Mendeley

Mendeley just ate ~2.5h of work.

Mendeley is a free (for now at least) program that aims to do much what Endnote, Zotero, and Papers do, but to do so better. It's main edge seems to be that you can outsource your reference library's metadata, and even the .pdfs themselves, to their cloud and thus carry them around from computer to computer without having to continually update lagging versions of Endnote that run on different machines. This seems like a good idea so I figured I'd try it, especially since Endnote has a very annoying habit of freezing my lab computer.

Mendeley's good ideas:
1) Keep reference metadata and .pdfs in the cloud for maximum portability.

2) Automatically parse .pdf data.

3) Parse and display all references of all .pdfs added.

4) Full text-searching and user-editable tagging.

5) Social sharing of your library, notes, and metadata with other users. This seems like it'd be really useful for grad students in the same lab, post-docs in a new lab, and collaborating prinicple investigators.

Sounds good in theory, right? Yeah! However, even for a beta, Mendeley is rather clunky and awkward.

Mendeley's awkward dance moves:
1) Syncing the reference metadata I added (tags, abstracts, notes, etc.) to the cloud completely erased everything I had added. Sure, the .pdfs are now in the cloud, which is convenient, but ALL my notes about the papers are gone like dust. So is all of the cleaning up after Good Idea #2.

2) I didn't expect this to be perfect, and I was fairly satisfied that it worked perfectly in ~15% of papers and got most of it right in 75% more. But now that I've fixed it, and then lost all of that in syncing it, I'm not eager to go back and have to do all of it again.

3) Usually works. Doesn't seem to recognize most, or any in some cases, of the references in papers where the references are formatted at 50% the font size of the text. Haven't tried adding files or notes to references yet, or clicking through to their abstracts.

4) Works, but sometimes pulls in "accepted day X, month Y, year Z" or pieces of correspondence information as well. And not all papers have keywords set aside for this kind of parsing, which the program shows as a big angry exclamation point.

5) I have yet to try this. I figured I'd give it a spin after syncing by data, but now...well, not right now.

I'll most likely give Mendeley another try sometime soon, especially if the bug of deleting corrected metadata (and yes, I remembered to save) when syncing gets fixed. It looks promising and I hope that it is able to remain free (or at least, free for beta adopters?).

At the moment, I'm just glad that I didn't rashly delete my Endnote library.

UPDATE:
I contacted Mendeley about the problem and we're working on it. Hopefully their fix will work. Also, they apparently Google themselves daily, so beware (they're watching).

UPDATE 2:
Fix worked. Now I have 2 folders, one with raw extracted .pdfs, the other with my annotated .pdfs. However, I'm not sure how I'm going to maintain them both.