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Looking for PIM / Thesis Writing Software for the PC

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Posted by Peter
Oct 21, 2009 at 09:21 PM


No worries Edwin, and happy to hear that you find it useful.

To answer your (not dumb) question: In the process of brainstorming and catching ideas I generally open a new doc and try to stick with it. However, sometimes the ideas get too cluttered, or they branch off and start to develop into something distinctly different. That is when I like to have the experience of a clean slate. Sometimes I even create one or two quick notepad txt files because it’s so much simpler than starting up Word. Initially I save these new files on the desktop rather down in some folder under MyDocs because I’m not sure how they will all fit together or how I want to categorize them. Then, over the course of several days or sometimes weeks, I go back through these docs and ‘weed’ them and cleaning them off my desktop. Sometimes this involves cutting and pasting from several into one and then deleting the originals. Sometimes this involves collecting several doc/txt files together under a new theme and then creating a new folder with that theme’s name. Sometimes I try to put the desktop files into preexisting folders under MyDocs. Sometimes I make the new folders a subfolder of a preexisting folder under MyDoc. The upside of this workflow is the level of spontaneity it allows and the on-the-fly recording of ideas. The downside is the clutter and often disorder.

I hope this answers your (not dumb) question and good luck with your project! ;)

Edwin wrote:
>Hi Peter,
> >Your work flow descriptions are so helpful to my Word addin project! Thank
>you so much!
> >Maybe this is a dump question, but may I ask, by “creating new drafts
>every week or so and end up with loads of file versions scattered across multiple
>folders”, do you mean that it is a consequence of that fact that you have to save
>previous versions the files? Thank you.
> >—
>Writing Outliner - Word addin for


Posted by Peter
Oct 22, 2009 at 12:32 AM


Hi Dr Andus!

Thanks for your comments on work flow and I think it is a very useful discussion (although it perhaps should be broken out like the ‘aesthetics’ one). A few comments / questions…

I’m wondering if you’ve even compared Surfulater with Zotero’s ability to grab web material and turn it into bib source refs? (I think Evernote and/or Mendeley do this as well but I forget which one just now.)

Also, I’ve never used Bonsai or Whizfolder but they look like identical outliners to me. I’m curious why you start with Whizfolder and then move everything over to Bonsai. Why not just stick with one or the other?

Dr Andus wrote:

> >I’m also a PhD student, with a similar interest in designing a work flow that is
>supported by appropriate software tools…


Posted by Dr Andus
Oct 22, 2009 at 10:22 AM


>I’m wondering if you’ve even compared Surfulater with
>Zotero’s ability to grab web material and turn it into bib source refs? (I think
>Evernote and/or Mendeley do this as well but I forget which one just now.)

I’ve only just recently discovered that Zotero can take screenshots of websites, however that doesn’t want me to switch over to Zotero. For my research I need to capture hundreds of websites and organise them into categories. Sometimes I need a snapshot of the whole website, sometimes just an image or a snippet of text, and Surfulater can handle that very well. I like the fact that my websites (which for me are my primary research data) are separated from my academic references (secondary research data) in EndNote. The only thing I use Zotero for is to capture bibliographic reference off websites like Amazon, which I then transfer into EndNote. Which is not to say that I’m not impressed by Zotero, it’s just that I’ve been locked into EndNote before Zotero came about and the current set-up works for me.

>Also, I’ve
>never used Bonsai or Whizfolder but they look like identical outliners to me. I’m
>curious why you start with Whizfolder and then move everything over to Bonsai. Why not
>just stick with one or the other?

Bonsai is more focused on the task of outlining, which it does beautifully, I absolutely love it. It is excellent for constructing the overall outline of a text, as it allows you to create hierarchies, colour-code the various levels, collapse them, move them around, zoom in and out of branches. So one can construct really complex outlines and then follow them while writing. One could use Bonsai at any stage of the research process but I prefer to use it at the very end, to construct the very final clean outline, which I then use for writing the paper in Word. So I don’t move over everything from Whizfolder. Rather, I use Bonsai for extracting the clean ideas from the jungle that is stored in Whizfolder.

Whizfolder has different functionalities when it comes to outlining. The key difference is that Whizfolder allows you to develop each topic (item) within an outline into a piece of text, while there is no convenient way to do that in Bonsai (which is not a gripe, I like Bonsai’s simplicity as it is). In Bonsai, you just have the topics. Bonsai is good for creating the skeleton, while Whizfolder allows you to add the meat. I happen to use the two ‘inductively’, i.e. gather the data and analyse it by developing text in Whizfolder and then extract the outline at the end into Bonsai.

But this combination could be used ‘deductively’ as well, i.e. by developing an outline in Bonsai and then adding the meat in Whizfolder, although it would make a bit less sense, as you could probably do all of that in Whizfolder alone. As I’m doing qualitative research, the ‘inductive’ approach works for me better. While I love Whizfolder as well for what it can do (great for capturing and organising ad hoc writing snippets and quotes from PDFs and as a general conceptual database of the whole project), the content becomes pretty complex. So it helps to extract the core ideas into Bonsai, which is just so simple and it’s so quick and easy to manipulate the elements of the final outline (though I still have version 4).



Posted by Alexander Deliyannis
Oct 22, 2009 at 12:40 PM


I am at the final writing stages of my MBA dissertation and I must say that for it, like for several professional projects in the past, information management software has been worth my investment; I don’t know how I could have organised my material any other way.

That said, I started with a relatively complex setup, but in the end only the essential tools survived. Nowadays, my setup is similar but simpler than Dr Andus’:

- Surfulater for gathering all relevant information; I found most journal articles in HTML form as well as PDF, so I would usually grab the HTML and link to the PDF in my hard drive.

- Brainstorm as my writing environment; I find it indispensable, as others do GrandView, but I must say that at this size and level of complexity of texts, the lack of editable outline view becomes an issue. In any case, I have found nothing better in helping me to focus on the actual writing.

Some notes on workflow:

- I used Evernote to capture material whenever I was away from my main PC; when back, if it was relevant, it would go into Surfulater.

- I built a common outline of keywords (tags) in all three programs, which I found very useful in organising the material consistently. Maintaining this structure across the programs has been the greatest hussle.

- I did purchase an academic license for Endnote when I began my studies, but ultimately I did not use it or any other bibliography manager. I learnt Harvard referencing well and find it much more convenient to keep my references (as titles) along with the rest of the material in Surfulater and Brainstorm. Both programs can sort titles for my reference list; they also support cloning, which is great for keeping references in context in more than one places.

- I find Brainstorm’s “namesakes” (the program automatically recognises identical text entries and makes clones out of them) extremely useful to maintain flow in my writing. If something is missing while writing, I can type “citation needed” and go on writing; later I will navigate ‘sideways’ (left/right arrow jumps through namesakes) through all the “citation needed” entries. I can do the same with keywords. It’s very similar to referencing stuff in a wiki, but without the markup.

- Similarly, I find some of the smart touches of Surfulater’s latest versions very useful; e.g. highlight of titles is visible in the outline, so I can mark and quickly see what material I’ve been through.

- For some time I tried UltraRecall because it could index PDFs but found it much less convenient than Surfulater for the full range of material. PDF-Xchange is great for annotating PDFs but mostly I make the annotation in the HTML version.

That’s it form my part; I’ll post one more comment in the aesthetics thread and the go back to my writing :-)


Posted by Lucas
Oct 22, 2009 at 05:04 PM


Dr Andus,

Thanks for describing your setup. The distinction between creating the meat and creating the outline is useful. I actually find it easiest to generate text hierarchically to begin with (in a single-pane outliner like Ecco Pro, OmniOutliner, or Microsoft Word), but the resulting text often becomes unmanageable. I end up generating lots of complex hierarchies of text with various themes reiterated throughout, and ultimately it becomes extremely time-consuming to organize all the text, even though I produced it very quickly. Now that I have begun using ConnectedText, my workflow has changed. Instead of generating text in a hierarchy, I create a new “topic” for each significant idea (like in Ideamason). I can still indicate all the hierarchical relationships among my ideas using the built-in functionality for assigning topic relationships and categories (and this actually allows for richer webs of connection than a straight hierarchy does). The initial task of creating text takes longer, for me, with this method, but the overall time for a writing project becomes significantly shorter, because the text I generate is much more manageable and better organized. (And the dividends pay off even more when one is faced with a new writing project on similar themes, and it turns out half the work is already done.) The next stage with this method is very similar to what you describe doing with Bonsai, only it does not requite a separate program. ConnectedText has a built in Outline module that is designed for arranging existing topics into an outline for export (to be worked on, for instance, in a word processor). Anyway, it seems that the workflow here is somewhat similar to what you accomplish with WhizFolders and Bonsai.

So, what I am learning is that while I love the freedom of generating text in a single-pane outliner, I get better results when I am forced to separate the text I generate into discrete topics from the get-go. And this becomes even more palatable when I still have the freedom to assign complex hierarchical relationships (including bi-directional ones), as in CT. When I used outliners, I was always in search of robust “cloning”. But with a wiki like CT, I suddenly have infinite cloning. I can make any topic a parent and/or child of any other topic.



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