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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

 


Posted by Peter
Aug 16, 2012 at 07:21 PM

 

Steve, I forgot to thank you as well. My post was directed to you too (along with the rest of the forum). I’m on my way to check out the Scrivener forum now…

Oh and Jim, I take your point about using a single DT database with a select number of file but without indexing (at least for beginners). However part of my challenge is setting up the darn thing and locating the relevant files on my computer (and eventually an older computer that I haven’t used for while). I purchased the DevonSphere Express which searches the entire computer. However you can only select one file at a time to move! I complained to Devon and hopeful they’ll improve it to allow multiple file section (or include it in DT but I suppose that’s less likely). That way I can start building a well defined DT database.


Stephen Zeoli wrote:
>Peter wrote:
>> Thanks Steve, this is very helpful! The export feature you mention for
>Scrivener would certainly give it an advantage.
> >This Tinderbox feature was hinted
>at on the Scrivener forum (I believe). There seems to be a lot of communication and
>cooperation between the two developers, so I am hopeful this is indeed in the
>works.
> >For me, one of the biggest drawbacks of Tinderbox remains its arcane (to me,
>anyway) export functionality. I’ve even had a communication with Mark Bernstein
>(the developer) about it and he assures me it is easy, just a matter of creating some
>export templates. Still, I can’t quite get my head around it. Fortunately, it is
>pretty easy to export to plain text and I can usually make do with this. Still, a
>dedicated Scrivener export would be brilliant and make the two applications a
>perfect match.
> >Steve Z. 

 


Posted by Hugh
Aug 17, 2012 at 01:11 PM

 

Peter wrote:
> >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.

Sorry, my mistake. Tinderbox is an outliner, although far from the traditional kind. When I wrote that it could be used for “creating by jotting down random notes to see what they add up to”, I was really stressing the second half of that phrase, rather than the note-taking. Tinderbox is an application that excels in the generation, ordering and linking of ideas (that are manifested as notes). There are numerous better note-takers, in the sense of getting notes down.

What I wanted most to do was to differentiate Tbx from data managers and storers like DevonThink; some people do start off by thinking that DT and Tbx are substitutes, but when used for the purposes for which they have been designed, they are in fact complementary.


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.

Plenty of people do indeed do without. Tbx, although it has an unusual pricing model, isn’t cheap initially, and its learning curve is steep. OmniOutliner Pro is much easier to learn but isn’t cheap either. The outliner NeO, when I last looked, was very inexpensive. A less expensive outliner option I should have listed is Opal.


> >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.


Omnifocus is a yet another species of creature in the jungle. It isn’t a note-taker; it’s primarily a task manager, probably the grand-daddy of Mac task managers. Useful and powerful, but with a moderately steep learning curve. There are several cheaper, or even free alternatives, most of them on the web.

As note-takers, Notational Velocity or nvAlt remain good choices. One reason for this is that they can sync via Simplenote to other note-taking and writing apps on iPhones and iPads. Users seem to rate this functionality highly. The two applications are also free (or donation-ware, I forget).


>
>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.


As I implied above, Tbx has truly excellent data management capabilities in the sense of data manipulation, but not data management in the senses of capture, filing, storage and retrieval, which are what Devonthink is good at.


> >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.


Conceptually they are close and even overlap, but my experience of the Mac is that its user interface and the ways in which it assists interoperability between programmes encourage one to use the best tool for its role in the workflow, rather than to seek out a “Swiss-army-knife” “jack-of-all-trades” solution. That is certainly one of the assumptions behind the development of Scrivener - that one writes better if one gets the ideas and words right first, with the formatting and polishing left until later, perhaps for another application. For this reason, it exports to many formats, including those used by word processors.

Scrivener declares explicitly that it itself isn’t a word processor, in the sense of providing full formatting and layout. Most of its tools are designed to help in getting the ideas and words right, although it can format work simply, and more and more users appear to be carrying out the entire writing and formatting process within it, but mainly for purposes like e-books. The doctorate students and other academics who use it appear to value the qualities of Scrivener in the ideas/words phases of their work, but I doubt very much whether its formatting tools - it has virtually no layout features as such - are up to the requirements of finally outputting a thesis.

>
>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).


That is my experience too in writing long-form factual pieces. In fact the process is often one of moving constantly backwards and forwards between different “modes”. But that doesn’t mean that the tools you use cannot be distinct and appropriate for different processes: the Mac interface encourages this. I often have nvAlt, Devonthink, Scrivener, Tinderbox and MS Word all open on my computer at the same time. As I mentioned in another post, I believe Tinderbox will talk to Scrivener pretty well, Scrivener exports successfully to Word, and DevonThink stores all the files you put in it in their “native”, original form, so that they can be successfully retrieved whenever you need them.


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 see DT as less a “mother-brain”, and more as a “mother-bin”. I believe it happily indexes Dropbox folders.

>
>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

Hope this helps.
H

 


Posted by Alexander Deliyannis
Aug 17, 2012 at 08:53 PM

 

Peter wrote:
>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.


Like Hugh, I will agree with your conclusion that the various stages tend to overlap; in fact, I would say that the procedure is, to a significant extent, recursive. Sometime ago Dr Andus started a thread on a similar viewpoint http://www.outlinersoftware.com/topics/viewt/3906

With this in mind, I would focus on minimising the number of apps used, and not so much ensuring import/export across a broad range of tools. My experience says that one can spend innumerable hours moving material from one program to another instead of doing real work.

A few years ago I did my MBA dissertation and was initially quite concerned about getting my software setup right and tried quite a few of the tools. Fortunately, quite early in my dissertation and in a rare display of maturity, self-discipline and CRIMP control (rare, and probably the last) I decided to stick with just two programs. What those were is probably irrelevant to you as they are both Windows programs, namely Brainstorm and Surfulater. However, the reasons for my choice might contribute to your own selection:

- I chose two programs that are completely complementary; Surfulater is very good for collecting existing material and organising it with folders, tags and in arbitrary order. As a ‘mother bin’, it could be the equivalent of DevonThink in your case (though without the ‘intelligent’ features). Brainstorm, on the other hand, excels in text manipulation and is a minimally styled but powerful writing environment; its text cloning feature means that I can write and rewrite stuff, while still maintaining the link to the original reference.

- I chose programs that I was already familiar with and could use transparently in my workflow. If you are not accustomed to the tools that you intend to use, you have an additional reason to use as few tools as possible.

Just my 2c.

 


Posted by Dellu
Nov 7, 2012 at 01:40 AM

 

Hi Peter and Steve
I found your posts quite brilliant and helpful. I am also starting up my phd in linguistics, exactly in Peter’s situation. I tried almost all the apps you guys mentioned. Here are my observations so far.

1. I use Mendely for some preliminary works; to collect and rename my PDF files into a Dropbox folder. it is not the best reference manager; has a lot of flaws specially for Latex. But, the Watch Folder and Rename features are really helpful to cleanup my computer. I drop all my newly downloaded files into a dedicated folder, then Mendeley automatically sucks the papers in it, recognizes the metadata, rename and put it in another folder in dropbox. All my 2000 articles are beautifully renamed by Author-year-title format; easy to search them in Spotlight (alfred).
2. Bibdesk and Jabref are good enough for bibliography (I also don’t like Zotero), for Latex. But I use Papers for its Magic Manuscripts feature (amazing).
3. Devonthink is indispensable for its artificial intelligence; recommends related papers.
——-
4. Tinderbox is too complex. Plus, it has limited capability to import various file formats. I tried to import word files and Scrivener documents. It rips of the images in the files. It is poorly integrated with other applications, generally; seems to work best only with text files. Exporting to other format is also equally messy in Tinderbox.

5. There is one crucial feature that the Circus Ponies Notebook offers that all other note-taking applications, except Microsoft OneNote, don’t. The ability to tag (mark) points deep inside the text. When I am writing a long note, I always want some way of tagging some key points that I want to remember latter. All the note-taking tools could tag files, but never bullet points, or paragraphs. Notebook and OneNote can do that. It is called Keywords in the former and tags in the latter applications.  Notebook also has a MultiIndex system, another way of finding your crucial points using keywords. If you like tagging your specific points in your extended notes, I think, there is a reason to use Notebook. I still am not satisfied how Notebook syncs with Devonthink. But, I think there is not better note-taking app right now, unless you want to use Scrivener for everything. Here is a good article on the difference between Scrivener and Notebook, http://www.organizingcreativity.com/2012/02/outliner-in-scrivener-vs-outliner-in-cpn-structure-scrivener-vs-content-cpn-outlines/.
———
I am not still satisfied about the workflow; the sync between Devonthink and Notebook is so clumsy.

have you guys (specially Peter) developed a good workflow yet? Can you update us if you have come up with better solutions with the general workflow?

 


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