organise the rest of your workflow.

  2. Rachel Mackay says:

    HI Macademise, what a great blog! I will be looking up a number of the software applications that you mention. I’m currently involved in my first research project and have settled on Sente and Docear for managing my literature and mapping my ideas. Then I write up in WORD – haven’t really spent time exploring alternatives to that. It’s still quite clunky to get it all to work together but I love both Sente and Docear. The best thing about Docear is that it will automatically import all your PDF annotations into the mind maps. From there you can organise them into topics, ideas etc.,and link them together. You can use the mind maps to do your outline for your writing and have all your quotes and notes right there just by dragging and dropping them to each topic you want to write about, then when you want to see a quote in context you just click on it in the mind map and it opens the PDF up to the exact place the quote came from. The downsides – 1. Docear can’t recognise annotations made in Sente because of the way Sente files them so at the moment I am using Adobe Reader for this. 2. The Bibtex export to Docear doesn’t work properly, again because Sente adds additional unnecessary info to. 3. Docear does have it’s own reference manager but I don’t find it nearly as easy to use as Sente. 4. Docear’s cite to Word only works on Windows not mac, so I use Sente for this feature. Overall I love both these programmes and would highly recommend you have a look at Docear. I still have some work to do on getting the integration working a bit better though.

    • macademise says:

      Hi Rachel, thanks so much for your comment. I haven’t tried Docear but what you describe sounds really smart, so I’ll check it out. I extract annotations through iAnnotate or GoodReader on my iPad which works very well – but there’s no automatic way to stick them in a mind map. For writing up I strongly recommend Scrivener, which I’ve written about here. It’s by far the best word processor I’ve encountered for academic writing.

      • Rachel Mackay says:

        Thanks I will have to look at Scrivener. The interface between Sente and Docear (or lack of) is beginning to drive me crazy. So I am trialling just using Docear as my reference manager as well. Unfortunately it is not nearly as polished as Sente which is a shame. In the end I decided that the mind map functionality was far more important than anything else.

        • macademise says:

          Yes, since discovering Scrivener I have never looked back. I do a lot of mind mapping, too, but in separate apps (NovaMind and Curio).
          Would you be interested in writing a guest post on this blog about your experience with Docear, when you’ve tried it out for a little longer?

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