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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