zeb
I bought PB a few weeks ago as a way of organising an unwealdy folder of pdfs of research papers - I recently started a PhD. I just love the way can now find my way around them much more easily, and can see the interconnections between the papers really well - and link each paper to a whole number of relevant thoughts really easily.

What I'm wondering is if there are any message board members who've used PB for a literature review for a PhD or other large research project who can tell me about how you've used it.
  • One of the things I am wondering about is moving from the mind map to a linear plan for the literature review. Any hints?
  • Also, what routines do people have for managing and updating the Brain alongside keeping bibliographic databases (I'm using EndNote) up to date. I'm pasting notes between the 2, which doesn't feel efficient.
Anyone have any other ideas about research projects...
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gcoulthard
Wish I had some more ideas for you, but all that I can add is that I also use PB for managing research PDFs and EndNote for bibliographic details. I have 300+ references in my main EndNote file, but found its ability to manage research notes terrible. I have also tried the following apps:

1. ConnectedText, Wikidpad, ZuluPadPro - great personal wikis, but ConnectedText doesn't have a WYSIWYG editor, Wikidpad never really made it to primetime, and ZuluPadPro is a great "notetaker" but is not great at managing the big picture

2. MyInfo, MyNotesKeeper, TreePad (and other tri-pane outliners) - great RTF editors and good at laying out hierarchical structures, but not great at linking free-form notes and seeing relationships

3. MindManager, Compendium, cMap VUE - great mindmap generators, but not great at capturing research ideas and notes on articles

4. IdeaMason, Biblioscape - like EndNote, these are good reference managers, but also try to be "composition managers" also. IdeaMason has potential, but feels like a 1.0 product (even though it is in release 3.5) and hasn't been updated in over a year. Biblioscape is quite powerful and almost made me jump from EndNote, but it doesn't manage the styles as well as EndNote.

5. WebResearcher, Surfulater - used to store notes about Websites, blog entries, PDFs, and other information

So, having said that, here is what I do:
1. Use PersonalBrain to see the "big picture" and organize hyperlinks, resources, topics, and relationships; too bad the notes feature wasn't stronger!!!
2. Use EndNote to capture bibliographic information
3. Use WebResearcher to capture Web-based data/articles/research data
4. Use MyNotesKeeper to write and manage my topics and notes and PDFs (added to each note as attachments)

What I would prefer:
1. Use PersonalBrain for the big picture and linking to disk and Web resources
2. Use IdeaMason or Biblioscape for a 1-stop shopping for references and notes

Hope that helps,
Glen

p.s. Currently PhD ABD at Purdue University (how about you?)

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mgm921
Hello,

Thanks for sharing your methods. I am just starting my doctoral coursework and purchased PB to organize citations (quotes) and notes. I am curious how you are integrating a separate note software (My Notes Keeper) into your PB.

I took another look at Biblioscape after reading your post. I hadn't looked at the software in a couple years. Many new features. I downloaded a trail to look at again. I work in APA for almost everything. Currently use EN (Endnote) for my bibliography records and paste citations into my notes for a thought (topic). I figured that would allow me to reformat the citation use the EN Cite While You Write.

Sincerely,
Michael



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gcoulthard
Just to let you know, I'm using the EndNote X2 for Windows and it's very good at integrating with Word 2007 -- which is why I'm using it over Biblioscape.

As for using PB with a notes program, I use PBs ability to hyperlink to MyInfo topics directly from my brain. So, after hierarchically laying out my paper or topics in MyInfo, I right-click a topic in the outline pane and choose "Copy Link to this Document." I can then paste that link into PB. This works well even with MyInfo closed, because the program is launched, the appropriate file is loaded, and then the relevant topic is selected. It all works very seamlessly.

Hope that helps,
Glen

p.s. Ahh..., if only I was a software programmer and could create the perfect "frankenstein" biblio-notes-brain program.

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zeb
Thanks both,

I'm not familiar with all of the programmes mentioned in your posts, but that's given me some leads and ideas about ways of working.

I suppose I had hoped someone would say 'no, you're missing a trick, here's what you have to do...', but you post are useful, nonetheless. Now we shall just have to wait for a Frankenstein programmer to read this thread!

BTW, in answer to your query, I am a few months in to a study on nascent musician entrepreneurs (Birmingham City Business School, BCU, UK) and currently at the literature reviewing stage. I shall probably be back on the boards next year asking if anyone is using PB in grounded theory analysis...

Regards, Zuleika
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Shiiko
One good resource for bringing separate information (articles, notes, etc) together and keeping them indexed within PB is a Wiki.   Here is information about how to create a Wiki. 

http://forums.thebrain.com/tool/post/thebrain/vpost?id=2015054
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pascalvenier
After using for a while a custom Filemaker database, I switched to using Devonthink, a Mac application. I have however started a couple of month ago to live in PersonalBrain and transferring all my bibliographical references in my Brain.

The protocol I follow for each bibliographical reference is the following
1. Create a thought following the following format: [Author's Surname, Year] for example [Doe, 2008], [Doe, 2008b]
2. Write the full reference in the Notes sections.
3. Copy the full reference and past it in the label section.
4. Creating a jump to a thought with the Name of the author.

I use a type for References and another for authors, with different colours, which make distinguishing references from authors faster.


@Shiito The idea of a wiki is an intriguing one which I shall seriously look into.
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mgm921
The idea of combining a outside 'hierarchical' scheme that can tie to PB's networked views is intriguing. I believe the networked view that PB presents has the best advantage for seeing novel and innovative connections. The downside is transferring the information into outline format for writing the paper(s). Of course cut-and-paste works, but is tedious. It would be nice to export the topics in outline format along with their respective notes. I have seen this mentioned in some other threads. I am also "toying" with PowerPoint slides as 'note cards' and they drag and drop into the PB notes section, but as images not editable text. <sigh>.  Another outliner, Whizfolders, pastes hyperlinks into PB and works as Glen describes with MyInfo. As an aside, I do use EN X2 with Word 2007 and enjoy the integration.

Sincerely,
Michael

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JosefBetancourt
One thing that is rarely mentioned is a different category of information organization and applicable here,  called the Concept Map.  An example is cmap at http://compendium.open.ac.uk/institute/   I guess PB is a mashup of mind mapping and concept mapping, but I think it really created its own new thing.

--- Josef





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agnor
gcoulthard wrote:

p.s. Ahh..., if only I was a software programmer and could create the perfect "frankenstein" biblio-notes-brain program.


I thought about that--really, honestly thought about that.  And then I plonked down my money for PB, because I'd rather use software than spend years writing my own

Though I am very interested in programming "around" PB (I have some threads about using Perl and whatnot) and in the PB API once it comes out (nudge nudge).
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agnor
Great thread here, everyone.

I'm not in an advanced degree program yet but have been trying for years to frankenstein different programs together.  Right now I'm experimenting with embedding wikis within PB (great for very narrow, content-reliant data) and also using Compendium and Mindmaps within PB.

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ShelleyHayduk
Now with version 4.5 you can copy your outlines into PersonalBrain and copy your Thought text "Past Outline" to past Thoughts back into a word document.  This way you can move pretty quickly between your documents concepts in your Brain.

You might want to consider creating Thought types for different types of citations or research sources not only will this help delineate and provide you with additional meta data but you can run reports on this from PersonalBrain then take your reports on certain types and export them out to word, excel etc.


Shelley
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jataylor
I love this feature.

This is one that I've been waiting for, and I knew that our friends at TheBrain would get around to incorporating it sooner or later.

Thanks!

John A. Taylor
PB Pro 6
Win XP, Win 7
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gcoulthard
Perhaps, I'm missing something from Shelley's post. When I use "Copy a thought," all I get is XML when pasted into Word or Excel. When I use "Copy as text," I just get the text from the currently selected thought. How would I "Copy as text" and get the content's of the entire branch for pasting as an outline into Word or Excel? -- Glen

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jataylor
Glen,

Press CTRL and click on your Parent thought then on the child gate (the dot at the bottom of your parent thought).

This opens the selection window.  Right click on all these highlighted thoughts and select Copy as Text Outline.

Then in your Word or Excel document select paste (CTRL-V) and you'll have your outline.

John A. Taylor
PB Pro 6
Win XP, Win 7
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