Academic research- what are the best tools and workflow techniques?
Started by Carrot
on 11/16/2011
Carrot
11/16/2011 6:11 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.
MadaboutDana
11/16/2011 6:58 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
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
Stephen Zeoli
11/16/2011 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.
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.
Pavi
11/16/2011 1:12 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.
Dr Andus
11/16/2011 1:12 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).
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).
Carrot
11/16/2011 3:42 pm
Thanks for your replies.
Everyone?s comments and suggestions are very helpful and encouraging. I had not really thought about the advantages of having information duplicated to some degree. It seems that Bill raised a good point. - it encourages reflective thinking about the data.
In fact, the applications themselves have forced me to conceptualize my data in a certain way. For example, Freeplane mindmapping provided me with a good way to map out the belief system of the religious group that I am studying. I was even able take my laptop with me to the villages, and show my informants the ways I had categorized their beliefs, and ask them if my categories made sense or not.
I?m not sure how I would have done that with another tool like a tree-structure outliner. I don?t think it would work as well.
Pavi, thanks for your reply. I will look at your suggestion for using Zotero and UltraRecall. I wish I?d bought UltraRecall right at the beginning. It seems immensely flexible. I?m wondering if myBase can be substituted or if its too simple a tool. It seems very good at captureing webpages (includes access date and URL) TreeDBnotes is very nice, but it lacks a web-clipping tool and so this cripples its usefulness to some degree.
Dr. Andus, thank you for encouraging me to rethink my assumptions that there is a ?best tool? and ?best method?. Of course in hindsight I see that every project is different. But its very helpful to hear about the the methods used by others. No need to re-invent a well-established process.
The process you are using sounds quite similar to mine in fact. You are using VUE to model your arguments and workflow, while I am using Freeplane for those purposes. (I?d thought about VUE or Compendium, but found Freeplane easier to figure out). And I?m using 2 outliners, and AtlasTI for coding.
And I?m using a huge widescreen monitor as well, and always have open 2 outliners, AtlasTI, LibreOffice and Freeplane. I'll mull over about everyone's advice again and let it seep in :)
Thank you all very much for the discussions and suggestions here!
Everyone?s comments and suggestions are very helpful and encouraging. I had not really thought about the advantages of having information duplicated to some degree. It seems that Bill raised a good point. - it encourages reflective thinking about the data.
In fact, the applications themselves have forced me to conceptualize my data in a certain way. For example, Freeplane mindmapping provided me with a good way to map out the belief system of the religious group that I am studying. I was even able take my laptop with me to the villages, and show my informants the ways I had categorized their beliefs, and ask them if my categories made sense or not.
I?m not sure how I would have done that with another tool like a tree-structure outliner. I don?t think it would work as well.
Pavi, thanks for your reply. I will look at your suggestion for using Zotero and UltraRecall. I wish I?d bought UltraRecall right at the beginning. It seems immensely flexible. I?m wondering if myBase can be substituted or if its too simple a tool. It seems very good at captureing webpages (includes access date and URL) TreeDBnotes is very nice, but it lacks a web-clipping tool and so this cripples its usefulness to some degree.
Dr. Andus, thank you for encouraging me to rethink my assumptions that there is a ?best tool? and ?best method?. Of course in hindsight I see that every project is different. But its very helpful to hear about the the methods used by others. No need to re-invent a well-established process.
The process you are using sounds quite similar to mine in fact. You are using VUE to model your arguments and workflow, while I am using Freeplane for those purposes. (I?d thought about VUE or Compendium, but found Freeplane easier to figure out). And I?m using 2 outliners, and AtlasTI for coding.
And I?m using a huge widescreen monitor as well, and always have open 2 outliners, AtlasTI, LibreOffice and Freeplane. I'll mull over about everyone's advice again and let it seep in :)
Thank you all very much for the discussions and suggestions here!
Pavi
11/16/2011 3:59 pm
Hi Carrot,
I am also a more recent convert to Ultra Recall, and wish I had adopted it sooner. I was using Mybase and EPim, and previously testing many, many others including treebdnotes. UR can replace mybase and treedbnotes, although some features are not there (like password vault, but of course you can make your own). It is powerful, flexible, and can be used for many purposes.
It seems you already have a Mybase license - I am not sure if it can embed word files and export in a merged format as UR does (per my post in another thread). Also, customization using attributes and forms make UR customizable, and I am not sure about how to get this functionality in Mybase. However, these features might not be needed for your academic work. I have forms for things such as: article submission, passwords, account logins, doctors visits, correspondence, etc. as I use UR for personal, professional, GTD, research (with logical links back to the relevant folder in professional) and e-mail archives.
Basically, whatever setup you are comfortable with will work, but it might make you more efficient (minus the learning curve) to choose tools that suit your thinking processes and workflow better.
Best, /Pavi
Carrot wrote:
Pavi, thanks for your
reply. I will look at your suggestion for using Zotero and UltraRecall. I wish I?d
bought UltraRecall right at the beginning. It seems immensely flexible. I?m
wondering if myBase can be substituted or if its too simple a tool. It seems very good at
captureing webpages (includes access date and URL) TreeDBnotes is very nice, but it
lacks a web-clipping tool and so this cripples its usefulness to some degree.