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Starting a PhD Thesis (Read 28950 times)
olonoff
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Starting a PhD Thesis
Dec 9th, 2007, 4:46pm
 
Hi, my name is Neil Olonoff and I am just beginning a dissertation. (My field is knowledge management and the topic is "Creating Knowledge Management: Social Construction of a Paradigm" although here I'm only interested in issues concerning research and Tinderbox.)  

I've downloaded the demo and just ordered the product from Eastgate, and am eager to get off on the right foot, so that I don't make major mistakes at the start, and have to re-do a lot of work. Incidentally, I'm also working on a brand-new iMac, which complicates my newbie status because I'm a long time PC user who has only recently (1 month) begun using a Mac. Another story entirely!

Basically, my source materials are books and approximately 1,000 electronic research papers, mostly pdfs. I've got all the papers in one folder.

The process I envision is to use Preview and Zotero for browsing pdfs. Then copying, pasting and note-taking in Tinderbox, using one master outline for the entire thesis. Eventually, I will export to Word, and so I'll have to find the best possible HTML template which preserves my outline as well as outputting note titles, text, etc.

One of my concerns is the difficulty of going "back and forth" from a Word doc to a Tinderbox environment. Is this something I should contemplate doing only at the very end in one massive export? Of course this question is a year or two ahead!

Does anyone have experience with this type of process ... researching and composing a large document in Tinderbox and then "publishing" in a word processor? I've got Word, but is there a better word processor for the application?

Finally .... references / endnotes. Zotero can capture some, but not all of these. I haven't even looked at how this might be done in Tinderbox or how they might transfer to the word processor. Again, any suggestions on tools and output methods?

I've done enough preliminary research and reading to feel confident that Tinderbox is fully competent to the main task; creating the body of the document. But I haven't even skimmed the surface of agents and prototypes, and I suspect that at least one prototype note will be essential to my task. So I'm at the very beginning.
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« Last Edit: Dec 09th, 2007, 4:48pm by olonoff »  
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Mark Bernstein
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Re: Starting a PhD Thesis
Reply #1 - Dec 9th, 2007, 9:48pm
 
My first advice would be, simply, to not get too far ahead of yourself.  Tinderbox is designed for flexibility; it EXPECTS you to get the structure wrong the first time.  And the second time.  That's why they call in research!

The hard work here will be gathering ideas, exploring their connections, and figuring things out.  So, you want to take lots of notes, and you want to be sure that the notes are connected to the sources, and that you know how to find the source again if you need to.

Yes, in a year or 18 months, you're going to be deep into HTML export.  And cutting and pasting like crazy.  And you'll be wrestling with EndNotes or Bookends or Zotero for the references.  And, even when you're almost finished, you're going to have piles of facts that need sourcing or additional evidence.  

Some things to remember:

a) The research is the point. Don't worry more about the tools than you do about the work.  Don't waste time by failing to master your tools, but don't invest too heavily in automating everything.  Programmers say, "You ain't gonna need it": you can spend a week automating a chore that would have taken you all afternoon.

b) Keep good backups.  REALLY good backups.  Be confident that you've got three copies of all your work in three different places.  Don't skimp, and don't forget or postpone backups.  I've known people who lost dissertations and books in disk crashes, burglaries, fires.  Be fanatical.

c) Imagine how your dissertation will look.  Get the specifications early.  If you don't know anything about HTML, or you don't know how to really use Word, grab a decent book on the subject.  You don't have to read it right away: you'll know where to find it when you want it.  Same thing for _The Tinderbox Way_.

d) Start thinking early about ways and means to publish parts of your dissertation work.  Conferences, journal articles, magazine articles, Web sites.  Talk this over with your advisor.  

e) Think early about how you might want to use these notes, not just for the dissertation you're planning, but also for other publications, for conference talks, for preparing to teach this material, for your festschrift.  Be nice to your biographer and your biographer might be nice to you.

f) Ask questions.  Lots of current and former dissertation writers in the Tinderbox world!
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olonoff
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Re: Starting a PhD Thesis
Reply #2 - Dec 10th, 2007, 5:05am
 
Mark -
Thanks for the thoughtful reply. Somehow I get the idea you've been there!
Much appreciated.

Neil
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Willem Smelik
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Re: Starting a PhD Thesis
Reply #3 - Dec 10th, 2007, 1:29pm
 
Mark Bernstein wrote on Dec 9th, 2007, 9:48pm:
My first advice would be, simply, to not get too far ahead of yourself.  Tinderbox is designed for flexibility; it EXPECTS you to get the structure wrong the first time.  And the second time.  That's why they call in research!

The hard work here will be gathering ideas, exploring their connections, and figuring things out.  So, you want to take lots of notes, and you want to be sure that the notes are connected to the sources, and that you know how to find the source again if you need to.

Yes, in a year or 18 months, you're going to be deep into HTML export.  And cutting and pasting like crazy.  And you'll be wrestling with EndNotes or Bookends or Zotero for the references.  And, even when you're almost finished, you're going to have piles of facts that need sourcing or additional evidence.  

Some things to remember:

a) The research is the point. Don't worry more about the tools than you do about the work.  Don't waste time by failing to master your tools, but don't invest too heavily in automating everything.  Programmers say, "You ain't gonna need it": you can spend a week automating a chore that would have taken you all afternoon.

b) Keep good backups.  REALLY good backups.  Be confident that you've got three copies of all your work in three different places.  Don't skimp, and don't forget or postpone backups.  I've known people who lost dissertations and books in disk crashes, burglaries, fires.  Be fanatical.

c) Imagine how your dissertation will look.  Get the specifications early.  If you don't know anything about HTML, or you don't know how to really use Word, grab a decent book on the subject.  You don't have to read it right away: you'll know where to find it when you want it.  Same thing for _The Tinderbox Way_.

d) Start thinking early about ways and means to publish parts of your dissertation work.  Conferences, journal articles, magazine articles, Web sites.  Talk this over with your advisor.  

e) Think early about how you might want to use these notes, not just for the dissertation you're planning, but also for other publications, for conference talks, for preparing to teach this material, for your festschrift.  Be nice to your biographer and your biographer might be nice to you.

f) Ask questions.  Lots of current and former dissertation writers in the Tinderbox world!


I agree with all of the above—including the caution to experiment and automate too much. Been there, done that. I might add the following in reference to publishing.

These days, Tinderbox, Ulysses and TeXshop are the apps I have running constantly. I could not do without any of them. I really need to keep note-taking (Tinderbox) distinct from the actual writing project (Ulysses). The resulting workflow makes me very happy, each day again.

I do a lot of preparation in Tinderbox, but the real writing in Ulysses. Ulysses has the advantage that you can organize your writing easily in one project file, write and revise without too much distraction (including the full screen option), and afterwards export in rtf, Word, or LaTeX-format. You do not need to decide exactly how it will look like; you can always change the format later. Theoretically, in LaTeX you can even change the formatting of references automatically, but I do not use that feature, as I have a fixed set-up; I just copy and paste from the free BibDesk reference manager. I never use Word, unless someone sends me a Word file. But if I need to submit in Word-format, I still can, even without using it.
As for PDF's, I use Skim (free again) and DevonThink.

Re: Backup, consider Mozy for online backup (free up to 2 Gb and useful if your house is burgled or burnt down, as Mark suggested) and Retrospect for really reliable and incremental backups. Firewire backups are much faster in my experience than USB.

All the best

Willem



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Lew Friedland
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Re: Starting a PhD Thesis
Reply #4 - Dec 18th, 2007, 2:13pm
 
Just to add my 2 cents. I've used Tinderbox for a long time for both notetaking and writing. Also have supervised a fair number of Ph.D. dissertations, so am familiar with the entire process.

I want to second Mark's comments.  Don't get too hung up on the tools and the system. Tinderbox is a marvelous tool for unstructured notetaking, and in the beginning of the process, that's what you should be doing. It's beauty is that you don't have to worry too much about how notes are tagged, categorized, or cross referenced. Of course, the one thing you probably do want to make sure of is the source of your notes. There are a number of ways for doing this in Tinderbox. Some folks have fairly complicated systems for cross referencing Tbx notes with Bookends or Endnote. I do think it is a good idea to keep a master bibliography in one of these specific bib systems for when you really start crunching sources. But the main thing is to create a simple note format that includes a source field or fields (author, abbreviated title) and make sure that you annotate page numbers, of course. Once you have this you can just let fly on your early reading.

One simple way of doing this is to create a book prototype that has author, title, page range (whatever else, but simple is better).  Then use this book prototype for a specific source (e.g. Jones, Knowledge Management, pp. 25-30).  The "onadd" command is very handy. If you start making sub-prototypes for every source it gets unwieldy.  But if you create a note, with a command in the onadd action:  "Author=Jones; Title=Knowledge Management" and leave pages blank, every note added under that note will contain that basic bibliographic information. It's a handy way of replicating information in notes without "breeding" prototypes.

Good luck.
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Lew Friedland
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Re: Starting a PhD Thesis
Reply #5 - Dec 18th, 2007, 2:16pm
 
Sorry, one more note. Re Willem's use of Ulysses: I use Scrivener in much the same way. Either one (and there are others, but Scrivener is cheap and has a great user community) is a very good way of moving from notes to the critical phase of drafting.  I strongly recommending using one or the other.  Both export to RTF.

I also use Devonthink for PDFs, web archives, etc. Also a great user community, very robust, and reasonable.
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olonoff
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Re: Starting a PhD Thesis
Reply #6 - Dec 18th, 2007, 3:05pm
 
Lew

You wrote:
Of course, the one thing you probably do want to make sure of is the source of your notes. There are a number of ways for doing this in Tinderbox. Some folks have fairly complicated systems for cross referencing Tbx notes with Bookends or Endnote. I do think it is a good idea to keep a master bibliography in one of these specific bib systems for when you really start crunching sources. But the main thing is to create a simple note format that includes a source field or fields (author, abbreviated title) and make sure that you annotate page numbers, of course. Once you have this you can just let fly on your early reading.

I'm at work and don't have access to my iMac or Tinderbox, so going from memory. My situation is that I've got many books but also over a thousand papers in pdf or doc format. I've been experimenting with Zotero, Sente, Preview (still running Tiger) etc. I've been placing the filename in the Link field (I think I've got that right.)

But it still remains a multi application solution, like yours.

I guess I have a further question about "automating" the process of linking the pdfs and Tinderbox notes ... is there a way to use Automator to create a note from every pdf and capture the filename.  

thanks much,

Neil
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« Last Edit: Dec 18th, 2007, 3:05pm by olonoff »  
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Lew Friedland
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Re: Starting a PhD Thesis
Reply #7 - Dec 19th, 2007, 1:03pm
 
Neil,
Unfortunately, I don't do that level of automation. I do think that there is a way to do it, but someone more technically adept than me would have to tell you.  Hopefully, they'll do it in the list so then I'll know!
Btw, I do think Devonthink is a monster app for the management of large numbers of PDFs, etc. Not sure about Zotero (just don't know). But would strongly recommend DT.
Good luck,
Lew

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samuelarnold
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Re: Starting a PhD Thesis
Reply #8 - Dec 21st, 2010, 2:28am
 
we know, now a days the students have a lot of assignments to prepare. It become a burden. due to the language proficiency, they mostly depends online services to buy research papers, dissertations etc. try to write assignments your own and seek the help of an online service to correct your paper. this will help you to improve assignment writing capacity and make you confident.
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Paul Walters
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Re: Starting a PhD Thesis
Reply #9 - Dec 21st, 2010, 11:21am
 
I've been building increasingly long and complex exports from Tinderbox to HTML to Word, and would endorse Mark Bernstein's first post above:  don't export until you need to.  When the time comes, consider exporting chapters or other smaller sections of document rather than the whole thing.  The reason is that it is not easy, and quite time consuming, to go back and forth between Word and Tinderbox.  You'll gain flexibility and get more value (i.e., more time spent with Tinderbox; less time with Microsoft) if your exports are discrete and self-contained.
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mrkwr
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Re: Starting a PhD Thesis
Reply #10 - Dec 28th, 2010, 5:43pm
 
Too late for the OP I guess but a word of warning from personal experience: using file links to reference sources is not very robust because if you ever change the path to the files (e.g. the name of their folder or any enclosing folders), the file link doesn't just break it disappears so you have nothing to go on to rebuild it.  

It's easy to think you won't change the path but then a year later (say) decide to update the overall enclosing folder to reflect the new name of the dissertation or move the sources folder to a more logical place, only to find your 1000 file links have disappeared. Backups can help, obviously!

(PS: feature request, perhaps in a future version Tinderbox might retain the file name even if the link breaks so you could reconstruct the link?)
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Mark Bernstein
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Re: Starting a PhD Thesis
Reply #11 - Dec 28th, 2010, 5:45pm
 
If you have any sort of a backup, you can trivially recover the file links.  

And, of course, you should have backups!
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AaronS
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Re: Starting a PhD Thesis
Reply #12 - Dec 28th, 2010, 8:12pm
 
An interesting discussion. @MarkBernstein: Can you describe how one would go about recovering the file links with a backup? Thanks.
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Mark Bernstein
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Re: Starting a PhD Thesis
Reply #13 - Dec 28th, 2010, 9:08pm
 
I'd take a look at the XML of the tinderbox files.

Did you rename the volume? Or move the files to a new directory?
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Ella Evans
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Re: Starting a PhD Thesis
Reply #14 - Dec 14th, 2011, 2:02am
 
Good thread you have shared here.. thanks for that.. The last week i have just completed my thesis writing process with the help of online essay writing services. They helped me lot. One of the online essay writing reviews helped me finding them.  
Once again thank you for your quality post here..

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admin removed spam link
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« Last Edit: Dec 14th, 2011, 9:47am by Mark Bernstein »  
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