A question for my readers about software

I received an email question from Kevin that I’d like to open to the floor, as I’m curious about this subject myself. Can anyone recommend software to store and organize research material and notes while working on a project? I’ve heard writers rave about Scrivener, a word processing and project management tool for writers to help them keep track of ideas and research, but it is only available for Mac, so I have no personal experience with it (I use Windows).

If you’d like to share your software recommendations or describe your experiences with these types of programs, please do so in the comments to this post.

21 responses to “A question for my readers about software

  1. Although it isn’t specifically research-oriented, I’ve been very happy with Endnote so far (www.endnote.com). It clips from websites, takes text input, indexes PDFs, OCRs images, etc. And your notes are available anywhere either though the web interface or the downloaded desktop client. The search system is excellent and notes can be given as many tags as you want. There is a free and paid version, but both have the same features. When you pay you are allowed to upload more notes and get precedence for OCR.

  2. James Van Mil

    I use Microsoft OneNote 2007 for projects at work and my girlfriend uses it to plan for school (she’s a teacher). I haven’t used any other such software, but OneNote is well integrated with other Microsoft products. It also annotates content pasted from a website with the web address of the source.

  3. Celtx (http://www.celtx.com/)

    I’ve never used Scrivner, but Celtx is nice and seems like it has many of the same features. Plus its free!
    For Windows/OSX/Linux

    P.S. Lisa, I’m really liking this blog. Keep it up!

  4. Zotero (www.zotero.org). Firefox add-on and completely free.

    The video tour is great (http://www.zotero.org/videos/tour/zotero_tour.htm). It looks like 1.5 is coming out soon, which will allow you to sync with other computers.

    I tried Endnote. Zotero is Endnote++.

  5. The Web (or is it now a lower-case generic word?) has revolutionized research. Just so, word processing has revolutionized note taking and organizing. I dump everything into a single word processing file. The search function retrieves things in a blink. Word has a good outlining and tagging functions, but the great thing about word processors is that they let you do ad hoc searches without the need to guess at categories in advance.

    Your advice about not waiting to begin writing is right on the money. In the same way as writing and research are interconnected, writing and organizing are a single process. You revise your tagging and outlining categories as your work develops. I think the most useful thing about doing it this way is that you quickly spot gaps where you need to do additional research.

    If you get a separate program, the must-have function is proximity search. For years, I’ve used Zyindex, which searches even large files instantaneously and takes you directly to each hit.

    An online almanac is better than a straight Google search for lists (Vice Presidents’ wives, World Series winners) and odd, uncategorizable stuff (Roman/Julian calendar changeover), though Wikipedia has pretty much taken that over.

    Like your site.

  6. Loving this blog.

    For a forthcoming book on drug-resistant bacteria (click link in my name for more!), I am using DevonThink to organize research materials, FileMaker for timelines and contacts, EndNote for the bibliography and, umm, endnotes, OmniOutliner to maintain a materials index — and, sadly, Word to write. I want to love Scrivener, but it does not handle endnotes well, and since this is a science-y book, good cites are essential. (For fiction, screenplays etc. I hear it is brilliant.)

    DevonThink (Mac only I believe) takes almost any file type, stores it and renders it searchable. I have Web pages, pdfs, PowerPoints, RTF, plaintext, etc. etc. in it. It also has a little fuzzy AI going on that searches for similars in the whole database, plus generates a concordance for any document. Crazy, really.

  7. To date, I love Google Notebook. In the past, I really liked Backpack, and it’s still a fine solution, but I find that Notebook works better for me in my specific use cases.

  8. I’ve used Nota Bene for a very long time. It’s ideal for academic writing and editing because it formats text and citations for any style guide.

    You can keep notes on every entry in the bibliographic data base and search through all of them by key words.

    The word processor itself is as fully-featured and as powerful as Word Perfect and far better than MS Word (both of which I have also used for many years). Nota Bene handles special alphabets easily, including Hebrew and Arabic, which it prints on screen from right to left.

    There is also a very active and highly experienced userlist full of people who can give great advice about ways to use Nota Bene to help with research and writing novels, technical papers, academic papers, articles, theses and dissertations.

    I’ve tried other outlining and bibliographic software but nothing has the range of features. I wouldn’t switch to another program.

    Your blog is one I’ve thought about writing for several years. Thanks for doing this work!

  9. Aaron, thank you! I suspect that I will very soon wonder how I ever managed without Zotero.

  10. NoteTab light is useful and simple. Multiple tabs so you can have many, many documents open at the same time. Plain text.

  11. I have used Scrivener and Notebook, but I’m in a dual-OS (Mac OS & Windows) environment so I like something OS-neutral and USB-key compatible.

    Lately I’ve been using Tiddlywiki which is a single HTML file with javascript that works like a wiki (searchable, tags, etc). You interact with it through any web browser.

    There is also a Firefox extension that lets you snip webpages or sections of text and keep them in the wiki for later. And if you want to keep your wiki online, there is TiddlySpot.com

    It’s a bit of learning curve, but once you wrap your mind around it, it’s a great little tool, OS-neutral, browser-neutral, and portable.

  12. I was on leave last semester to work on a book project, so before launching into the same old routine I researched the current options for an academic research/writing work flow. In spite of my 12 years using Endnote, I decided to abandon its limited benefits and to use DevonThink as the throw-everything-in-it database and then Scrivener for the actual writing process. Scrivener has completely changed the way I write. I would recommend spending some time reading the threads on the Scrivener forums to educate yourself (not only about that program, but others as well). But the bottom line is that DevonThink is amazingly powerful, and Scrivener alone is worth the switch to Mac.

  13. For a “throw everything in it” database I use Yojimbo (http://www.barebones.com/products/Yojimbo/) — I haven’t used it for writing but I expect it could be used that way. I’ve briefly tried Scrivener but I didn’t see how it would be any better than my previous process of having two WP documents open, one with a draft and one with notes. Maybe I should give Scrivener another chance.

  14. Scrivener has been a wonderful tool for my writing. The full-screen mode is a great feature (available in many other similar programs), especially when I’m writing fiction.

    For notes, I’ve recently downloaded Evernote. It has a desktop program plus a Web site that it synchronizes to, so you can access your PDFs, pages, photos, etc. from anywhere with a connection. It’s available for Mac and Windows: http://evernote.com/
    So far, I’m quite happy with how it’s organized.

  15. The third cheer for Zotero. (Thanks, Aaron and Cheryl.) Endnote was good in its time, but with web access changing, and Firefox leading the way, no better way to handle research than with Zotero. My only concern is export for the next generation of tools.

  16. A tool I like for taking notes and organizing is freemind (http://freemind.sourceforge.net).

  17. Stef–I looked into Yojimbo. It had an attractive interface, but as the URL name suggests, it’s pretty bare bones (compared to DevonThink). You should really give Scrivener another try. The problem is that their tutorial really doesn’t give the academic writer enough of an idea for work flow. For that, I had to read a lot of threads on the forums and experiment, but I’ve ended up with a system that is helping me manage a full-length book project in ways that Word documents (no matter how many windows I open) never could.

  18. Kevin Rowney

    I’m the “Kevin” mentioned in the original post that started this conversation thread. Thanks everyone for these great suggestions, and thanks especially to Lisa for posting my question. I’ve been a FreeMind user for several years now, but with all of these great options I think its time for an upgrade.

    Again, thanks to all!


  19. Lisa,

    First, I’d like to thank you and Matt for a lovely afternoon the other day. We thoroughly enjoyed your company.

    While hanging out with you we’d been discussing “organizational software” and my brain went on hold and could not remember the software I use. It’s a product called OneNote from Microsoft (XP and Vista only I believe). OneNote is sort of Office’s bastard cousin as it doesn’t come with most of the normal office application versions, but is an office app. Onenote pages never have to be “saved” they’re updated as soon as you modify them, and the format for storing info is free-form, allowing you to combine graphics, text, written or drawn information (if you use a tablet), scanned info, web snippets, graphics, links, etc. OneNote pages can be organized into multi-dimensional folders and subgroups so you can define your own “filing system” and all info is indexed and searchable. More info can be found at http://www.microsoft.com/onenote. OneNote is a bit pricy if you’re buying it separate from office 2007 ($99 retail list price, $90 on CDW). Student licenses through colleges are way cheap as it’s included in the home/student edition of office.

    There is a try-before-you buy time limited, fully operational license version available for download if you don’t want to commit to the price without testing it. Inexplicably OneNote is included only in the rather inexpensive home and student version of office ($149 list for word, powerpoint, excel and onenote) and in the uber expensive Office ultimate suite ($680 list). I find it to be an awesome tool, and well worth looking at. I would pay the $100 for it if I didn’t already have it.

    It’s always seemed weird to me that Microsoft doesn’t include it in more versions of office and promote it as a replacement to more cumbersome storage technologies in windows like file folders of word documents, using Outlook PST files, or other organizational structures.


  20. A fourth cheer for Zotero. Really wonderful. I admit, the open-sourcey-ness means I’m ideologically predisposed to favor it, but I think there are good reasons to be optimistic about a program that can be developed by and for fellow researchers.

  21. A yet another cheer for Zotero. I have just discovered it and had dropped by to share the news. Good to see it’s already being covered and well received