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Looking for PIM / Thesis Writing Software for the PC

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Posted by Manfred
Oct 20, 2009 at 12:10 PM


if the keyboard is bad, don’t use it. If the Interface is bad, don’t use the application either. But perhaps there is a difference between how something feels and how something really is. Even if a tool does not at first “feel” right, it is not necessarily bad. It maybe you (or me) that is the to blame, not the tool.

In other words, sometimes you need to change the tool and sometimes you need to change yourself. The latter is harder, I know. But this fact does not mean that it might not be worth it.

Life’s full of choices like that. Far be it from me to suggest that everyone should follow my example. It’s just that a do have a definite view on some things (including on the usefulness and functionality of ConnectedText), which you might (or might not) want to take into consideration. 


Posted by Cassius
Oct 20, 2009 at 03:46 PM


Gee, when I did my Ph.D. dissertation (mathematics) there was no software to use.  I did 99% of my research while lying in bed until 4am each night.  I also typed most of the draft in bed using an Olivetti light-weight typewriter with two exchangeable keys (for the math symbols).  I guess I’d do the same today, but with a light-weight laptop in place of the Olivetti.


Posted by Manfred
Oct 20, 2009 at 05:23 PM



As I said: “What does aesthetics have to do with researching and writing? When I wrote my dissertation I really wanted an IBM Selectric, but not because it was available in different (attractive) colors, but because its correction system was better than anything else available.”

P.S.: Perhaps there should be a thread on the “Aesthetics of Outliners and Pims


Posted by Dr Andus
Oct 20, 2009 at 11:33 PM



I’m also a PhD student, with a similar interest in designing a work flow that is supported by appropriate software tools. Unfortunately I’m still far from a fully integrated and streamlined work flow and each time I try, I do it slightly differently. However, so far I have assembled the following tools to support this process:

- EndNote to store and categorise references and link to PDFs;
- Adobe Acrobat and now PDF-Xchange Viewer (thanks guys!) for annotating PDFs;
- Surfulater for capturing website content and organising it into categories;
- Atlas.ti to analyse data (I haven’t got to that stage yet);
- Whizfolder for organising ideas and reading notes into hierarchical categories, capturing snippets from PDFs (using the excellent “Watching Clipboard” function), linking to PDFs and any other file with research data, and any ad hoc writing and outlining;
- CmapTools for quick conceptual mapping;
- Natara Bonsai for developing hierarchical outlines to be used for writing the final draft (building on material captured and organised in Whizfolder and the conceptual maps in CmapTools);
- MS Word for writing.

Out of all of these, I am really happy with and couldn’t or wouldn’t want to live without Surfulater, Whizfolder, CmapTools and Bonsai. I’m hoping that Whizfolder will become the nerve centre of the entire dissertation, although I haven’t fully utilised it yet, as I’m only just moving into the data analysis stage of my PhD. Still, for some unexplainable reason, I find working with Whizfolder strangely satisfying…

I’ve tried out too many mindmapping, notetaking and wiki tools to remember them all. The above are what I ended up with after 3 years of searching and experimentation. I have to say I’m not very patient, so if a software doesn’t immediately make sense, I quickly move on. I’m intrigued for instance by Ultra Recall but I just couldn’t figure out what it’s really for and how I could use it as part of the research process.

Anyway, I’d be also interested to hear about how others map their qualitative research analysis and writing processes.



Posted by Edwin Yip
Oct 21, 2009 at 02:34 PM


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 writers.


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