workflow – for the mac. some hints for pc.

[UPDATE: I have added and changed a few things here after working with the apps for a while now. Mostly I would say I cannot image life anymore without Dropbox, and Devonthink is an amazing power tool for anything relating to research, especially since I imported all my archival material and OCR’d it. Evernote still has a place in my workflow, though, as easy-access collection of ideas, notes and concepts organized in low hierarchy. Scrivener is the BEST writing program ever. Period.]

This is the result of a workshop we had in Princeton to improve our workflow, or rather, to collect some notes on things one can do to streamline research, organize thoughts and make the mac look pretty. I apologize for the missing links to the programs, I will try to update those, and obviously all the missing information – but if you google the programs, or look for youtube videos, that should give you a sense of how they work, and what other people think of them.

It’s by no means a complete list, but I thought I’d post it anyhow, for people to look some things up. Feel free to ask, comment, or dismiss some or all of it! And if you think of buying some of those: It is always worth checking out educational discounts. Just saying.


– store whole documents, not just parts of PDFs for later teaching purposes.
– keep clean copy for teaching
– first survey of secondary literature: arrange excerpts in logical order as preparation for writing; you will need to return to literature later in the process


Dropbox. I have said this before, but please, get Dropbox, everyone. It really is worth it. I store everything on Dropbox. This means I store it on my computer locally in a folder that is synced with Dropbox; on my Macbook Air I have opted for “select sync” (found under settings) as to not download all my GBs to the little harddrive. Dropbox folders in finder are synced with online storage, but files are also stored locally (hence they can be included in time machine backup; and can be accessed when offline). I also store my Devonthink database on Dropbox, and there are some things you have to be careful with, i.e. do not open your database simultaneously on two machines!. Other than that, for anyone working on more than one computer, or with an iPad, or really for ANYONE, Dropbox is the way to go. It means you can scan directly to your file system from anywhere with the web interface. Or it means you start working at a document at school, and just keep working on the same document at home – and no frantic copying required a la “which version was the latest one, let’s make another copy.” This does not mean, however, that backing up is off the list. Syncing is NOT a backup. I still back up with Time Machine, and the Dropbox folder in my finder is included in the backup.

UPDATE for the workflow regarding data organization with Dropbox/Evernote/Goodreader on iPad:

I have all my texts in one folder on dropbox called “texts,” in folders with names of authors (if you want, you could copy this folder to your harddrive to keep clean versions of your pdf files). If I need to have the texts in other folders to know where I read them or to link them to a project, I make an alias of that text. In Goodreader, this dropbox folder in its entirety is synced to my iPad, with the option of deleting files on Dropbox switched OFF, but with the settings for uploading changed/marked up files ON… and with the option of deleting files on the iPad ON (otherwise when you clean up or so, you have everything double due to the syncing). so far this works well – Evernote is only used in my case for ideas I have on the go, for the papers or projects (I then give the notes as title the name of the project I use in the Finder/Dropbox, plus an extension declaring what it is…)


Classical Workflow
use ref manager to locate secondary material (EndNote, Zotero, Bookends)
annotate pdfs and take notes (Skim or Sente)
Import notes into database (DevonThink or Evernote)
Outline argument by organizing notes (omnioutliner)
Write (Nisus Writer Pro, Pages)

Process Workflow – using all programs simultaneously
Import Primary Materials (DevonThink)
Annotate primary materials and take notes (DevonThink)
outline argument (Omni Outlier Pro)
write (Nisus, Pages)
research (Bookends, EndNote, Zotero etc)


EndNote can update the information through a link to word, in case you change the information/correct it; whether it can do that in pages/iWork is not clear to me.

Zotero can not do links, or at least not to my knowledge – once the information leaves zotero, it is on its own. Could become a problem down the line when handling large bibliographies (future dissertation, I am talking to you.)IFLASH
flashcard program; make your own, and study better/harder/more organized.


Filemaker can be used as database for images; images stored locally, but could be stored remotely; database links the images and provides information. Problem here is that filemaker is (after 3D Studio Max) the least intuitive program I have ever used. If you don’t have someone making a database for you, be prepared to spend some time. But – there are some things that only filemaker can do. So analyze your needs, and your abilities, your friends and you patience, and then try it.

Alternative version with Finder: for the dissertation, you could store the images as pdfs in folders according to project; storing a pdf of the chapter in the same folder;  (this means for every project you would have to duplicate the image – multiply storage); the new version of word is stable in handling images, so that is off the table; archival images are stored in folders (without further classification); working i.e. with memory/mnemonic devices; always include images with title as citation (for later reference) – you will hate yourself if you don’t do this.

Some people use Excel to document archival material, some use the file structure of Windows/Mac OS and uses file structure names according to archives in the wiki to take notes on those folders; another tip: take a photo of the box/take a photo of the file/take a photo at the end, save it as ONE pdf file – this will save you some tears.


Create your own Wiki: to structure your work, your thoughts and – as a colleague said – to talk to yourself, you could build your own wiki system. Here you can plug in all your references, your ideas, and cross link them. It requires a little bit of tech knowledge, but generally the systems offered are easy to handle. A wiki can help updating and rewriting the abstract etc; use the structure of the dissertation to organize things accordingly; brainstorming and re-linking to other folders; creating a network or material; Big plus is you can use it to actually construct a way to organize your own network.


website (bookmarking websites; specific pages of googlebooks) (image database) (drop in image-links you encounter on the web); write on stuff that you want to put out as an exercise; (dictionnary etymologically)


notational velocity (Mac) and iNote (iphone); automatically shows similar files; simple interface adn search mechanism that links the files together; including shortcuts for marking particular stuff (i.e. with *** or so) makes the search function work better for your own priorities.
mnemonic devices instead of note taking while reading
Evernote: simple note taking; manage links/images; taking quotes and stores them.
Instapaper: storing things for later;


Program Skim: free pdf annotater for taking notes before you write
iPad (see here also my post for iPad apps): “iannotate” for pdfs


Devonthink: I was hesitant at first, because it is a complicated program, and expensive. But it is amazing, and saves a ton of time once it is up and running. It is worth figuring out the differences between importing files (=the database makes a copy, which is stored in the database-logic, hence less obvious findable in the finder) and indexing (which means you link the file to the database, but leave it generally stored in the file system of your computer). There are pros and cons for both versions, I use generally indexed files, since I also use my iPad to work with my pdfs and text files, and have all of that synced via Dropbox; one more thing to remember is that you might need to access your files from a different computer at some point, which might not have devonthink installed – if you have everything IN the database, this might be difficult. [UPDATE: I now use “import” for archival images – while keeping a copy on an external drive – and pdf/OCR them, and “index” for text files and all other files that are related to writing as such. So far this seems to work, since I don’t usually access the image files without looking for information through Devonthink anyhow; I would recommend re-naming the files in Devonthink for better locability to respective archives etc, but keep the original jpg name as part of the file.] I use one huge database for everything/all the material, and then create a project specific database for each profject; DevonThink has an exceptional OCR program, which I use to OCR all my archival images, which makes them searchable for names and events or keywords. While this is not 100% reliable, of course, it gives invaluable pointers for research. If the organization seems too complicated, dump everything in the inbox if you start using it until you know how it works.

The good thing is: if you decide to leave DevonThink, you can export the whole thing with a folder hierarchy according to the one you have created in the database; hence, you lose nothing in trying. There is a version for the iPad, but it is not perfect yet, people say, so I have not started using it.

Evernote: Evernote can do a lot of the stuff DevonThink can, i.e. web clippings, pdf storage etc., but is limited in size and does not have the amazing, AMAZING link and search function that makes DevonThink worth its money.

UPDATE: Evernote has flat hierarchies (you can do tagging and nesting notebooks, but not much more), and a horrible text edit function (read: none) on iPad, but is quick, easy, and very accessible. The fact that I can sync it across all devices means whatever I need to jot down is available for later (actual) work. It also means I can write down notes on texts, ideas or questions all in one app, and can pretty easily find them later. I do have to say thought that so far I only work with several hundred notes (not thousands, as others), so it is still fairly easy to keep an overview. How this will work once I collect much more material I don’t know, but that’s a question I have for more than just Evernote (read: how does one REALLY structure teh material for a whole dissertation?).


Outlining in general was a new idea to me, but I have to say it totally works. Just the freedom of brainstorming ideas and then shuffle them around without scrolling through endless textblocks is very liberating.

Omnioutliner: work through a body of material and highlight the stuff you want to include; and then organize it in the outlining program; you will never keep the outline as is, but use it early and often; use it posterior as post-outline to analyze/re-evaluate your argument; material in the database;
how do you save versions? just as date-labelled files.
see also Scrivener: different view (but maybe also more options? does real footnotes; and allows for comments that translate into word documents)


Scrivener: I LOVE this program. Love it. It is a combination between an outliner, a writing program, and a database. It generally organizes your work in a binder, so you always see the document structure while working. It also has a folder for Research (bibliographic material, pdfs etc) and one for Notes (where I dump anything that comes to mind, but has no place in the paper yet). This way you can keep your paper-to-be clean, and your word count straight. Scrivener can do footnotes and comments, and it can export to almost any format you might need or want. It has a function called “project targets” where you can set your goals and monitor yourself – useful – and a composition mode where you have minimum distraction and maximum focus – beautiful.

To sync it with the iPad you will have to work with something like Elements (see my iPad app post) until they publish the promised iPad version. Scrivener autosaves, and you can take snapshots of the document before daring bigger changes; It allows for split screen (either with the same document or with a different one); image insertion and scaling. Watch the youtube videos to learn how to use it (“how to write a research paper”).

Nisus Writer Pro; does a good job in saving things in .rtf; I don’t use it personally, but it has been recommended by people I trust on this. It is suitable for the last stage of writing, when you have to track changes, and fine tune your formatting – Scrivener is not great at that last step.

Pages (iWork): I use Pages for all notes on secondary sources, and for the final formatting, if necessary. I like its clean interface, and it never, never crashes, but it is a bit annoying having to export to .doc format everytime you exchange stuff.


Dragon Dictate: use it for interview transcriptions or note taking via audio; works quite well;


My Little Pomodoro – break timer with stats; it does work!
Freedom: blocks websites you specify for a time you specify. It’s helpful.


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  1. By Crunch Time – and how to survive it. on August 22, 2012 at 3:57 pm

    […] to edit a paper with only the trackpad.) As mentioned in other posts, I use the writing program Scrivener. If you don’t use it, you don’t know what you are missing. I seriously think it has […]

  2. By my favorite iPad apps on August 22, 2012 at 4:05 pm

    […] UPDATE for the workflow regarding Dropbox/Evernote/Goodreader on iPad (see also here): […]

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