Sunday, April 20, 2008

Managing references 2: The search

This is part 2 on managing references. Here is part 1.

So I needed to find some software to manage my references and citations that would overcome some of the recent changes in my computing preferences. The change to MAC and my adviser's and university's preferences resulted in a switch to Office for MAC, and this made reference manager obsolete.

I searched the internet, and eventually came on a Wikipedia site that compared several reference managers. I found this very useful, because it provided a lot of information on a single webpage, allowing me to narrow it down pretty quickly.

I first made a list of managers that would work on my MAC:
1. 2Collab
2. Aigaion
3. BibDesk
4. BibSonomy
5. Bibus
6. CitULike
7. Connotea
8. Endnote
9. JabRef
10. Papers
11. RefBase
12. RefDB
13. Zotero

Moving on to the next table on the page, I realized that I wanted to be able to share my database with my adviser and colleagues. This might not be necessary but I don't like to be restricted. The boss uses EndNote, so the software needs to export to EndNote. This cut the following options from the list: 2Collab, Aigaion, BibDesk and CiteULike. The import format options did not remove any additional programs. Nine programs left.

Citation styles. In my field several different styles for in-document-citations and lists of references are used. I'm not entirely sure which one I'd like to use, but again, more options are better than less. And if my style is unavailable, being able to define my own might help. BibSonomy, Connotea, and JabRef were scrapped. Because Bibus still allows user-defined styles, it's hanging in there. Down to 6.

1. Bibus
2. Endnote
3. Papers
4. RefBase
5. RefDB
6. Zotero

Not all of the table provide useful information for the elimination process. The next one that will help me bring down the number of choices is wordprocessor integration. That is a BIG plus.

The restriction that EndNote does not work on the 64-bit versions of Windows, is of no consequence to me, there is no information on Papers, and I'm too lazy to go find that out right now. If Papers becomes a serious option, I'll have to go back and look at that. But at this point we say goodbye to RefBase and RefDB. We have the following left:

1. Bibus
2. Endnote
3. Papers (keeping this Word-integration thing in mind)
4. Zotero

The next set of tables don't change anything to this list, so we go back to the first table where the prices are listed. Price is important, but I'm willing to pay some for great functionality. And as a student, I do often get deep discounts. That is why price only now comes into play.

1. Bibus-free
2. Endnote-Academic version roughly $100
3. Papers-$24-42
4. Zotero- free

I was really interested in taking a closer look at Zotero at this point. Free sounds great, but m ore than anything, the integration in FireFox, the browser I already use anyway, sounded intriguing. Clicking on the Bibus link, I read that Bibus' functionality of MAC is limited. It should probably have been eliminated quite a while ago based on this. Bibus is out. Papers was 29 Euro, not unreasonable, if it's good I'd be happy to pay that. Endnote, being the most expensive of the options, even as a student, was eliminated. So this left me with Zotero. I'm trying it out right now, and I reserve the right to hate it, and go back to the list to choose something else. But with free you can't go too far wrong. If it doesn't work out, I can simply remove it, nothing lost but some time, right?

To be continued....


CAE said...

I've only ever used Endnote, because that's what my institutes have had and I'm too cheap to buy anything to use at home.

Don't use Endnote unless you absolutely have to. It's fine once your references are imported, but that process is maddening and time consuming. Yerch.

ScienceGirl said...

I love Papers (bought a student license last summer), but I write in latex, so I don't know how it would work for you...

Sydney said...

I'm a new grad student (yay for plant pathology, too!) and stumbled upon this, but I will definitely come back to this when I write my thesis on my Mac!

makita said...

Hi Sydney,
So far Zotero is working out ok, except that it doesn't have a definition (or one just like it) for MPMI. You can design your own, but that is more than I have time for right now.

I'm also anxiously waiting for the word plug-in for Mac Word '08. But it's working fairly well.

It does make sense to choose a program early, so you can add reference in as you read them, instead of collecting them all when you're almost done. That takes too much time away from writing.

Thanks for visiting!

n9mjg said...

I don't understand why you eliminated Aigaion. I was able to export 150 references from Aigaion into endnote with no difficulties.

makita said...

Hi n9mjg,
I had found a website that listed properties for each reference manager that listed options, and according to that Aigaion was not an option. Do you find it a good program otherwise? I've stuck to Zotero so far, and I like it, but the plugin for MS Word for MAC is still not available on the standard version, only on the versions that are being tested.
Thanks for the comment though.

Anonymous said...

There is something called Sente 5, or YEP, try them, you might like it. Especially Sente is more powerfull.