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Workflow on Mac (Mountain Lion) for PhD Thesis

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Posted by Peter
Aug 16, 2012 at 06:17 PM


Thank you both for your input. Hugh, in your first post you suggest that TBX can be used both for note-taking and analysis but then in the second post you propose that TBX is mainly for outlining/structuring so I’m a bit confused. Perhaps you could clarify a little more. I’m still trying to figure out if I can do without a dedicated outliner and only use scrivener combined with (cheap) mind-mapping app link MindNode.

I also appreciate your workflow model, however I would have to modify it somewhat (essentially flip it) to adopt it more to the “grounded” approach I use in my work. So rather than moving Structuring > Drafting > Formatting/polishing, plus Data Managing and Storage, Citing and On-the-fly Note-taking, mine looks something like this:

A: “Primary Data Management/Analysis” - in my case “qualitative” e.g. interview transcripts and field notes. Here I have something like Atlas.ti in mind however I would like to move over to a mac app and come up with a way to incorporate DT.

B: “Secondary Data and Literature Management/Analysis” (“Citing”) - including amassing references (citations) and pdfs but one could include other secondary source materials such as photos, video, audio, etc. While I think a ref manager app remains useful I also hope to get DT involved in this mode too.

C: “Notes/Annotations” (“On-the-fly Note-taking”) - usually during reading the above but also out walking, lying in bed, etc. So I find note-taking application independent (incl. pen and paper). However this eventually creates a problem when searching across-applications/computers to find connections in multiple places. We might call this the “googling inside out” problem. Notational Velocity is a nifty little app but it doesn’t address real-life practices of ubiquitous notation. This is where the issue of syncing and phones apps is particularly urgent. I’ve seen reference here to Omnifocus.
D: “Building Semantic Associations” (“Data-Management and Storage”) - which attempts to address the “googling inside out” problem noted above of searching through the hard drive. DT seems like the obvious choice here, but TBX also has Data Management capabilities as far as I understand.

E: “Outlining/Mind-Mapping (“Structuring”) - I now see roughly two options here. Either one chooses a dedicated outliner (e.g. OmniOutliner, Circus Ponies Notebook, TBX?) that includes a mind-mapper component, or or one uses the built-in outlining capabilities of a word-processor like Scrivener or Word and add a (cheap) mind-mapping app to work more visually. I’m leaning towards the latter combo but still on the fence. Thanks for the MindNode tip Hugh. I’ve used the Lite ver but might upgrade to the Pro but both incorporate OPML.

F: “Writing” + “Layout” (“Drafting” + “Formatting/polishing”) - Conceptually I think these are pretty close but I do recognize the advantage of drafting in Scrivener and exporting to a word processor, e.g. Word. One could even produce a polished layout in something like InDesign but that’s generally over the top for most journal submissions - reference to your post Jim in particular.

The key point through all of this for me is that these modes/phases tend to overlap. For instance, note-taking/annotation is done during data analysis as well as reading, building creative associations, writing (and the other way too). This suggests the need to export/import across various modes/apps (in this case note-taking) as well as “googling inside out” in the apps/computer. So I suggest the more one can integrate this process, thereby limiting the number of apps needed to work the data, the more efficient, productive and creative one can work. This is the role I hope to give DT, if not now then perhaps eventually. But for DT to play “mother-brain” then all of its “child” apps need to export/import/sync with it! Here Dropbox might be an important component as well.

I’ll check Scrivener’s forum as you suggest Hugh. Hopefully there are some keys there. I recently posted on the Zotero forum and apparently there is a plugin for dropbox: http://forums.zotero.org/discussion/16827?page=1#Item_16