How do you organize your research
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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 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.
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.
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 http://seedwiki.com/ and http://stikipad.com/ looked really good, but that was a while ago so things might have changed since then.
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.
Also, the main discussion board ("Phorum") at http://www.phinished.org/ has a lot of tips on different organizing tools and strategies.
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.
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?
This weekend I found out about http://www.bubbl.us and www.thinkature.com - 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 http://www.zotero.org/ 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.
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'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.
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'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?
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).
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: http://en.wikipedia.org/wiki/Comparison_of_wiki_farms. 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....
For those like me who want a wiki that doesn't require being online, this is another useful Wikipedia chart: http://en.wikipedia.org/wiki/Comparison_of_wiki_software
1. Luminotes (https://luminotes.com/) 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 (http://www.flyingmeat.com/) 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 (http://hogbaysoftware.com/products/writeroom). 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.
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.
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.
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 http://luminotes.com
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.
1. Mac only, and
2. A little buggy (it's pretty new software)
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.
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.
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?