This post has been updated 9 November 2013: added JabRef
Routine work should be automatized. I remember writing my master thesis using a not so legal copy of Endnot X, which had a terrible memory leak. As a result, I had to restart my computer every hour - which took about 10 minutes! I didn't smoke cigarettes, so what a waste of time... However, the best part of my thesis was probably the bibliography.
Today we get all the fun for free. You may get rid of your boxes of EndNote and Reference Manager. They're too expensive and little innovative. There are two fresh, hip reference managers that rule the scientific world nowadays: Zotero and Mendeley. There is an additional and traditional tool I use with them when doing LaTeX-work: JabRef. I discuss pro's and cons, so you should understand why I choose for Zotero. Both are excellent research tools, but the functionality sticks to managing references. There may be broader tools to manage all of your research, such as One Note or Citavi. I don't know these programs and I am not a big believer.
Zotero
This program meets your needs. It integrates seamlessly with Word 2007 and syncs its catalogue (the references) with your free account at the Zotero server. Data can be synced with the Zotero server or your
WebDAV server of choice. I use
4shared.com.
The good
- Elegantly exports to many formats, including the files in a nice way. As a consequence, you can always return on your steps and use your old reference manager.
- Neat integration in all major webbrowsers
- BibTeX can be synced using the AutoZotBib plugin and the Spartan or the RobinTan translator.
- It is open source
The bad
- Each file has its folder and folders have nonsensical names, ruling out the use of Explorer
- Interface is old fashioned, ineffective
- Automatic indexing is lagging pdf import and unintuitive to turn of
- Doesn't sync with Mendeley: you should work via RIS files that include the file path.
Mendeley
A proprietary copy of Zotero, that should sync with it, as well as with a BibTex-file, zo it could act
as a bridge between those programs. The file manager is neat, quick and accurate. I regret Zotero
doesn't sync back, so I could do part of the job in Mendeley. Mendely offers 1000 MB free cloud storage, which is nice. Prices go up after that, but for lightweight users, it may be a good deal.
The good
- It syncs with Zotero. However, for large sqlite.data files, this becomes cumbersome and slow, as the syncing is continuous.
- It natively syncs with a BibTex file, which is very good
- The interface is nice and let's you read pdfs in the left pane, while having the reference column to the left.
- You can always revert your decision, via RIS files as said before
- Search results go quite deep into the references and are neatly shown
The bad
- The browser integration is limited to a bookmarklet. This means you have to press and see whether you can import straight from the browser. If you do, you only download to your Mendeley account. Importing to your desktop program is a second step. I understand the cloud approach, but soon you'll leave free territory (considering a HD as free storage).
- A deal breaker: there is no way to sort search results! What if you want a chronological overview by author? What if you want to see what journals were published in? These are common desires!
- The thing with syncing large libraries.
- It's proprietary and they've slowed down on updates.
JabRef
JabRef is a totally different breed from the first two. It is to Mendeley/Zotero what TexMaker is to Word. You basically get a list with references, screen wide, optionally linked to fixed folder paths.
The good
- It's blazing fast to open and quick to search through.
- Your database is a text-file, there is nothing to slow it down.
- It's a bibtex file, which all software can read and what you need in LaTex.
- Put it on Dropbox, google Drive, and the like, and you are always in sync.
- You choose an appropriate bibtex key you will remember.
The bad
- It doesn't auto-catalog, manage, or rename pdf files.
- If you use several bibtex files, it is not obvious to move references from one to the other, except by export/import.
- It doesn't auto-create the bibtex keys.
- It doesn't ocr for references.
Workflow
I use Zotero and JabRef. Zotero manages my literature in the same way iTunes manages my music collection. It is useful though, to make/export a small bibtex file when you finished a paper. It's faster and it secures your references. Also, sometimes Zotero skrews up the references (say, names with multiple uppercase characters), and you can solve this in JabRef.
A few ways to make the most use of Zotero:
- Make a dump folder for new documents. I do this by quarter.
- Use three kinds of tags:
- Some generic terms: TO DO, CLASSIC, STARS
- The paper's keywords or theme
- Some nickname, or the project or institue the paper comes from
- Use the notes, but do not overinvest in this, because it is too software specific and you'll lose notes and folders one day for sure. I generally give up why I downloaded a paper or who sent it to me.
- Do not catalog other things than literature. It could replace explorer, but you'll waste your time.
- Make a folder for each project, with two subfolders: a) literature, and b) references. In references, you keep what you reference to in the paper.
- If you write several papers, make several references folders.
- Export the references folders to bibtex for survival. Polish with JabRef, and edit the bibtex files when you later pick up the work on the paper. By then, your library will have changed and will mess up your paper.
- Example of the latter: Zotero auto-assigns bibtex keys, say AuthorYearA/B/C. If more articles are imported, those will change and you'll be miserable.
Some non-workflow related hints:
- Use a cheap WebDAV server to sync. It works well, won't mess up your database like dropbox would.
- Go through the pain of setting up Firefox if you're on mac.
- Solve the Bibtex export problems.
- Spent your free time tidying up your database. It's your comparative advantage.
Online sources
