How do you organize your research

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How do you organize your research

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Editado: Jun 6, 2007, 6:02am

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.

Editado: Jun 15, 2007, 7:47am

While I was doing my undergrad history research paper three years ago, I would take notes while I was reading the book and wrote down the page number that I saw the information. 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.

Jun 9, 2007, 11:04pm

I did notecards for my thesis. I kept them all in a black box, organized by chapter and then by section. It seemed to work well. I also take notes on everything I read (for my studies) in one of my notebooks. Things get copied down a couple (or a few) times, but by the time I sit down to write, I know my research really well.

Jun 10, 2007, 1:17pm

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.

Jun 16, 2007, 1:41pm

#4: 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.

After reading your post, I downloaded a personal wiki, and I've been trying it out with some light summer research. I'm really liking this so far! So glad you mentioned it. I won't be able to give it a full test until the fall, but it looks like it'll really be helpful.


Jun 17, 2007, 1:34pm

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.

Jun 18, 2007, 5:51am

I never thought of using a Wiki, but I think that could be a great way to organize my notes. Which Wiki are you using?

Jun 20, 2007, 4:38pm

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.

Jun 25, 2007, 6:29pm

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.

Jun 25, 2007, 6:37pm

Gwendydd, thanks for the wiki idea! I've been trying out pmwiki over the weekend, and it seems really promising. (Especially compared to my current 'organization' scheme for my dissertation, which principally involves a series of legal pads.)

Jun 26, 2007, 5:09pm

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.

Jun 29, 2007, 10:03pm

Thank you, Gwendydd. I learned something today. I was worried. It was getting late. For me, a project begins in chaos and I am not eager to shut the door too early, lest I leave an idea beggin. But then it's order I need. Always looking for experiments in connecting ideas, and you advice and tips and lesson will take me a long way.

Ago 12, 2007, 5:26pm

Sorry to resurrect a old thread, but I thought I'd suggest another software option: EverNote. 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.

Also, the main discussion board ("Phorum") at has a lot of tips on different organizing tools and strategies.

Ago 12, 2007, 6:06pm

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.

Ago 26, 2007, 5:15pm

I work in a lab, and I'm required to keep a logbook. I have separate binders for different types of data (western blot images or films, bar graphs, microscopy images), protocol, or product sheet for all the reagents I use. I scan the images, or keep a PDF files of manuscripts in my computer.

I also keep a very detailed Moleskine notebook for my research/literature review. I use the freeware Bookends for Mac for keeping track of citations.

Ago 27, 2007, 9:53am

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?

Set 30, 2007, 4:30pm

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.

Nov 3, 2007, 5:45pm

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.

Nov 10, 2007, 10:50am

In a pinch to get a research essay going, I abandoned my notebook, which is a haphazard collection of ideas, research, references, notes, lists and whatnot, & started throwing all the little research tidbits on the firefox extension, (as per link by byzanne in #17). I still love my notebook but I'm too tired to decode everything in my various handwriting styles...

I'm in the process of adding my scribbles as "notes", and I tag them so I can find each bit when I'm organizing the essay. This in lieu of putting notes on cue cards, the m.o. of high school research. Haven't actually tested the efficacy of this yet but it looks like it's going to work.

Nov 10, 2007, 10:54am

Zotero is AMAZING!!!!! Thanks Byzanne for the tip!

Nov 10, 2007, 11:29am

Yes, thanks for all the neat tips and links in this thread, esp. Gwendyd and Byzanne for the links to some social collaboration tools out there. I'm definitely going to check them out!

Editado: Nov 10, 2007, 12:51pm

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.

Nov 15, 2007, 1:28am

Organise? Uhh... yeah. Organise. I might try that.

Nov 17, 2007, 3:54am

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.

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Editado: Dez 16, 2007, 6:53am

I've been looking for methodology&software for organizing scientific research and research resources for few weeks. I've just started my PhD study and I need to organize my research much better.

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.

What I've used so far:
1) total commander with a lot of plugins:
- essential for maintain and organize hierarchical folder structure
- commenting files, folders (CTRL+Z)

2) Firefox with addons: I save bookmarks in hierarchical way, but few day ago I've started testing some tagging addons due to need N1b.

3) Freemind: mind-mapping to collect reaserch information, make notes, find new ideas. You can put links to web pages, files and folders, make some notes, relations between information (links between nodes).
But I notice that mind-maps are better for brain storming and finding new ideas than organizing information, because it grows to fast.

4) Few weeks ago I've started testing tagging software (tag2find, taggtool, ...). Tagging is wonderful and promising idea to describe&organize files (media, docs) because one can categorize file with multiple tags (instead of single folder name). But tagging software is still under development and there is problem with backuping/moving tags between computers.

5) I've started testing "research tools" (e.g. docsvault, askSam) but I need more time to tell something about it. Maybe somebody else use it?

6) Now I've been testing Zotero (thanks byzanne). It works as a firefox plugin. REALLY GREAT tool for needs: N1b, N3, N4, N5, N6.

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)

But doing web research that way I see that I loose connection between bookmarks (firefox), "hard disk" and notes (freemind). I sometimes put *.url of the page to the folder, but I double my work and waste a lot of time.

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.

Do you know such a tool?:)

I wonder if I should change my methodology. I feel that I save too much web resources on my disk. I made a assumption that this resource would dissapear when I will need it. But it takes me too much time to organize it (need N1).

What's your methodology to do scientific research?


Editado: Dez 15, 2007, 5:09pm 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.

Jan 16, 2008, 3:55pm

I'm really behind the curve, but I recently discoverd Zotero, and am now crazy in love with it.

I feel like Mommie Dearest: NO! MORE! LOOSE! PAPERS!

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).

Jan 21, 2008, 2:38pm

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.

Jan 21, 2008, 3:13pm

Answer to message 28:

There are companies out there that host wikis. A wiki is software that lets you (and, if you want, other people) very easily create, link, and edit webpages. It also keeps a complete record of all the changes that you (or other people) make to those webpages, so it's really easy to undo changes.

There are several companies (often known as wiki farms) that will let you start your own wiki - your own space on the internet where you can keep notes, link pages, etc. Wikipedia has a list of the companies that do this and a chart comparing their features: A couple of years ago, I did a bunch of research for some friends of mine and recommended Seed wiki or Stikipad, but that was a few years ago so I'm sure things have changed since then and there might be better options out there. But you can go sign up for a free account with the wiki farm of your choice, and start creating web pages with all your notes and thoughts and research.

Does that answer your question? If not, I'll be happy to provide some more information....

Jan 21, 2008, 10:29pm

I have been inspired by this thread to set up PmWiki on my Mac laptop. Unfortunately there are problems with creating files that are titled with non-English characters (àéîøü). It only occurs on disks with HFS+ format (i.e., most Macs), and it's because PHP (the language PmWiki is written in) does not encode its letters in Unicode but in the older ISO standard. And I see everyone's eyes glazing over, so will stop explaining the problem. ;-)

For those like me who want a wiki that doesn't require being online, this is another useful Wikipedia chart:

Jan 22, 2008, 12:57am

I was also motivated to set up a wiki on my Slackware laptop by this thread. So far, it's proven pretty useful. I used Mediawiki, so it looks exactly like Wikipedia, except I use a motivational image by Jorge Cham in place of the Wikipedia globe. It was a snap to set up. Unfortunately, it's also PHP, so wouldn't help with your problem.

Jan 22, 2008, 1:44am

I'm glad that wikis have been so helpful to people! I certainly can't imagine how I would keep all of my notes organized without mine. I also use PmWiki - it's one of the most customizable and flexible ones, although it doesn't have all the bells and whistles that Mediawiki has. I also run mine on a web server, because I like being able to access my wiki from wherever I happen to be (and I have two levels of password protection on it, so I'm not worried about security).

Jan 22, 2008, 11:47am

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.

Editado: Mar 21, 2008, 11:42pm

Wow I am going to have to read more of this thread and will try out MediaWiki tonight on my mac or my Debian machine.

I used Blogger and a blog and make DL html lists in my blog posts for books I am borrowing or reading this allows a month by month search when I need to find a citation for an idea I know came from someone else. In the DT field I have my standard citation and then I keep notes in the DD field.

I am now starting a thesis and am using RefWorks from school but also librarything, Visualbookshelf in facebook, some notes in Second Life, and learning BibTex because I am right now planning on completing a LaTeX template for my thesis. The template came from my school.

Off to try Wiki's

Oh my main tools are various pen and ink note books and printouts.

Mar 23, 2008, 11:29am

I did set up MediaWiki on my Macbook and it took about 8 hours but the instructions on the MediaWiki site worked fine.

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..

Thanks for the tips.

Mar 27, 2008, 4:10am

I'm the Luminotes developer, and I thought I'd jump in and comment on your comment on Luminotes. :)

Firstly, table support is definitely on my near-term todo list. I also wanted to point out that you don't have to click any menu or use the mouse at all to create a link.. Just hit ctrl-L. In fact, you can do most things completely with the keyboard. Just hover over the various toolbar buttons to see their key combinations. Since you originally posted this in January, Luminotes has gained several new features, so I encourage you to check it out again.

If anyone has any suggestions that would make Luminotes better for research, please feel free to contact me. See my contact info at

Mar 27, 2008, 10:42pm

dhelfman --Thank you for posting the link. MY one question would be how much pure text can one upload and link in 30 mg?

Mar 27, 2008, 11:22pm

medievalmama: If all you're entering into your wiki is plain text with no formatting, you could probably fit about 20,000 pages of text before running out of room. When you start formatting the text, such as using italics and lists, that takes a bit more room. And when you upload files into your wiki, that uses up additional room as well. Depending on the size of the files you upload, they may take many times the space of all of your wiki text.

Mar 31, 2008, 5:55pm

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.

Abr 2, 2008, 5:58pm

Just passed my specialist exams -- wish I had something for them. Now on to the "little book".

Jun 27, 2008, 4:00am

Hekpful info for novice researchers and teachers of novice researchers

Jun 27, 2008, 10:25am

Zotero is great for organizing books & articles for research projects. In addition to being FREE, it is also easy to use...kind of like

Jun 30, 2008, 10:44am

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)

Jul 13, 2008, 12:39pm

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.

Jul 13, 2008, 11:40pm

I have just finished my Masters thesis using Zotero. I only one problem and that was trying to work on two computers (home and lab) with the MS Word macro. Importing and exporting isn't what you'd really want to do with it.

In the end I didn't have a problem since I ended up working from one computer (lab) and backing up the data on my home and USB drive for safe keeping.

I highly recommend it and would use for my PhD.

Jul 30, 2008, 11:25am

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.

Jan 28, 2011, 12:06pm

Jan 28, 2011, 4:35pm

As an undergrad I did papers with note cards, as I learned in high school (1975), and Zotero. When it came time to write the note cards were the most useful. I could sort into categories then shuffle them into a rough outline. I could take notes anywhere but they had to be legible, something my handwriting is not.

Zotero solved the problem with my handwriting but it was difficult to organize even using tags extensively. The first paper, where I used note cards, had a very difficult argument to make and I don't thing I could have organized as well as I did using Zotero. Cutting and pasting made note taking very easy for any online sources and the automated harvesting of data made keeping a bibliography very simple.

The beta of the next version is available at The Center for History in the New Media and I am going to play with it before I officially become a grad student. Hopefully organizing data has been improved.

What is the learning curve like on the personal wikis and what are their pros and cons?