Horses for courses: Voodoopad, Tinderbox, Curio, Devonthink, etc

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Posted by Prion
Mar 3, 2013 at 10:34 PM

Thanks for the welcome and your replies. I think I should clarify my intention and background a little.
Yes, few tools are better than many, at least if that’s too many. With this thread I would like to encourage fellow CRIMPers with a roughly similar background to share their choice of tools and experiences. I am not new to dabbling around with tools (I should add that I am using a Mac) and trying to design workflows but each tool has a couple of strengths and weaknesses hence tools and workflows are intertwined and cannot be viewed in isolation.
One of the experiences that I have made is that the interface of a program is important to me. Sente for all its strengths (a wonderfully competent reference manager, the note taking and cloud syncing are working really well)....I found it intimidating in the long run and switched to Papers, which is less powerful but feels more balanced to me. The core functionality is there in Papers, there is little I do not use and little I am missing (with cloud syncing being the one big exception).

The tools I am using the most are in the heading of this post but I’d like to hear what you are using and how. I, too, am taking notes about my workflows. Whenever programs are concerned, I turn to a big Tinderbox document where I have stored this kind of information for a long time. Workflows about concrete projects are often stored in more or less free-form Curio documents although they can get too free-form at times for my liking. I am recently experimenting using Voodoopad for this purpose, too. It forces me to into a more linear structure and is a lot less spontaneous but that may actually be a good thing in the long run.

Tinderbox is another candidate on my list of things I am re-evaluating. I have a love and hate relationship with this program. It is uniquely powerful and when it works it is a joy but it also seduces me to waste days fiddling around with it. Its interface is often criticized for being not very Mac-like but I don’t know. I find it not very inspiring but on the other hand some UI decisions are just wonderful (linking!). On the whole, though, I am nowhere near what Steve Zeoli and others can do with this program while experiencing a lot less friction, too.

I guess, the one thing I haven’t quite decided on yet is where ultimately every piece of information is to be found in my system, the hub of my note-taking universe if you will. Right now, there are several locations I need to search, not-so-trusted systems living side by side on my computer. One way to simplify for me was to abandon taking notes about research papers inside my reference management program itself.

This post is getting too long already, I’ll stop here

Best regards
Prion

Posted by Dr Andus
Mar 3, 2013 at 11:33 PM

Prion wrote:
>I guess, the one thing I haven’t quite decided on yet is where
>ultimately every piece of information is to be found in my system, the
>hub of my note-taking universe if you will. Right now, there are several
>locations I need to search, not-so-trusted systems living side by side
>on my computer. One way to simplify for me was to abandon taking notes
>about research papers inside my reference management program itself.

I don’t use a Mac, so I can’t help on that front. But in terms of having everything (important) in one place, I think that can be achieved now, though it takes 1) the right software, 2) the right workflow, and then 3) discipline to stick with 1 & 2. In this regard I would suggest that a wiki can serve as such a system. It has two benefits for academics: 1) it can serve as your slip box (index card, Zettelkasten) for notes, quotes (basically everything essential), and 2) it can provide links to pretty much everything else that can’t be imported for whatever reason.

Also, sometimes there are good reasons not to put everything into the same database. I keep all my academic etc. notes in ConnectedText, but I keep my academic journal PDFs in EndNote. I only link to those PDFs from CT that are truly relevant. So there is a virtual filter set up (in my mind), to separate the wheat from the chaff. For the same reason, I keep webpages in Surfulater, rather than in CT. I can link directly from CT to a Surfulater item, if necessary.

My main principle though is to bring everything important into CT in text form. For this reason I don’t keep notes in my bibliographic manager (EndNote). Those notes would be important and there is not much one can do with them in EndNote, while in CT they can be linked, categorised, and found in searches. Similarly, although I read journal articles in PDF form, eventually I import selected quotes and annotations into CT. The point is to avoid duplication of effort. I found out the hard way that poor note-taking (keeping them in the PDFs or handwritten in books) results in having to do the work again…

Posted by Dr Andus
Mar 4, 2013 at 11:13 AM

I just remembered that I came across a Mac-based academic workflow here before:
http://drosophiliac.com/2012/09/an-academic-notetaking-workflow.html

For comparison, here is mine (very similar, just different tools):
http://drandus.wordpress.com/2013/01/10/academic-writing-workflow-with-connectedtext-freeplane-and-outline-4d/

Posted by Stephen Zeoli
Mar 4, 2013 at 12:31 PM

Prion,

I am not an academic, and do not do much—if anything—that would qualify as scholarship. However, I am working on a local history book that requires me to capture notes and documents (mostly PDFs) for my research. I’ve tried to keep the workflow for this fairly simple: dump all research into Devonthink. Then pull what I need, as I need it, into Scrivener as I’m writing.

I don’t have thousands of documents, so I don’t even worry much about organizing the research in Devonthink other than I may add a tag or two, and I have a separate DT database for this project.

I will take a side trip into Tinderbox if I need to think through the logic or the flow of a chapter, and I’ve created a Map view of the timeline I’m dealing with, annotated with the primary sources I want to use for each period of time. And I may use Evernote as a ferry between my devices, if I happen to find something worthwhile when I am not actually at my MacBook—which is frequently the case. If it is a document I find, I will put it in a special folder in Dropbox as the ferry to my MacBook/Devonthink.

While I have my issues with Devonthink (e.g., I hate the interface), it is the data manager I most trust on the Mac platform. I would use Yojimbo for this (because I like the cleaner interface), except that you can only have a single database, and I like keeping my projects separate.

Steve Z.

Posted by Prion
Mar 4, 2013 at 10:23 PM

Thanks for the concrete suggestions, I actually saw some of them already but noticed some new ideas upon re-reading them, thanks.

I learned that there are some things I absolutely need to keep separate.

1) Task management is not the same thing as keeping a project structure. In the list of things that need to get done I just keep the tasks with very little background information. I know what project a certain task comes from when I see the task and new tasks are generated when reviewing the current status of each project with all their data and this takes place outside my task manager.
This was quite a liberating insight for me.

2) where to store pieces of information is not my biggest problem. Like Steve Z. I use Devonthink as my data warehouse. Other software would probably work, too, as long as it provided custom URL for every piece of information I deposit there, that is crucial for me and I use these custom links a lot.
Devonthink has a lot of things going for it but their implementation of tags drives me nuts. As a scientist set theory is probably deeply engrained in my brain and DTPO has a couple of oddities that makes using their tags like walking around with grit in my shoes.

3) The kind of information that I have the biggest problem finding a good home for is not the pieces of information as such but which connections I draw between them, this is separate from gathering the information in the first place and the most personal thing in the whole process. After a lot of trial and error I am coming to the conclusion that a wiki might be the best solution for this. Tinderbox, as nice as it may be otherwise, is too content with its splendid isolation to fulfill that role (I may keep using it for other jobs, though).
I evaluated Devonthink also as a candidate for the wiki, too, but although it knows some Wiki functionality (Wikilinks) it does not display backlinks, i.e. incoming links from other pages, which is crucial for me.
Voodoopad may not be as powerful as Tinderbox in that regard (what is?) but provides backlinks as well as custom URLs, talks to Spotlight, takes graphics more gracefully and may also scale better with size than Tinderbox.

Thanks for your comments so far.
Prion

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