Software for Academic Research

This is kind of an odd question, but I figure it goes better in this forum than anywhere else.

I am attempting to get more organized in assembling my Prospectus (and in the future my doctoral dissertation), and am finding that my current methods of organizing the large amounts of papers and sources are insufficient.

Are there any free or cheap solutions that would let me create a pseudo-database of papers, connect them by topic and other categories, and would let me attach my own notes to them? By database of papers, I dont mean the papers would be in it, I would simply need the abstracts and my notes, and I can organize the papers in my files alphabetically by author.

I was thinking of just making my own simply database in access to handle this, but I thought I would see if anyone has come across software that can do the sorting and connecting for me (and has potentially other interesting features).

Microsoft OneNote 2007, maybe? Ask someone to demo it to you, so you can see what it does. I recommend this only because of its freeform organization structure, and that you can paste gifs/word doc/excel spreadsheets on a OneNote page, and put your own notes right beside it.

If you’re using a Mac, you might try Papers ( It has a very nice interface for running literature searches (including saved searches), associating the results with pdfs (which can be tagged into collections), and providing space for notes and star ratings. Once they’re downloaded the pdf contents become fully searchable, so if you type in your own name you’ll see where you’ve been cited. You can even label individual authors as “competitors”, “colleagues”, etc - and there’s a pane that’s dedicated to keeping track of what they’ve been up to lately. Clearly they understand what academia is all about …

It’s not free, but there is a substantial educational discount. I don’t know of any comparable program for Windows, unfortunately. Before getting a Mac I would use Endnote for this purpose, but it’s much more expensive and much less convenient.

I’d suggest Endnote ( because it’s widely used, there are often massive databases available for it already at various institutions, the citation indices that I use usually allow you to download papers / searches in Endnote format, and it is available in both Mac and PC flavours. It’s fairly expensive normally, but if you’re doing a thesis at an academic institution then you can get an academic / educational discount and it costs peanuts.

There’s also Papyrus ( which I used for my PhD. It’s free, but DOS-based and a bit clunky (still works fine in XP, not sure about Vista) but if you can work around the kinks it’s just fine.

I’ve been using EndNote since I started graduate school, and it’s been a fantastic tool. There’s no way I can remember everything I’ve read, but EndNote lets you run freeform searches on whatever information you’ve bothered to enter on a given article or other reference. It also plays nice with Word, so I haven’t formatted a bibliography in years. It was, without a doubt, the best $100 I spent on grad school-related supplies. The automatic bibliography formatting alone was worth the price. There’s a demo at

I’ve been messing with OneNote for organizing my dissertation notes, and it’s a lot more effective than the mix of Word docs, Outlook tasks, and post-its that I used before. If you have an .edu email address, it’s only $60 as part of Microsoft’s promotion that lasts until later this month.

Neither is free or that cheap, but they’re both worth it.

EndNote. Get the student edition, which goes for about $100.

  • Alan

Man up. LaTeX + BibTeX.

I used Endnote for my dissertation as well.

It’s very wise to get organized early. By the time I started writing I had eight binders full of photocopied papers thanks to a budget that allowed for an undergraduate assistant and a copy card. Trying to sort all that out at the last minute would have driven me batty.

Make one of your grad students do it…

Oh, wait.

Never mind.

You aren’t the first to recommend it. I use LaTeX for all my presentations (I love Beamer), but I havent taken the time to learn BibTeX.

Which strengthens the “be organized early” argument since this is, in fact, the first thing that pops into your prof’s mind whenever something tedious needs doing.

Very rewarding to get the 5 pm prof lab drop-in “hey, did you see Y’s work on X?” and you can look on the computer and respond “yup, he basically found Z. I have the paper in my office, I’ll have undergrad make you a copy.”

I don’t know how it compares with Endnote, but I use The Journal for most of my writing-based projects in a way similar to what is described in this article. The application plays very nicely with Word. My instance is installed on a thumb drive. For stuff with more extensive references, I tend to manage the bibliographic items in separate categories and entries and link to them as needed from the other content. This is probably the one piece of software I could not live without.

I’ll second (third?) EndNote; I used it for my doctorate. Great stuff.

I used NoodleTools for a while, and it was OK. Their product looks a lot more feature-filled since I last looked at it.

[quote=Wader;1305859]You aren’t the first to recommend it. I use LaTeX for all my presentations (I love Beamer), but I havent taken the time to learn BibTeX.[/quote

BibTeX is not hard at all. Also, depending on your area, you can probably get references in BibTeX format in the same place you get a paper.

And, Beamer is love.

BibTeX is one of the only two reasons I can think of for using LaTeX in the first place, the other being complex math typesetting.

Also, if you are affiliated with a university, EndNote can be a free download from their IT department. No need to pay $100.

Which in an Economics program is a necessity

BibTeX is good for creating a bibliography, but I don’t think it is quite the right tool if you want to organize your notes on a huge number of papers, which you can then search nicely by keyword.

When I got MY Ph.D., I just chucked the clay cuneiform tablets in a pile and had my slaves sort through them before going down to the river to draw my water for the day.