Friday, August 27, 2010

Paper managing software

Endnote has pissed me off for the last time (I hope)! Now that I have a really large library, it is difficult to find things in it. I sometimes have formatting issues, and it can be annoying to add something to the library. Basically, the software is layer on layer of new stuff on old, and it is just not working for me anymore. Now that I am finishing up an old collaboration (where we used to send each other drafts with Endnote libraries), I am taking this chance to try something else.

Lots of people recommended Papers to me (since I have an old Mac in my office), but I find I am using the Mac less and less (since my lab instrumentation is all Windows based, and I like to look at the raw data occasionally). It looks like I will probably start hooking my PC subnotebook up to my big monitor. So I want at least a cross-platform solution.

I decided to try out Mendeley, and I like it so far. I let it grab my paper data out of the pdf files, which took a little while. Once set up, I found that while most of the details it grabbed were correct, I do need to look at entries before using them. Rather than wasting time fixing stuff, I am fixing entries as I use them. There is a tool to look papers up by title in Google Scholar if the data grabbed from the pdf is incorrect, and that is pretty handy.

I am not used to using anything but Adobe to read pdfs, but the ability to add notes to my papers (and highlight text) seems like it could be pretty handy. It is also possible to share annotated papers, which I may eventually do with my group. I signed up for the Web account, but I don't know if I will use it. For now, I just want something that can insert references properly into my manuscripts (I am not a LaTeX person) and search through my library of pdfs.

I'll post a more extensive review after I use Mendeley for the manuscript I started yesterday. Anyone else have paper/reference management software suggestions?


sciedgrrl said...

i heart zotero for managing references. i used it for my dissertation with open office and it was essentially a breeze (other than the part where i had to write a dissertation).

just today i found out about pdf-xchange viewer which is free software for annotating pdfs. i'm hoping to try it out for paperless grading purposes this semester.

Venkat said...

I have used just EndNote so far for all my papers. Whenever something happens that I don't expect/comprehend, I assume its because *I* don't know EndNote well enough. So haven't got pissed off enough to think of switching :]

Professor in Training said...

Self-confessed MacFreak. EndNote for writing. Papers for reading.

Female Computer Scientist said...
This comment has been removed by the author.
Female Computer Scientist said...

After having tried many different reference management software packages, I have a deep and profound love for Mendeley. I love it so much I would pay them money to use the service if they started charging.

I run the desktop app on my work and home computers, and just drag pdf files into it. I have a "read me later" folder, a "cite me in XYZ manuscript" folder, etc. I just drag and drop and deal with it later.

Last I heard Mendeley is working on supporting dropbox and also the iPad soon, which means even more super love from me. :). Right now they have an iPhone app, which means I can keep my entire pdf library always in my pocket. This is a really cool feature.

Zotero is also pretty fantastic, and plays very nicely with Mendeley, so you can always use both.

GamesWithWords said...

Keep us informed on how well Mendeley works for citations. I similarly hate Endnote and have never used it for managing PDFs (I like Papers). I tried switching to Zotero for a while for citations, but the best I can say about it is it doesn't really work (that's nicer than "doesn't work at all"). Problems include the fact that if you have the same author listed on different papers with a full name on one (Noam Chomsky) and an initial on the other (N. Chomsky), it'll insist on writing out the entire name on every citation -- even if only one of those papers is actually cited in the manuscript you're writing. Endnote doesn't have the problem.

So I found that it took more time to fix Zotero citations than to simply do everything by hand. But I got tired of doing things by hand and went back to Endnote. I keep my Endnote library in Dropbox and have no problem using it from my different computers.

prodigal academic said...

Thanks for the comments, everyone.

I used to be a MacHead, so I kind of wish I could use Papers, but I really need PCs (some of my core instruments are still on WinXP!)

FCS I hope I am as happy with Mendeley as you are! So far, no weird glitches, but I am writing up the results and experimental first, so not much citing going on.

GWW, I will definitely post a more extensive review in a few weeks after I've finished my draft and sent it to my fellow authors (in case they have issues using the citations as generated).