Citation Software Recommendations?

[iLikeTrees]

I discovered that the citation software I had in my undergrad had a 2-year license and expired as I'm in the final stages of my MS thesis writing. (booo!) I had Sente (I got it for free) but wasn't super-impressed, so I'm wondering what other grads out there use and recommend. I don't really know what's available and the one I've heard about most is Endnote & I've heard mixed things about that.

I'm doing my writing on a Mac and I'm in a science field, so recommendations that suit those two specifications would be great. Thanks!

[hellopsy]

I discovered that the citation software I had in my undergrad had a 2-year license and expired as I'm in the final stages of my MS thesis writing. (booo!) I had Sente (I got it for free) but wasn't super-impressed, so I'm wondering what other grads out there use and recommend. I don't really know what's available and the one I've heard about most is Endnote & I've heard mixed things about that.

I'm doing my writing on a Mac and I'm in a science field, so recommendations that suit those two specifications would be great. Thanks!

I like www.zotero.org/ -- it's free, supports tagging and resides in the browser (one click to download and it can also save webpages easily). You need Firefox though, so if you're using Safari on your

Mac you'll have to switch.

[timuralp]

For making bibtex entries, citeulike.org is cool. If you write your papers in latex, the bibtex entries are awesome. Also, check out bibdesk. My friend using OS X loves it. And finally, wiki has all the answers: http://en.wikipedia.org/wiki/Comparison_of_reference_management_software but you must choose... wisely.

[Jae B.]

I also use Zotero, after a friend recommended it to me. So far, so good. I use it on Flock, which is a browser based off Firefox. I also make use of the syncing and online library, but I can just export or copy my citations into a file and use Dropbox to access them anywhere -- I'm trying to avoid buying extra storage space.

But I have come to terms with the fact that, no matter what, making formal citations is always going to be a drag. I love the simple citing in journalism: "According to...." "...said."

Edited April 18, 2010 by Jae B.

[aginath]

EndNote was constantly making Word 2008 on my Mac crash. Since I never bothered to use it, I uninstalled it. At the recommendation of an old undergrad friend who just finished up his PhD, I looked into Zotero. LOVE.IT. Seriously. I can tag all of my references so that they can be cross-used and I can create lists that are specific to one project. The bibliography export is quite nice, too.

[aginath]

Speaking of Zotero...

http://www.zotero.org/blog/standalone-zotero/

Standalone Zotero

Posted April 15th, 2010 by Sean

We’re excited to reveal that the Zotero project has begun preliminary development of a standalone version of the research software that will interact with browsers other than Firefox. Code has already been committed to Zotero’s open-source repository that provides a glimpse of how this new version might work. This proof of concept is allowing our developers to study how best to integrate Zotero with other popular browsers like Google Chrome and Microsoft Internet Explorer. Of course, Firefox is still an excellent web browser, and we’re confident that it will remain so for years to come. That said, we also want to provide the Zotero community with the opportunity to use other software when they choose to do so, or when they face institutional barriers to using Firefox.

[Genomic Repairman]

Bite the bullet and get EndNote X3. I run Office 08 and Snow Leopard and everything works fine. The program is great and if your PI has an endnote library you can copy it to yours. Besides you usually get student discounts.

[Strangefox]

I would like to talk some more about Zotero.

I've read these two posts about it from ProfHacker:

http://chronicle.com/blogPost/ProfHacker-101-Getting-sta/22829/

http://chronicle.com/blogPost/ProfHacker-101-Getting-sta/22845/

And I am finally going to try it out. One thing that interests me a lot: how does backup work there?

The second post says: "When you enter your Zotero credentials in the preferences pane (1), you make it possible to make your library and notes visible to others (if you wish) and to sync them across multiple computers (so you always have a backup!)."

Backup is an essential thing bor me. I don't want to spend lots of time building my Zotero database and then use it because of a stupid glitch. So I would like to know if Zotero's backup is efficient.

[rising_star]

I haven't had any problems with Zotero syncing between my computers, so I assume that means the backup works. It does have to be connected to the internet to sync (obviously). If you edit a reference on multiple computers, you'll have to select which version to retain when you sync.

[Strangefox]

I haven't had any problems with Zotero syncing between my computers, so I assume that means the backup works. It does have to be connected to the internet to sync (obviously). If you edit a reference on multiple computers, you'll have to select which version to retain when you sync.

Thank you!

Another question. The ProfHacker post says: "For syncing files in your own library (2) you can use Zotero File Storage (currently limited to 100MB), or a storage service that supports WebDAV. (Since my library contains a lot of files, I’ve opted for the latter.)"

I think I would prefer the second option, too. But I have never heard of this WebDAV storage. What sites have it, which would you recommend to use?? I wonder if I can use GoogleDocs with Zotero - I have enough storage space there.

EDIT: BTW, I found info about backups: http://www.zotero.or...ort/zotero_data

Edited July 25, 2011 by Strangefox

[MoJingly]

I just downloaded Mendeley, and after messing around for a few minutes, I feel like it's going to really simplify my life. I really like its interface. I read about it on the "What software do you find indispensable" thread.

[Strangefox]

As for me I have been "messing around" with Zotero all day long today I really like it. I've read about Mendeley too but I decided to start with Zotero. I think its functions are more important for me now. I am glad that I found out how to back up files (not only by syncing them, but also by copying storage directory to another storage device. So now I can be sure that my carefully accumulated database won't be lost all of a sudden.

I really liked Zotero and I liked organizing my references - PDF articles and Amazon links of books. I have not explored all options yet but those that I have figured out all seem extremely helpful.

[newms]

I just downloaded Mendeley, and after messing around for a few minutes, I feel like it's going to really simplify my life. I really like its interface. I read about it on the "What software do you find indispensable" thread.

Yeah, I think I'm going to be using Mendeley as well. Zotero and Mendeley are both free but the additional storage seems cheaper with Mendeley, and more people in my field seem to use Mendeley than Zotero.

[Strangefox]

Yeah, I think I'm going to be using Mendeley as well. Zotero and Mendeley are both free but the additional storage seems cheaper with Mendeley, and more people in my field seem to use Mendeley than Zotero.

And what are Mendeley's primary functions? For some reason (something I've read) I believe that I don't need Mendeley now, but may be I'm wrong...

[newms]

And what are Mendeley's primary functions? For some reason (something I've read) I believe that I don't need Mendeley now, but may be I'm wrong...

Mendeley and Zotero seem to do pretty much the same thing - reference management, just that Zotero seems to be Firefox based (they're developing a stand-alone app as well as integration with other browsers) while Mendeley has a stand alone application. They both have online storage that allows you to sych with 'the cloud' for access on multiple devices, but Zotero's free plan has 100MB while Mendeley's free plan has 1GB. Mendeley has a comparison chart of reference management software here, but keep in mind that they wouldn't be impartial. Wikipedia has a comparison of reference managers, including Mendeley and Zotero, here.

[Eigen]

Bite the bullet and get EndNote X3. I run Office 08 and Snow Leopard and everything works fine. The program is great and if your PI has an endnote library you can copy it to yours. Besides you usually get student discounts.

I'm going to second this, except I'd recommend X5 as opposed to X3 (updated for this year).

Endnote seems to be by far the most widely used and robust reference manager- it has a good web-access component, gives you web-space to backup your full texts attached to their respective references, and gives a wealth of customization options.

Citations are easy to download, and easy to edit- you can simply write new citation styles and reference styles in addition to the thousands that are already out there- most journals even provide "endnote" reference styles for use with their submissions (at least in the fields I'm familiar with).

The newest version (X5) even supports viewing/editing/annotating PDF documents within the program, so you don't have to use anything else to manage your references.

While I'm not directly recommending it, the other program that is relatively frequently used (along with Mendeley and Zotero) is Refworks. There's also Scrivener and Papers for macs, iirc.

[Strangefox]

I'm going to second this, except I'd recommend X5 as opposed to X3 (updated for this year).

And if, say, I am using EndNote X3 and I want update it to X5 - do I have to pay for that or it's only this one sum (around $100, you wrote earler) that I pay when I buy any version that is out there, and then all updates are free?..

[Strangefox]

Mendeley and Zotero seem to do pretty much the same thing - reference management, just that Zotero seems to be Firefox based (they're developing a stand-alone app as well as integration with other browsers) while Mendeley has a stand alone application. They both have online storage that allows you to sych with 'the cloud' for access on multiple devices, but Zotero's free plan has 100MB while Mendeley's free plan has 1GB. Mendeley has a comparison chart of reference management software here, but keep in mind that they wouldn't be impartial. Wikipedia has a comparison of reference managers, including Mendeley and Zotero, here.

Thanks a lot for the links!

BTW, can you download reference info from websites (like Amaron) with Mendeley? Zotero has this feature and I think it's great.

One more BTW: I've just had a quick look through "What software do you find indespensable" thread and a couple of people wrote that Mendeley had crushed soon after they had installed it. So be sure to back up your annotations.

Edited July 26, 2011 by Strangefox

[Strangefox]

People using Zotero, tell me:

Do you use their storage plans that are for purchase? Or do you use WebDAV storage sites?

[Strangefox]

One thing that worries me: when I choose a reference software (be it Zotero, Mendeley or Endnote) and start building my reference database, that probably means that it would be very difficult to switch from one of them to another down the road, right? I won't be able to transfer references - I will have to start anew! That's a disturbing thought A lot depends on my choice!

UPDATE: "I will note that the “Import from Zotero” feature worked seamlessly; I seeded my Mendeley account with all of my Zotero data so I would have something to work with as I worked through the tool. Given the syncing abilities, it would be possible (and not terribly difficult or time consuming) to, say, work with Zotero as your primary tool yet sync with Mendeley so as to increase the content in your field and just add to the community in general. If you’re looking to try Mendeley and you already have a Zotero account, I recommend importing your library in this way and playing around with the data you’ve already collected."

(from here: http://chronicle.com/blogs/profhacker/using-mendeley-for-research-management/25627)

Edited July 26, 2011 by Strangefox

[rising_star]

I downloaded Mendeley, played around with it for a few days, then stopped using it. The same thing happened with CiteULike. Strangefox, do you see any advantages to using Mendeley vs. Zotero?

[TheSquirrel]

I never managed to like Zotero. Its user interface is terrible. I have yet to find a software that does the things I want it to do: organize my PDFs into categories, allow me to type notes about them (not ON the actual PDFs), and which has a decent, uncluttered, user interface, and which does not force me to keep a browser open in order to use it. If Zotero evolves into an actual program rather than a browser extension/add-on, and changes a few things in it, I'll consider using it, but as it stands, it's kinda annoying (though probably one of the least annoying out there). Mind you, I use Firefox, and it's usually open, but I still don't like how it works within that, and not as a separate program. One HUGE turnoff, and probably the main reason I will not use Zotero, is that it does not seem to let me save or print my notes (I like converting them into PDF and keeping separate copies of them as well) in a normal fashion. It seems to open the generated report into the browser, but when I print THAT (or convert it into PDF), it shows the zotero link at the top, as if it has been printed off the web. I also don't understand the advantages of having it all stored online, and don't feel comfortable with the idea. I like to keep my stuff local. I like how you can turn off the syncing feature on OneNote. I don't need it, I don't use it, and don't want to be forced to use it. I'd like to save my notes and references on my computer, into one file (or a notebook, as in OneNote) and be able to back them up.

I also don't like how you have to put all that time and effort into uploading and organizing your references on one program, when it's not that good, and then being forced to continue using it because it's not compatible with other programs and you can't move your stuff as a result.

I recently tried OneNote, and I like its note-taking and sub-page/sub-section, etc features, but it's not good for organizing files and then taking notes on them, not to mention that it doesn't have the tag feature that Zotero and others have. Sigh. I also tried Mendeley and Qiqqa, but I didn't like either of them. I don't remember, but one of these two does not allow printing, and one of them only allows you to take notes on the actual PDF file. If I had wanted to do that, I'd be using Adobe Acrobat Pro, which I already have. Lame.

Edited July 26, 2011 by TheSquirrel

[rising_star]

I also don't understand the advantages of having it all stored online, and don't feel comfortable with the idea. I like to keep my stuff local. I like how you can turn off the syncing feature on OneNote. I don't need it, I don't use it, and don't want to be forced to use it. I'd like to save my notes and references on my computer, into one file (or a notebook, as in OneNote) and be able to back them up.

I also don't like how you have to put all that time and effort into uploading and organizing your references on one program, when it's not that good, and then being forced to continue using it because it's not compatible with other programs and you can't move your stuff as a result.

You'll discover the advantages of having it stored online once you have a hard drive randomly fail and you lose a year's worth of references.

As for exporting, you can export your EndNote library to Zotero or vice versa. Same with Mendeley. So, it's not like you're stuck with one program, unless you really want to be.

[Sparky]

Question for people using Mendeley or Zotero: is there a way to add fields to the entry type templates? Like in the case of a translation of a book, and the original, in one entry (which neither of the two supports, as-is), or the series and series number of a book (which Zotero includes by default but Mendeley doesn't).

I want something standalone, but I'm willing to deal with the unstable alpha/stable browserish Zotero if I can make it include all the info I need. #*($&@#$ citation formats that require listing a text's entire publication history in one entry...

[Strangefox]

Strangefox, do you see any advantages to using Mendeley vs. Zotero?

Well, I was looking for such advantages but it seems that both of them, being good in general, have lots of advantages and small disadvantages so that whether a person chooses to use one or another depends more on personal tastes and idiosyncrasies. I like the fact that I can export my data from one to another anytime. It means that I can start working with Zotero now and if later I find out that I like Mendeley more, I can always switch to it (or to EndNote - in another comment you wrote that you can export data from Zoreto to EndNote and vice versa and that is great!). I think I will stick with Zotero also because, as I've written somewhere else, some people in another thread had written that Mendeley software is still being developed and sometimes it crushes with unpleasant results for users.

I will probably buy 1 GB of Zotero storage space later. $20 a year seems a good deal to me. Moneywise, Mendeley is better than Zotero when we are talking free space (only 100 MB with Zotero and 1 GB with Mendeley) but when it comes to bigger storage space they are practically equal - $60/year for 5 GB at Zotero and $60/year for 7 GB at Mendelay. Of course there is 2 GB difference but I don't think I will need more than 5 GB anyways.

Of course there is EndNote with unlimited (?) storage space but it does cost more and I don't believe that paying $115 for it once will be all I will have to pay. There will be updates which I won't be able to get for free as with Zotero. Anyway, if Zotero was so much worse than EndNote, I believe people would not be using it and prasing it.

And you are using Zotero, right? Are you satisfied?