Software Bleg

So. I’m thinking of seriously rebooting my rather shambolic note-taking, research and organizing practices, and I want to think consciously for a bit about what kinds of software or IT solutions out there fit my habits as well as some of my new aspirations best.

The first criteria for me really has to be forward-compatibility, relatively mainstream and well-supported products. I’ve got a bunch of dissertation notes that I took in a custom-created Hypercard database, so let’s just say I learned a hard lesson about not venturing off the pathway too much.

What I’m really looking for is:

1. The best way for me to keep a record of research materials consulted during research that can then be exported as citations in a variety of publication formats while also keeping very clear when and where I consulted these materials.

2. The best way for me to keep tightly connected notes on those materials where I can link to the citation record but can also keep notes of varying length and detail, including direct quotations with page numbers where it is clear to me that those notes are quotations.

3. The best way for me to keep a record of books, articles and other materials I’ve read which are not directly connected to research, with some kind of searchable tagging system that correspond to some of the subject categories I have in my own head. This isn’t important for a specific research project, because everything I’m looking at there, even speculatively, is by definition connected to that project. But when I’m reading more broadly, or in my field of specialization, I do want to have some way to tag or mark my thinking about where this resource fits in my own head (is it good for a course? helps me thinking about a problem I’m concerned with? links distantly to a research project?).

4. The best way for me to take notes connected to this more speculative kind of reading. This is where I’m a bit frustrated right now. I just don’t take these kinds of notes any longer, but I used to. I have a filing cabinet full of articles I read in the late 1980s with no searchable index, just tabs on files, and notebooks full of thoughts about these articles which I’m sure I will never put into electronic form. If I’m going to start taking these kinds of notes again, I want them to last and be useful.

5. The best way to log incoming work like requests for recommendations, connected to a calendar or schedule.

6. The best digital “to-do” list, linked to a calendar. I want room both for ongoing reminders that need to be checked off each day (“write a hour a day on X project”) and specific projects or meetings that have deadlines.

This entry was posted in Academia, Information Technology and Information Literacy. Bookmark the permalink.

17 Responses to Software Bleg

  1. whoganRI says:

    I’ve waged a long — mostly fruitless — battle toward finding the right tools for these kinds of problems. I’d be very curious to hear what you finally settle on. I use OmniFocus (Mac only) for the ‘to do’ parts of your requirements, which links with iCal. That combination has been very functional and easy to maintain and use for the year I’ve been using it.

    The notetaking issue (esp for speculative reading) poses the more interesting dilemma, I think. The problem for me has always been ‘how to keep ideas and information I come across during speculative reading accessible to my mind when I’m writing?’ My favorite scholarship invariably impresses me for its wide-ranging reference — I always wonder: how does this scholar store all that stuff about subject x in her mind and think to make note of it when she’s writing about subject y?’

    Anyway, in my own work as an English professor, I’ve tried End Note, which made citation easier, but didn’t solve the information storage/accessibility problems… actually, the best solution I’ve tried is a fairly low-tech one: I keep a ‘readings.doc’ file in MS Word: each semester, or season, I start a new one. I keep notes about anything I read, on any subject, in these big files. The notes I take in these files are searchable and I use the document map feature to see author/title info quickly. The virtue of keeping big, multi-subject readings files is that it preserves the possibility of drawing (and perceiving) linkages between a book I read, say, on Irish history, and one I might read on print culture in the early 20C, or popular music in the 1920s.

    When it comes time for writing, I scan through the last few seasons (or years) of these readings files and try to recall anything that might touch on my current writing subject — if I find something, I print that part out and start unwieldy notes files in good ol manila folders for that particular writing project.

    For the ‘keeping quotations and your own reactions to them separate’ problem, I just put quotations from my reading text in bold and write my response to that quotation in regular face type.

    Boy, I’d love to hear how other scholars solve these perennial problems. I know there’s no ‘holy grail’ tool out there, but I’m sure there are better ideas than the ones I’m currently using.

  2. k8 says:

    I use EndNote. The newer versions allow for more storage (say, of pdfs, images, articles, etc. It allows tagging. I use some archival sources (I’m in comp/rhet with a focus on print culture and literacy) and I have plenty of room to take notes about the sources/authors of my documents or where I found them, etc. EndNote is easy to use with Word, which for me is a huge plus. Because I’m in an interdisciplinary field, it really helps out when I need to switch citation styles. It has an initial learning curve, but once you get it, it is fairly simple.

    One thing that helps when tagging or creating subject terms is to keep a master file of the terms you’ve used and be consistent. My MLS is showing here, but it is just a matter of cataloging materials in a way that is consistent and accessible.

    I also keep large notes and citations in reading/research files in Word. As long as I insert citations as I take notes, there is no problem whatsoever in terms of keeping it separate from other text. I might format it it differently to distinguish it from my own writing, but that is rarely necessary.

    As for calendars – I can’t point to one and say it’s the best, because I’ve only used a few of these. I’ve had good luck with google’s online calendar/organizer. I just don’t use it that much because I like to have written lists/post its/etc. out in front of me on my desk.

    I won’t go into my complex system of physical files that are color coded within each sub-category.

  3. librarygrrrl says:

    Zotero sounds like it might be a nice fit for items 1-4 on your list. Features include: create multiple collections of items, tag items, items have “date added” and “date modified” fields, attachments are part and parcel of each item, there is an extensive note-taking and annotation function, you can take snapshots of web pages for offline consultation and marking up, etc. etc. It also has citation creation features and EndNote-like Word and Open Office plugins. Future versions will allow for synchronization across machines. Needless to say, I’m a fan. It’s from the folks at the Center for New Media and History –

    I’ve also heard interesting things about EverNote but haven’t tried it myself. I don’t think it has the citation capabilities you’re looking for, though.

    I use Google Calendar for logging requests and “stuff I need to get done by X date”, as well as to manage my personal outside-of-work life (involves a lot of hockey games for some reason…)

    For to-do lists, I still struggle. Remember the Milk is one that I’ve tried that integrates quite well with Google Calendar and GMail.

  4. Do you use a Macintosh? If so, I highly recommend OmniFocus for #6. It’s worth every penny, even though it’s a version 1.0 product. (1.1 will come out soon.) I was an alpha tester, but I have no other connection to the company.

    For #1 and #3, I use Bookends, which is a competitor to EndNote. It has fewer features and it’s Mac-only, but the developer (one guy) is generally quite responsive to users’ feedback. And he fixes bugs without expecting you to pay for an upgrade.

    For #2 and #4, I have tried several solutions. I’m currently using DEVONthink Pro Office. At present one can’t link directly to a document in DevonThink, but that functionality will come with version 2. DevonThink can accept hyperlinks to a Bookends reference, so I can link notes to the reference that way.

    As far as distinguishing direct quotations, paraphrases, and my own thoughts, I use a technique that I learned from Constantin Fasolt at the U. of Chicago when I started grad school. I carefully mark notes as reading notes or as thoughts. For reading notes, I always use the following protocol: Anything in quotation marks is a direct quotation. Anything in square brackets is my own comment or reaction, unless it is inside a direct quotation, in which case it’s an interpolation. Anything else is paraphrase or summary. It’s a low-tech method but it has served me very well. With a modern text parser the stuff in square brackets could be automatically highlighted, but I prefer to use highlighting in rich text documents as a way to call attention to important points.

    One big plus of DevonThink Pro is its artificial intelligence: it can suggest documents in your database that resemble the current document, and it can also suggest where to file a document based on an analysis of its contents. It’s not perfect but it does help me draw connections with things I have noted before, making it more likely I will return to them.

    And sometimes, I’ll just skim over my old notes.

    A final thought: I recently got a Fujitsu ScanSnap scanner, and I have been scanning my old notes on paper and saving them with descriptive filenames and tags. It’s amazingly fast, and it makes it much more likely that I’ll use the notes. Perhaps when handwriting recognition gets reliable, I can even convert them to searchable text.

  5. Oops, forgot to mention that OmniFocus is great for #5 as well. It has a quick entry window, and you can also set it up to process incoming emails that contain tasks, so if you’re away from your computer, you can email yourself a task. Some people use Jott so they can create a voice note that gets emailed to OmniFocus and turned into a task. There’s also an iPhone version.

  6. Timothy Burke says:

    Yeah, actually in a way, I’m not so worried about distinguishing things as quotations, as I’m insanely careful about that in my note-taking. I just want something where the note-taking portion isn’t so constrained that it keeps me from using my own very meticulous conventions.

  7. Laura says:

    I’m going to vote with Zotero myself. Not only is it a simple plugin for Firefox, but it allows you to store copies of the files you save. You can save files from the library databases, from web sites, from Amazon, from YouTube, etc. They’re beta-testing a server-based version too. You can tag stuff, save it into folders, add notes and more.

    For the speculative reading, Devon think works well. I don’t use it myself, but I’ve heard really good things about it and have always wanted to try. I’ve been using for some of this, but it has obvious limitations.

    For calendar/reminder tools–I use Remember the Milk. There’s a gmail plugin that’s great. I can have my list up right next to my email. You can set due dates and have it emailed to you and sent to your cell phone. Another good option is Airset, which I used for a while, but might be better suited to your needs.

  8. Timothy Burke says:

    Zotero seems great to me for citation storage, but I’m worried about its links to note-taking, which is critical for me when I’m doing research AND when I’m reading speculatively or to catch up in my fields.

  9. Rob MacD says:

    The thing that makes these conversations fun is the same thing that makes them inconclusive: this stuff is so personal and what makes a program click or not click is so subjective, it’s hard to predict what anyone else will or won’t like. Case in point: Zotero. In theory, I should love it. I respect the philosophy behind it, I know half the guys who wrote it, and I’ve got a huge grudge against Endnote for its catastrophic failure in the last days of my dissertation. But tiny little things – the size of the text boxes, the fact you have to click twice to move from one field to the next – create just enough friction that I can’t make it my home environment.

    So, with the caveat that all this stuff is idiosyncratic and personal:

    For 1 and 2, I use Endnote. The Notes fields in Endnote are plenty long and flexible enough for any kind of notetaking you might want to do. I do not use the features that let Endnote slurp bibliographic data off library sites – the intentionality of deciding “yes, this is part of my current research project” and typing the bibliographic data in is a necessary part of my process.

    For 3 and 4, and every other kind of note taking, I use Info Select. Info Select is a weird program with an ugly interface and a lot of unnecessary googaws, but at its heart it applies the Gmail philosophy – “search, don’t organize” to notetaking of all types. The great thing about Info Select is its blazingly fast full text search, which, like Google, renders redundant a lot of the organizing and tagging and foldering you might do. So if I read something cool or have an idea or get a business card or find a recipe or hear a funny limerick or anything I might ever want to remember again, I just type it into Info Select and include in the text itself a few plausible tags by which I might remember it later. No muss no fuss – it feels like just writing something on a scrap of paper and shoving it in a huge drawer – except that at any future date I can just type “limerick” or “recipe” or “cool” or “Timothy Burke” and every relevant scrap of paper is instantly returned to me. It also has a tickler feature, so I can tag a note to make itself scarce and then come back and wave itself in my face at a given future date and time. In the long run, this is the only paradigm that I can see working for me. I don’t want to have to devise some system of tagging or organization now that has to cover every possible query or project I might take on 10 years from now.

    For the To Do list part of 5 and 6 I use MyLifeOrganized, a great and highly customizable To Do list program that has the added virtue of playing very nicely with GTD, even the demented half-ass version of GTD that I practice.

  10. I’ve been made redundant by librarygrrrl. Zotero and remember the milk were my rec’s. I cannot begin to tell you how dependent I have become on zotero. I don’t know that I’d be able to recommend anything that approached your notetaking requirements without knowing more about how you take notes, since you seem to indicate that you are very specific and idiosyncratic on this front.

  11. k8 says:

    I have heard good things about zotero – I meant to mention that before. I probably would have checked into it if it had come out sooner. By the time it was available, my dissertation research and I were already pretty invested in EndNote. I had actually considered making my own database in Access or Filemaker Pro until I realized that EndNote could handle the notes and types of searches that I wanted to do. I do, however, keep an Access file to keep track of people I need to remember to acknowledge when the time comes, along with a note about the help/service they provided.

    But, we all are idiosyncratic when it comes to research. Zotero is free, so it is easy to check out. There should be a free 30-day trial version of EndNote that you can download. A lot of these programs have free trial periods, so it might help to just play around with them and see if they do what you need for them to do.

  12. Timothy Burke says:

    In my last research project, I used FileMaker Pro to create two databases. One of “materials consulted” that had full citational data, the other “notes”. The thing I liked about the notes database was that I could spawn an infinite number of short notes linked to one citation where each note was a discrete record. When I’ve worked with EndNote, it seemed to me that I couldn’t do that–create multiple pure “note” entries or store a large number of discrete notes linked to a single citational entry.

  13. Rob MacD says:

    That’s correct – the Endnote paradigm is one note or entry per source. You can create discrete notes of the kind you describe with Zotero, but the interface for finding and interacting with them is not elegant.

    Here’s where personal idiosyncracies come in: I can’t imagine why I’d ever want to divide their notes up into infinite discrete entries.

  14. Timothy Burke says:

    Yeah, it’s not necessary. It’s just a convention I got used to early in my work, where each entry was a discrete thought, quote or comment on a particular source material as I read through it, as opposed to a single long, continuing block of text containing all the comments and quotes from that source.

  15. I’ll throw my weight solidly behind Zotero, at least for numbers 1-4. I acknowledge that its citation management is a bit more advanced than its note-taking abilities (which, as Rob MacD noted, is not elegant), but you can tailor the note-taking to your needs and customs. It’s easy to assign any tag you create to both individual notes and sources, so you can easily categorize discrete entries/comments. And of course you can use the search function to quickly scan through tags, sources, notes, etc. The documentation and support is very good, and the team at CHNM is constantly upgrading and improving the software, which updates automatically. I’ve used Zotero for everything from my entire senior thesis to my current application process for grad schools (ie. capturing faculty member pages, program requirements, etc.).

  16. elnjensen says:


    Thanks for raising this interesting set of questions. I’ve wrestled with this as well, and am still trying to find the system that works for me. Regarding your first few items, I’m not much, as the needs for citation/quotation management in the sciences are pretty different from your needs.

    For the others, I use two programs mentioned already: Evernote and Omnifocus. I use Evernote for generalized note-taking of all sorts – books I want to read, web pages I want to read later but not have to track down, links to papers I need to read for my research, and just general note-taking. For the latter, I like the fact that I can drag in images – say if I just made a plot or looked at a spectrum and want to note something about it. I also grab figures out of papers I’m reading (most of which are electronic now, so this is easy) and then have them there close to my notes. My main wish here is that I wish the editor were a little more full-featured, e.g. it has basic text styling (bold, italics) but no simple way to add hyperlinks (though saved web pages have active links). Seems like it shares a lot with Zotero though it doesn’t have citation management (it’s not an academic tool per se); you can, however, create your own arbitrary set of tags and apply multiple tags to any item. And it does have syncing to a central server, as well as off-line availability of notes. This is crucial for me these days – I’m tired of trying to keep things in sync among multiple computers; I want it just to happen automatically. (This is why I find it well worth it to pay Apple for a .Mac [now MobileMe] subscription to keep my calendar/address book/to-dos in sync among various machines.) One interesting feature is that it does text recognition in any images you save in your notes, and that becomes searchable too. So far this is more gee-whiz than actually useful for my own needs, but it could be of use at some point.

    For task/calendar management, I’ve been using OmniFocus and like it pretty well. After you learn a few keystrokes you can integrate it pretty tightly with Mail and iCal – a message comes in that has something you’ll need to deal with, hit a few keys, enter some tags into a pop-up, and you’ve got it archived with a due date set for later reference. The latest version also syncs among multiple computers.

    I’ll be interested to hear what you decide to try out.


  17. Interesting further comments. I have avoided Zotero because I am very reluctant to rely on a browser plugin for a major scholarly research tool, for two reasons. First, Firefox does not play well with Macintosh services, since it is not a Cocoa application. Second, if an operating system upgrade makes the browser or its plugin architecture incompatible, what happens to my data? Bookends, Journler, and DevonThink all allow exports to standard document types; I wasn’t able to find out from the Zotero website whether it could also export data to other formats. (The FAQ has a brief entry on exporting, but it does not mention whether exports are only to Zotero’s format or to other formats too.)

Comments are closed.