My daily readings 02/07/2012

  • Remember to study color coding

    tags: Research Note Endnote

    • I just finished the first research project I have done in years. With that being said, I tried four different ways to organize my research notes, note cards, notebooks, just writing in the margins of my books with a pencil, and typing them into MS Word. I haven’t really figured out a great system of organization, but I would love to hear some of yours.
    • If I had made a Xerox of pages from a book, I used a highlighter. If you’ve made Xeroxes of stuff, make sure you write down the source!

      Finally, don’t forget to keep a running bibliography! You can add (or delete) the books and materials you’ve used over time. Keep that separate from your paper; you’ll be printing enough out pages as it is! When you finish the paper, add the bibliography at the end.

    • I used to use notecards, but ran into problems when I needed the same notecard for different projects simultaneously. So I started using Endnote–it’s basically just a big database, but it really helps to organize all of your notes. You can use Endnote to essentially create notecards, but then you can add keywords and you can search through them, so it makes it much easier to work on multiple projects. Endnote also automatically generates footnotes and bibliographies for your papers–I find that this saves me a whole day of work on a 20-page paper. Endnote definitely has its problems, and there is other software out there that does similar things, but I have found Endnote to be a big life-saver.
    • I am currently working on my dissertation, which is by far the biggest research project I have ever had to do. I have a couple of different simultaneous organizational methods that seem to work together well. I use Endnote to record general notes on each book/article I read, and to keep track of what I need to get the next time I go to the library and what search terms I have used to find the sources I have found. In addition, I use a wiki to keep more specific notes. You can get free wikis from lots of different places, and essentially have your own tiny wikipedia. What I really like about using a wiki is that I can link pages to each other, and reorganize my notes as I go. If I were using a traditional notebook, it would be full of cross-references and revisions and would get really confusing and bulky. But with the wiki, I can link different ideas to each other, I can assign categories and tags to each page, and it’s really easy to revise my notes. I guess it’s a good indication of how habits of thinking have changed with the omnipresence of computers–my brain naturally wants links and tags, and the old notecard system just doesn’t cut it for me any more.
    • I should also add that the other great benefit of using an online wiki is that you don’t have to worry about backups: provided, of course, that you are using a reliable wiki server. It’s really nice to know that if my laptop died tomorrow, all of my research notes would still be stored safely on my wiki.
    • I’m in the very fortunate position of having a computer-wizard partner, so he has set me up with pmwiki ( He runs it off his own server, and does all the administration, so I know it’s well-cared-for and the backups are reliable. Pmwiki is pretty streamlined (as opposed to mediawiki, which can be really bulky), and incredibly customizable.

      If you or someone close to you doesn’t have the computer-savvy to run your own wiki, I did a bunch of research into wikis a long time ago and thought that and looked really good, but that was a while ago so things might have changed since then.

    • I’ve been using OneNote since work pried my hands off of InfoSelect. But a wiki is an interesting idea because there is access from anywhere — even a public PC. I think I’ll try a free stikipad account to see how it works for me. I am intrigued by your saying that you link pages — is that a common feature among wikis? I’d like to hear how you do that and if you can do it on the fly — rather than organizing things in folders etc such as OneNote does. OneNote is pretty great for web research — cut and paste and it records the URL etc so you can go back. Thanks for the suggestion.
    • I’m glad my wiki suggestion has proved so helpful! I’ve been using wikis for a year or so now for my research, and have found it to be a really useful tool.

      Scrivener’s Lot – wikis all let you make links among pages on the fly. You know how when you use wikipedia, every time an article mentions a person or a place or an important concept, it’s blue, and you can follow the link to the article on that topic? You can make your own wiki do the same sort of thing. Different wiki’s use different markup, but usually any time you put words in double-square brackets (just like touchstones on here), it makes a link to a page with that title. So then you can go create a page with that title. You can also have a more hierarchical structure if you want, or you can usually put tags or keywords on pages – there are lots and lots of ways you can organize your ideas, and you can usually have more than one organizational structure going on at once.

    • Always looking for experiments in connecting ideas
    • Like all notetaking software programs, it has some disadvantages, but I like the possibility of tagging notes, the search function, and the way that it links to websites or files from which you “clip” information in the notes.
    • I used photocopies and printouts of materials so I could highlight and make notes in margins. I always wrote all of the bibliography info for the source at the top of the first page of the material. This worked very well for me.
    • I’m working on a history PhD, with (arghh) thousands of individual notations, so my major challenge is keeping track of where the evidence comes from at the same time as collating them into subgroups.

      Something I found important was attaching sufficient reference details to the note to say months later who wrote it, even if you have a running bibliography such as Endnote. In the beginning I just used the last name and the page number, but then I discovered just how many authors out there share the name Brown, Allan, and of course Smith.

      I’m also a huge fan of colour coding. Who doesn’t get a thrill from baby pink and flourescent yellow?

    • I used Google documents a lot when I was doing my MSc dissertation (submitted last week!) and toward the end, found out about wikis here and used one to keep me on top of the fiddly little things that needed doing. Wish I had known about it earlier on in the process.
      This weekend I found out about and – both free – which look promising – they are being advertised as collaborative tools, but could be good for individual work too.
      I use Firefox which has an extension called Zotero which is great for collecting online bibliographic details. I have vague notions of one day doing a Ph.D. and am using it to keep track of useful reading.
    • For my latest research project, I took the books and wrote in the margins, underlined, made beginning-of-chapter notes, and so on.

      Then I took a cheap, yet cool, journal from the Barnes & Noble bargain racks and created a little book of sorts. I made a table of contents, an AP-style listing of my research books, numbered the pages, and started new sections to organize all of the notes as well as the project itself.

      I combined the two by taking the notes I made in my research and putting them into the journal, adding explanation and interpretation to show I could understand why these points were important / stuck out to me.

      By doing this, I had the notations within my research as they struck me in the moment, went through them again and re-examined them in the process, and collected all of the notes together in one location.

      This is how I write researched screenplays, now.

    • I just took the Zotero online tour, and it looks amazing! All I have to do now is come up with something brilliant to say about my topic.

      Is data stored locally (on your hard drive), and can it be backed up to CDs, thumb drives, etc.? Or is it stored on a network (the way gmail is)?

      I keep thinking back to the flyer I saw on my college campus back in 1992: A graduate student was offering a $500 reward to the thief who stole his laptop computer–all he wanted was to save a copy of his almost-completed dissertation to a floppy disk. We’re (hopefully) more careful now about backing up our files, but the risk of losing everything “at a shot” is the same today as it was 15 years ago.

    • I just finished another paper, and found that as useful as Zotero is for organizing quotations, I had to go back to the cue card method to actually get the ideas in order. They’re still scattered all around the apartment.
    • Needs:
      N1) organizing files and documents which cover few topics and/or are written by few authors
      N1b) organizing bookmarks (links) which also usually cover few topics
      N2) commenting files (e.g. commenting documents which I read)
      N3) making links (relation) between files/notes etc.
      N4) describing documents in some kind of bibliographic form
      N5) making some notes/todo list etc.
      N6) making some relations/connections between files, notes, web pages.
    • Up to now my research looks like this:
      – 90%: web research (google, citeseer etc):
      =saving files (articles + source codes + audio/wideo demo),
      =saving bookmarks in firefox
      =making some notes, relations in freemind.
      – 10% library/paperback research (writing some notes on paper or on mindmap)
    • I think that I need some ONE environment to organize local resources and web resources by hierarchy and tags. Something like: Zottero + files&folders linking and tagging would be the best. And then I would organize and search(!) resources in one place.
    • Diigo––has been useful for keeping research on a topic together. I especially like the ability to annotate web pages, tag and save on the web. It doesn’t, though, have the citation capabilities of Zotero.
    • I also ran across an interesting (if poorly edited) article comparing file management of mp3s and academic papers, as well as some ideas about where academic file management might be going (hopefully).
    • Can you explain “your own tiny wikipedia” and “getting free wikis”? It sounds interesting, but you have lost me completely!! I have a large, 3-section wall chart that is essentially a dateline with notes — 3000B CE-500 CE for antiquity (and teaching World Lit I & sacred texts for Humanities I); 500 CE-1660 for Brit Lit I and my comps; and 1900-present for my critics and their criticism + 20th century discoveries of ancient, classical and biblical lit. I have one set on my office walls and a bigger set the length of my hall at home. Somehow, tying books, criticism, and discoveries to historical events helps me store them in my brain longer.
    • Some more research on standalone wikis: I’ve narrowed it down to two options.

      1. Luminotes ( can be run from the server or as a standalone, which I plan to try. It depends on Python (so AFAIK there are no character îṣśüèš) and on PostgreSQL. Cross-platform. It’s distinctive in allowing you to edit a note without switching between browse and edit modes. You just start typing, as in a word processor. It lacks support for tables at present, but that seems a minor drawback. I like the simplicity, although I’d prefer not to have to click in a menu to create a link. It’s free under the GPL license. When you create a link there’s a brief preview of the linked page.

      2. VoodooPad ( is a Mac application with wiki features. Instead of HTML it uses Rich Text, and like Luminotes it allows you to edit without switching modes. Has a full-screen edit mode, or will let me edit in WriteRoom, my favorite total-immersion writing tool ( So now I’m evaluating whether VoodooPad is worth $30. For the less technically inclined, it is certainly the friendliest option. It also handles graphics much better than the others I looked at.

      One thing I’m bearing in mind is that VoodooPad is a company project while Luminotes is riding on one individual.

      There are several other wikis in various states of development. Some “personal” wikis put all their data in a single (X)HTML file, which seems likely to quickly become unwieldy. Others require lots of fiddling with a backend database, and I don’t have time for that. Strangely enough, PmWiki goes unmentioned in the charts on Wikipedia, although it seems to be one of the best options.

    • Have you heard of scientific notebook? It costs money but produces LaTeX files.

      I am using TexShop on my Mac for most math stuff. I am writing my actual thesis in a thesis template downloaded from the school. So the basic outline and formating are done by someone else and I fill it in. I am going to have to learn BibTeX.

      I have been able to export librarything to RefWorks but it took some spreadsheet conversions tricks like adding RefWorks tags by saving the librarything file as text and making new columns of the tags etc..

    • Since the thread is back…. I’ll mention that I’ve adopted Journler (Mac only; to help me gear up for comprehensive exams.

      I’ve backed away from VoodooPad because the RTF format doesn’t support footnotes — a fundamental flaw for research. Was hoping the Mac OS 10.5 update would include RTF footnote support, but no such luck.

    • I just found a really fantastic application called Papers for organizing pdf’s on your computer. One of the nicest features is that it integrates nicely with various online databases (PubMed, JSTOR, Google Scholar) to obtain metadata for your papers (automatically so, if your paper has an embedded doi). Two downsides:

      1. Mac only, and
      2. A little buggy (it’s pretty new software)

    • Response to Message 43:

      I’ve been using Papers for almost a year now. I haven’t ditched it (as I’ve done with other apps) because I really like it. The online databases are nice and you can even have it search through your library system so that you can actually obtain the pdf. It is geared more toward those in the biological sciences but it works for me as a health services researcher and a public health grad student. You can create ‘collections’ based on subject or whatever you like. There’s a student discount if you email your information. Papers isn’t a citation manager (I use Endnote for that and Reference Manager at work) but you can drag paper information into word. There is a free citation manager called Bookends (for mac only i think) but I’ve never tried it.

    • I’m working on my doctorate and I still do my notes the way I learned in high school. On notecards. One card per piece of information. And while that leads to a lot of writing and a whole lot of notecards, it makes it really easy to sort my notes. Old fashioned, yes, but it’s what works best for me.
  • tags: Note Wiki

  • tags: Note Wiki

  • tags: Startup life

  • tags: Note

    • Zim aims to bring the concept of a wiki to your desktop. Every page is saved as a text file with wiki markup. Pages can contain links to other pages, and are saved automatically. Creating a new page is as easy as linking to a non-existing page. This tool is intended to keep track of TODO lists or to serve as a personal scratch book. But it will also serve you when writing longer and more complicated documents.


       A “desktop wiki” means that we try to capture the idea of a wiki, not as a webpage but as a collection of files on your local file system that can be edited with a GUI application. The main focus is a kind of personal wiki that serves for all kind of notes: todo-lists, addresses, brainstorm ideas etc.


       But we want to go further then just a wiki filled with random content. It should also be possible to use you random notes as the basis for more structured data: articles, presentations etc. Zim will not include tools to layout a presentation or something like that, you should use your office suite of choice for that, but it should be a tool that can deliver all the content for a presentation in a form that only needs a template and some layout before usage. Therefore certain features normally not found in wikis will be added.

    • The editor allows you to organize your notes


       The ability to hyperlink pages is a powerful way of organizing content. This goes further than hyperlinks in ordinary web pages. One example of this is that zim keeps track of all links and for each page shows which pages link to it, making links bi-directional. You can also link webpages or external files, when clicked zim will open these with the appropriate applications.


       Since zim has the GUI layout resembling a note-taking application you can organize your pages hierarchically, allowing for example to group pages by topic. But because you also have wiki-style back-tracking of links you could also have a category system by using backlinks so a page can link to multiple categories.

  • tags: Education

  • tags: Book

  • tags: Creativity Consumption

  • tags: Mobile app design

  • tags: Education

  • tags: Design enterprise

Posted from Diigo. The rest of my favorite links are here.

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