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Workflow on Mac (Mountain Lion) for PhD Thesis

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Posted by Peter
Aug 12, 2012 at 03:12 PM


Hi all,

I am interested in your opinions on what the simplest and most efficient set of tools/apps is for a writer’s/researcher’s workflow. I am sure you get this sort of query all the time but my head is just swimming with all the choices out there. This is a desperate attempt at some final clarity! Here it goes.

I have consulted several excellent blogs on this already, including:


Here are a few tentative conclusions and articulated needs and questions…

To begin, I have a messy system and folder hierarchy that has grown like a cancer over the past several years. Therefore I’m interested in graduating to a more extensive use of doc tags (codes/aliases) to make use of the mac’s spotlight search. I have seen Tags ($30) and Tagger (open source) recommended. Does anyone have experience with one or both of these? Also, suggestions for feature/app that could help ease/automate the transition from folders to tags is appreciated. Do either of these apps do this? I have seen Hazel recommended for file org but somehow that just seems like overkill. I need a way to make sense from the mess but still live with it.

Reference Management and PDF annotation
Jennifer Claro makes a good claim for Bibdesk and Skim for bib/pdf management/annotation (see link above). Currently I use the Zotero standalone which opens the pdf in Preview to allow annotation. However Zotero doesn’t seem to search/index these annotations. She makes Bibdesk and Skim look pretty good together. Does anyone have experience with these or other set-ups for working with research pdf articles?

Export/Import/Sharing PDFs across apps
It is also important for me that the pdf database “talks” with other apps like DevonThink. See next…

Collecting and Outlining
While I have more experience using bib/citation/ref software I am less versed in outliners. I have never really used more than a simple mindmapper link Freemind, along with Word/Pages and Scrivener. However several of bloggers above make a strong case for Circus Ponies Notebook (CPN). Nevertheless, I am tempted to throw everything (mainly notes, docs, annotations, etc) into Scrivener or Word/Pages and create one big doc, perhaps with import/export to a mind mapper like MindNode for visual outlining. I think I understand the advantage of using a separate outliner like Notebook but at the same time I’m worried that too many apps will slow my flow and my concentration! Do people really think Notebook (and other dedicated outliners) really have a clear advantage? Are there any all-in-one or at least streamlined solutions out there?

If I start using DevonThink, perhaps I could just throw everything onto one of its rich text docs? It is difficult to know how well the latest DevonThink works since many of the reviews are based on earlier versions - pre 2.4 (see below).

Data Management and Idea Development (DevonThink)
While I am still on the fence about CPN for outlining, I am more convinced by DevonThink (I will probably go with Pro or Office). I am concerned however about the pdf reference/citation/annotation issue that people have posted about. There seem to be scripts that allow DevonThink to work with pdfs in an external folder (like Dropbox). I wonder if this works with Zotero/ Bibdesk? I’m not sure I would use dropbox much since I don’t work away from my mac for writing (e.g. on an iPad) so I assume a normal folder might also work? I just not clear yet about how to get DevonThink and a ref manager like Zotero to use the same pdf database and also search the annotations. (A screencast tutorial would be great!) Also, what happens if I accidentally more or change the folder? I guess DT wouldn’t know where they went?

For the actual writing I will stick to Scrivener/Word/Pages.

Bottom line is that I’m looking for a straight-forward and efficient paperless workflow to jumpstart my thesis writing! It’s just a jungle for a novice like me to figure out the best and simplest combination of tools for research and writing! I therefore certainly will appreciate any tips people have to offer! I am looking for an integrated solution, all the way from data collection and analysis to outlining and writing.

Kind regards,

PS Here are some additional apps that I came across in my search that might interest you, but then I suppose this community already know about them. Do any of these offer serious advantages over a system like Tags/Bibdesk/Skim/CPN/DT/Scrivener/Word/Pages?

Curio http://www.zengobi.com/products/curio/ - Wessels reviews it
Inspiration 9 http://www.inspiration.com/Inspiration - combines mindmaps, outlines and presentations
The Brain http://www.thebrain.com - a bit clunky and “Windowish” but somewhat innovative
Mindjet’s Mind Manager http://www.mindjet.com - expensive but this guy uses it with DT http://vimeo.com/33645437 - any success with other (cheaper) mind-mapping apps?
Qiqqa http://www.qiqqa.com - ref manager for windows on steroids and an intelligent search tool that seems to try to rival DT!
Docear - http://www.docear.org/ - Wessels reviews it



Posted by Daly de Gagne
Aug 12, 2012 at 10:39 PM


Peter, for what it’s worth, I use Mendeley, a free program, to manage my extensive PDF collection. It also stores them in the cloud, giving my backup redundancy to Carbonite and Dropbox, both of which contain my work documents.

Mendeley automatically adds any news PDFs OI have on my system, allows for tagging, etc.

A lot of material I acquire off the web. Non PDF goes into Evernote - which also stores my data in the cloud. EN is good for gathering material, but not much of an info manager apart from its tagging system. It does not even have highlighting of text, which for me is pretty basic. However, I work around it by colouring text which I would otherwise highlight.

From a writer’s perspective EN has one feature which for me is a deal maker - and that is that it allows me to have multiple open windows so I can scan docs I’m using for my writing.

I tried Scrivener for Windows but did not find it helpful.

My writing is either in EN, or in MyInfo, which provides me with columns for metadata, etc. MI also allows for multiple open windows. Unfortunately, it only allows for editing in one.

You may wish to look at a Swiss program called Citavi, which looks after references, etc, and may be one of the best of its kind.



Posted by Daly de Gagne
Aug 12, 2012 at 10:42 PM


Peter, I should add that Mendeley and Evernote will work on Mac. I am not about Citavi.



Posted by Stephen Zeoli
Aug 12, 2012 at 11:16 PM


Hi, Peter,

I can’t comment much on reference management or PDF annotating, as I don’t do much of that (I’ve been using Papers for that, but I haven’t leaned too heavily on it, so don’t want to make a recommendation).

I’m also not familiar with tagging software, so my comment may be off base. DevonThink can catalog all the documents in folders on your Mac, and you can use DT for tagging. I guess my question (for others to answer) is why do you need both tagging software AND DevonThink?

As for CircusPonies Notebook… I am not sold on that application as a great place to store lots of information. The notebook metaphor is intriguing, but it gets clumsy with a lot of information. At least that’s my experience. I also don’t think it is a very good outliner—serviceable, yes. But not the best option. My favorite outliner is Tinderbox, and it’s a great note application; however, you may not want to devote the time and effort into getting comfortable with it. If you want some insight into Tinderbox, I have a series of posts on my blog:


And a Mac Appstorm review:


If you don’t anticipate relying heavily on a complex outline, then you should be fine with the outline capabilities of Scrivener.

As for some of the other applications you mention:

TheBrain is a very nice application (but, as you observe, sort of Windows-oriented). It works fine on a Mac. It excels at organizing various pieces of information related to single topics. I think of it more as a super-charged Finder. I write about TheBrain on my blog too. I also wrote a review for MacAppstorm that you might find useful:


Curio is a nice “notebook” type of application. It is kind of a Swiss Army Knife. You can “explode” PDFs… that is, create a page for each page of a PDF and take notes relating to that page. You can build mind maps, do some basic outlining. If you like fiddling with your information, it could be a nice choice, but its very versatility is a bit of its undoing, so it doesn’t do any of those things as well as dedicated applications. I’m also not sure about how cohesive its exports are.

Anyway, I’m sure I have only added to your confusion with the above. If I were you and I were already comfortable with Scrivener, I would just get DevonThink and start using those two tools. They may be all you need.

Steve Z.


Posted by Peter
Aug 13, 2012 at 10:13 AM


Thank you for your comments. A few replies:

Daly, I will have a look at MyInfo and Citavi - thanks for the suggestions. I’ve tried both Mendeley and Evernote but a) I prefer not to work in the cloud (I think you can use both offline) but more importantly b) i just haven’t been satisfied with them. I think they’re loaded with too many bells and whistles for my taste. Zotero is really great, it just doesn’t do searchable annotation/tagging very well (at least I haven’t been able to get it working). I might try Sente now because it is a full-fledged ref manager but also incorporates OpenMeta tagging and the possibility to set up an external pdf database (both used with DevonThink for instance) http://code.google.com/p/openmeta/wiki/OpenMetaApplications

Steve, the point about tagging outside of DevonThink is that DT only searches within it’s database, not the drive(s). With a simple tagger app Spotlight (like Windows Search) can be used to narrow searches outside of DT. Tagger (and I suppose Tags) also permits Boolean searches. I guess it’s a bit like advanced googling for your computer.

Apropos Tinderbox, I’ve been reading through this forum and know it has some strong supporters;) I will check out your blog. BTW I found a great 30 min video of a researcher using Tinderbox for data analysis here: http://vimeo.com/8772338. The way he uses it reminds me more of something like Atlas.ti (which I find curious). My only concern is that it might take some heavy lifting to before I can learn it well enough. I will certainly keep it in mind. I guess it can be “programmed” to do some pretty powerful stuff but not sure it competes with DT’s more automated intelligent searching capabilities, the writing capability of Scrivener, or the slicker mind-mapping tools (many for free).

In the meantime I will explore Scrivener further, perhaps in conjunction with a mind-mapping software that uses OPML. I like to move between the more graphic and textual to keep the writing alive. That way I think I can make Scrivener work better for the more fine-grained “content outlining” - something like this: http://www.christopherspenn.com/2012/05/how-to-turn-mind-maps-into-ebooks-and-presentations-instantly/

Hopefully I’m getting things narrowed down a bit! More comments are greatly appreciated!



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