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Message started by mrkwr on Jun 28th, 2010, 5:59pm

Title: Using Tinderbox for a literature review
Post by mrkwr on Jun 28th, 2010, 5:59pm

I'd be interested to hear if anyone else has used Tinderbox to manage a literature review and if so could share any suggestions or tips. My current ideas are as follows:

I'm  putting a literature review together for a research project. I've so far got a bit over 110 source documents, a mixture or research articles, longer reports and web-clipped snippets (i.e. the usual stuff). The documents themselves are in DevonthinkPro.

I figured a way to export the document titles from DTP into Tbx, so this gives me a list of sources in Tbx. I may not end up using them all, so I'll put them in a "Possible sources" container to start with, and then move them into a "Sources used" contained once I've used them. (Or maybe create an attribute for this, not sure yet which would work best, see below)

I get to choose how the reference list is formatted in the final document, so by using the Author(date) convention it's easy just to sort the used sources and output as the final list. (Most of the DTP document titles are already in this format.) This also means that I don't need to do anything clever to manage the references within the text.

I then plan to write the text of the final document in "chunks" which I'll manage as one chunk per Tbx note. Each chunk (which may be one of more paragraphs) may cite one or more of the sources, so to keep track of where each statement comes from I'll do text links back to the sources. (These links don't end up in the final document, they're just to help manage the information in Tbx.)

The chunks then get rearranged into an outline structure something like this:

When I export it, the plan is to export the titles of the containers that correspond to the headings but just export the text of the notes corresponding to the chunks. That way I can use short titles for the latter to make it easier to visualise and reorganise the chunks in Tbx.

The downside is that there's nothing built in to enforce the two rules, that every source mentioned in the text should be listed at the end, and that every source listed should have at least one mention in the text. (I know I could probably do this using reference management software but I don't want to (a) buy more software and (b) have to learn how to use it at this point.) It's not very hard to do this manually using search, but if there's a relatively simple way to do this in Tbx I'd be interested to hear (e.g. each source will have a unique identified in the Author(date) combination, so perhaps each source note could have rule that said if it found itelf cited in the text and attribute was changed? but I can't see how to implement this in practice)

I'm pretty new to Tinderbox (though it's rapidly become an indispensable daily tool) so if anyone knows another way I'd really interested to hear.

Title: Re: Using Tinderbox for a literature review
Post by Jean Goodwin on Jun 28th, 2010, 7:02pm

Hi, mrkwr!  One thing that strikes me is that the "move from possible to used" activity could probably be automated.  Why not leave the sources in one place, and just click a Boolean attribute when you've used it?  That could get the source picked up by an agent, which could (e.g.) change its color, or even move it for you.

Even more elaborately, linking a source to a "chunk" could trigger the agent, which could then click the attribute, change the color, move the source....

I've done a lot of writing in Tinderbox, and the one thing I notice missing in your workflow is the extended pre-writing/brainstorming/re-arranging phase, which for me is what the application does uniquely best.  I may get several ideas from each source.  They may be pretty vague, so just trying to write them up in separate notes will take me forward.  Then how do all those notes relate to each other?  Can I begin to clump them together into proto-chunks?  That will likely lead to increase clarity about what I was trying to say, and thus re-writing of the notes.  How about cross-connections (links)?  Which comes first--which come later?  

For me, it's in this broad middle terrain between a pile of inarticulate sources and a hierarchical and logical outline that Tinderbox really shines.

Title: Re: Using Tinderbox for a literature review
Post by mrkwr on Jun 29th, 2010, 4:40am

Many thanks for the suggestion, Jean - I think your idea re automating the markup/moving of used sources is much better than mine, I will implement immediately.

I agree with you about the pre-writing phase, both about its important and the superiority of Tinderbox for this. That's kind of what I meant by "visualise and reorganise" the chunks, albeit not very articulately expressed.


Title: Re: Using Tinderbox for a literature review
Post by Mark Anderson on Jun 29th, 2010, 5:27am

Taking up Jean suggestion that linking a source to a chunk could make it 'used', here's part of the 'infrastructure' to do that.

First make a link type (Cmd+2, Link Types tab) called 'source'. If you want to use a different name adjust the code below accordingly. Now make an agent called "Mark sources" - the name doesn't actually matter but I suggest you make it a self-explanatory one. It also doesn't matter where you put the agent; being a back-of-house operation you can put it off away form your actual writing material. Give the agent this query code:


As to the action code, put whatever you need by way of telling you the note's used - different colour, different prototype, whatever.

The code above merits a little explanation as there's a degree of shorthand. The links() command returns a set.  Instead of making a set and testing if the set gets populated, here we just evaluate links(). It will be true for any note that has inbound links of link type 'source'.

To make the agent more efficient we can reduce the number of notes polled. For instance, lets assume that for each note that's a reference text chunk you've set the prototype "p_reference". Then we adapt the above to:

  $Prototype="p_reference" & links().inbound."source".$Name

Now, the agent first gets only notes using the '_reference prototype and checks their links.

Title: Re: Using Tinderbox for a literature review
Post by mrkwr on Jun 29th, 2010, 7:06am

Mark, many thanks. I knew something like this could be done but it would have taken me forever to have figured it out. I'm really struck also by the economy of Tinderbox, i.e. being able to achieve things that would be laborious in other ways with really tiny bits of code (once you know what you're doing!)

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