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Academic research- what are the best tools and workflow techniques?

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Posted by Carrot
Nov 16, 2011 at 06:11 AM

 

I’m working on a PhD and have been a fan of outlining software for some time.
However, now I’m finding myself confused by
a) inefficient work flow
b) lack of proper tools

I know many contributors on this site have a lot of experience and this has been discussed many times. Sorry for not being able to add anything new.

My current workflow and tools:

Citation manager: open source ZoteroHowever, I could switch to something if necessary

Freeplane: I created a thesis outline in FreePlane and use this to guide my writing.
Also, I created an mindmap of my understanding of the religious organization that I am studying.

TreeDBnotes: I have stored my field notes, transcripts, online articles in TreeDBnotes. I began using it first and have stored too much in it to bother switching everything to myBase now.
MyBase:  I use mBase 6 for storing clippings and copies of entire webpages. I’ve recently begun using AtlasTI to code my readings, field notes and PDF articles and PDF ebooks.

But now I feel torn. If I write in TreeDB or myBase, there is no way to automatically include citations.  I would have to write in TreeDB, then export everything to LibreOffice, and then add citations manually.

LibreOffice: If I write in LibreOffice, I can include citations, but I have no tree-structure to help divide my thesis into various sub-chapters and sub-groupings.

AtlasTI: At the same time as I try to consult my notes and data in TreeDB and myBase, I use AtlasTI running to query my field notes and PDF articles to search for appropriate material.

Is there a better way to to do this? I feel that I’m using too many tools that are not integrated, and scattering my attention.
I would greatly appreciate commenents and would like to hear about how you proceed.

Thank you

C.

 


Posted by MadaboutDana
Nov 16, 2011 at 06:58 AM

 

Specific: actually, LibreOffice does have an outliner tool, just like Microsoft Word - it’s called the Navigator, and depends on similar style-based conventions to Word (i.e. use of headings, subheads etc.)

More general: your workflow sounds very similar to many other workflows discussed in the forum. Most of us use a variety of tools - like yourself, for a variety of different, although often converging/overlapping purposes. I suppose having material in both myBase and TreeDBnotes is the only major parallel “flaw” (inasmuch as one can say such a thing), but personally I think both environments are excellent, although I would not advise writing your paper in either of them. My own advice would be not to use a data-gathering tool (such as the three you’ve mentioned) to author your paper - keep the authoring activity entirely separate (either in LibreOffice or, for drafting purposes, in something completely different like The Guide, a very simple outliner which allows you to set up links to specific documents/files/URLs, but also exports entire outlines to RTF and has a very powerful search engine so you can rapidly check back through what you’ve written). While it sounds ridiculous to run so many tools in parallel, you’ll already have noticed that many of us have found such diversity to be actively stimulating!

As your paper comes together, you’ll find you’re focusing more and more on your authoring tool, at which point Zotero will become your most valuable additional resource. Once you’ve finished the outline (assuming you’re using The Guide), I suspect you’ll want to bring everything together in a word processor (LibreOffice, OpenOffice, Word, whatever). I would hesitate to give any advice as to the best time at which to start incorporating citations (I tend to do that right at the end, using the process as a kind of final audit, but others will do things completely differently!), but as far as use of data is concerned, I would suggest using some kind of “tick-box” mechanism to cross out each valuable item of data in your reference databases as you incorporate it into your paper (the most obvious method is to move notes in the outline into a separate “Dealt with” folder as you insert their contents into your paper; doesn’t mean you can’t keep cut-down copies if you’re left with a few elements that still need to be incorporated).

Those are my thoughts. Having to jump between data sources is mildly irritating, but can in itself suggest further concepts and connections. So don’t panic - enjoy your elite status as a CRIMPer!

Cheers,
Bill

 


Posted by Stephen Zeoli
Nov 16, 2011 at 11:56 AM

 

So, just in case you didn’t read my other topic about IdeaMason, I’d suggest that if you’re looking for an inexpensive, all-in-one tool for this task that you try IdeaMason:

http://www.myideamason.com

It is far from perfect, but it combines all the tools you need for source-based writing. (But definitely try it before you commit to it.)

Steve Z.

 


Posted by Pavi
Nov 16, 2011 at 01:12 PM

 

Hi Carrot,

I have made some posts regarding this. I am in Academia and use:

UltraRecall to write (with embedded word files and citations), store research, notes, PDFs and webpages, project information and files, as an “electronic lab notebook” etc.
Mendeley as a citation manager and to read PDFs

That’s really all you need! Zotero works just as well as Mendeley, and embedding citations and exporting uses the same steps. I posted about how to do this: http://www.outlinersoftware.com/topics/viewt/3338/10
and here: http://www.outlinersoftware.com/topics/viewt/3344/10

Other programs might work well, but I prefer to have my research handy and integrated. Writing Outliner is popular and handles both Zotero and Mendeley (as far as I can tell) merging and Web Research 3 is great for webpages.I guess it’s a matter of using specialized tools and excel at a single task or one tool that is very good at many.

Best, /Pavi

Carrot wrote:
> >I’m working on a PhD and have been a fan of outlining software for some time.
>However,
>now I’m finding myself confused by
>a) inefficient work flow
>b) lack of proper
>tools
> >I know many contributors on this site have a lot of experience and this has been
>discussed many times. Sorry for not being able to add anything new.
> >My current
>workflow and tools:
> >Citation manager: open source ZoteroHowever, I could switch
>to something if necessary
> >Freeplane: I created a thesis outline in FreePlane and
>use this to guide my writing.
>Also, I created an mindmap of my understanding of the
>religious organization that I am studying.
> >TreeDBnotes: I have stored my field
>notes, transcripts, online articles in TreeDBnotes. I began using it first and have
>stored too much in it to bother switching everything to myBase now.
>MyBase:  I use
>mBase 6 for storing clippings and copies of entire webpages. I’ve recently begun
>using AtlasTI to code my readings, field notes and PDF articles and PDF ebooks.
> >But
>now I feel torn. If I write in TreeDB or myBase, there is no way to automatically include
>citations.  I would have to write in TreeDB, then export everything to LibreOffice,
>and then add citations manually.
> >LibreOffice: If I write in LibreOffice, I can
>include citations, but I have no tree-structure to help divide my thesis into various
>sub-chapters and sub-groupings.
> >AtlasTI: At the same time as I try to consult my
>notes and data in TreeDB and myBase, I use AtlasTI running to query my field notes and
>PDF articles to search for appropriate material.
> >Is there a better way to to do this?
>I feel that I’m using too many tools that are not integrated, and scattering my
>attention.
>I would greatly appreciate commenents and would like to hear about how
>you proceed.
> >Thank you
> >C.
> >
> > 

 


Posted by Dr Andus
Nov 16, 2011 at 01:12 PM

 

Carrot,

I’d challenge the assumptions in your question: 1) that there are “best tools and workflow techniques” that one could just adopt one-for-one, and 2) that one single integrated tool would be better than a carefully assembled arrangement of them.

Re 1) I suppose it’s possible to copy someone else’s behaviour and setup but I doubt it would lead to the most optimal (creative etc.) outcome. I think that each writing situation requires its own particular set of tools and workflow, which need to be discovered through experimentation. Although one may eventually be able to develop some kind of a stable setup and routine (I haven’t achieved that level yet).

Re 2), I agree with Bill that there are benefits to be derived from using multiple tools. See this earlier discussion about reflexivity resulting from using multiple outliners:
http://www.outlinersoftware.com/topics/viewt/3283

I’m finding that it is difficult to predict what the writing process will be for a particular writing project, hence experimentation is needed to find the optimal set-up. With a complex writing project like a PhD dissertation, I’m finding that there are a lot more interim steps between going from analysed data to final outline than I thought. At the moment I have 3 outliners (Natara, Noteliner, and Scrivener) open (and even an Excel spreadsheet to plan word count per section) and several VUE concept maps to model not only my argument but also my workflow. I’m finding the multiplicity of tools a positive thing, as it allows me to keep refining and distilling the argument as I use the various tools as mirrors, to some extent. What is essential though is having at least two monitors (one widescreen), so at least 3 software windows can be seen simultaneously (when necessary).

I also think it’s important to separate some distinct phases of the writing project, such as overall structure planning (for which I use Storybook, Scrivener and VUE), developing a topic outline (Natara Bonsai), developing a sentence outline (Noteliner), actual writing (Scrivener), and final editing (Word). Even these can be broken down further. Trying to do all those things in one software may slow things down because opportunities for reflection and improving things in smaller bits are lost. Also, the outlining and writing process is a continuation of the research process. I used NVivo for coding but it’s in the actual writing process that I’m figuring out what is important in the end and what it is exactly that I’m saying.

To summarise, my advice is to

1) experiment with a number of software to find an optimal arrangement of several software;
2) have 2 monitors to be able to construct a reflexive process using various software;
3) separate distinct writing phases and use dedicated tools for them (e.g. I’m glad referencing in Scrivener is awkward, as it forces me to focus on the writing process first, and then I can make the references pretty in Word, after I’m finished with the writing);
4) use ad hoc tools to bridge gaps where links between software are missing (I use Excel or PowerPoint for interim steps, or even an A3 size sketch pad. E.g. I found that rather than using the report tools in NVivo to extract findings it was just easier and simpler to take some screenshots of NVivo and review them in PowerPoint);
5) model the conceptual structure and record the workflow in a concept map (e.g. VUE).

 


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