Before I get down to business, I wanted to make some remarks about a post I a couple of days ago on having children and being exhausted. I really appreciate the frankness of the comments people left, but I suppose I didn't leave thing on a very positive note. I was pretty tired and this has been a challenging week, science-wise. I am trying to get all of our projects in a place that I can leave for a week over Thanksgiving and just write the manuscripts and that may be coloring my perception of reality. Still, so that none of you think that motherhood is all sleep deprivation, puddles of urine, and sore nipples, I want you to know that I am a total hero this morning because I have the unique ability to make duck shaped waffles. That's pretty cool. But, it's a skill I tell you. A skill.
Figure 1: Getting the duck in the waffle maker is the hardest part.
It's also cracking me up this morning that my son cannot say the letter "R" in English, but he nails it in Spanish. He can pronounce "Al rescate" like a champ, but it's still "Wescue pack, coming to the wescue."
But, now back to business. I have an inbox full of lovely questions and things you've sent me. So, I am declaring this "Ask Dr. Isis Week," where the focus of our time together will be answering your questions. Here we go with potentially the most controversial question I've ever answered...
Hi Dr. Isis,
Before I get to my question, I have to thank you for your wise, wise recommendation of Arikia's blog. What a great writer. I get almost as excited to see new posts from her pop up in my google reader as I do for your posts.
Here's my question. I've just completed writing my masters thesis (and got it accepted and formatted properly, and its now on its way to ProQuest for publication). But I spent HOURS typing out the references section. I do not wish to repeat that process. Ever.
I'm hoping you (and maybe your readers) can weigh in on citation software. Specifically, what software do you (and others) use, and why do you like it better than the other programs out there? (and which OSs are compatible? I have a MacBook Pro, and the lab computers are running Windows XP or Vista.)
If you do go ahead and use this for a blog post, I'd appreciate my name/email signature being edited out.
Thanks,
[Name redacted to protect this worshiper from the fallout associated with asking about bibliography software]
[Insert brief pause as Dr. Isis responds to the call of "Mommy, there are poopies here."]
Figure 2: An artist's rendition of the culprit.As for reference software, I suspect that many of us use the software that those around us use. I began using EndNote because, frankly, at one point in my career it came on my department PC. I am quite happy with it. I like that it formats references according to the specifications of a number of major journals and that there is a web-based option. I generally do most of my literature searches in Web of Science (I've written about that here), which allows for references to be easily imported into EndNote, formatted properly. I'd anticipate that these tools would be compatible since they are both Thomson Reuters products. I am also especially fond of the Cite While You Write feature that allows you to insert references and images using field codes that update as you change the body of the document. You can also format the reference section at any point in the writing process. (h/t to the University of North Carolina's Health Sciences Library for these great EndNote tutorials).
The issue I have been dealing with lately is how to manage our libraries. When I began, the lone ranger in our lab group, it was easy. I just kept my own library. Now that there are students, technicians, and rotating interns in the lab, I've been trying to create libraries in a way that is efficient for everyone. It seems a huge waste of time to have every person who comes into the lab start a library from the beginning and I've recently been all about creating an intellectual legacy. My solution has been to maintain two libraries. The first library is my personal library and is full of all sorts of shenanigans. The second is our publication library. We keep it in our folder on the department network and it contains all of the references from our publications. We update it as we publish, and that's it. Nothing else. People can download it to their personal computer and use it as a starting place to create their own libraries.
Or, they can say "screw it" and go all maverick with their libraries. Whatevs.
Figure 3: I'll be making my own library, little missy.I don't know that this is best way to manage a library, but it seems to work for us. I'd be interested to hear from my scientist readers though. Which reference software are you using and why do you like it?
Information Science
Life Science
Comments
Our lab only uses Macs which gives us some different options (though of course EndNote is also available for Macs). We've settled on using a program called Sente which has very reasonable academic pricing. Sente works with Word as you'd expect, but it also works with Apple's Pages and other basic text editors.
I prefer to write documents in Pages and use Sente for references. Many journals still insist that you have to send Word documents for the publication, but Pages allows you to save as a Word document.
I found EndNote annoying and buggy (particularly with the 'Cite while your write' feature). I also found it hard to keep up with EndNote's endless series of major updates. Sente is very stable and has some very useful features (which very possibly are also now in the latest version of EndNote)....and of course you can import references into Sente from EndNote.
Posted by: Keith Bradnam | November 8, 2009 11:42 AM
2 words: BibTex and Papers.
Posted by: Eugenie | November 8, 2009 12:08 PM
Having used EndNote, Reference Manager, Zotero, and Mendeley, Endnote is my choice for ease of use, cross-platform compatibility (we're both Mac and PC users) and, as has become increasingly important, more commonly used by the people I publish and collaborate with.
Posted by: New Asst. Prof. | November 8, 2009 12:14 PM
I'm also a very happy Sente user and wanted to add two things for the benefit of any Mac users considering Sente. The latest version (Sente 6) allows synchronization across multiple computers via the sharing of a small authorization file. This would make it a snap to keep a master library of references for a lab. Sente also allows you to keep multiple libraries, so those who feel the need to go all maverick-y and create their own could do so as well.
There are also other (non-Mac specific) options for keeping a master repository that might be worth having one of your little lab muffins investigate. Mendeley has an attractive and free desktop program that stores and synchronizes your references with an online library. This, plus the ability to network with other researchers (including one's own lab), would make finding key papers and synchronizing them with a shared library easy. Mendeley allows annotation of PDFs and works with a whole list of search repositories and scientific bookmarking sites (PubMed, JSTOR, CiteULike, etc.).
Zotero is another option that features an online library. It makes use of a Firefox add-on, so it's OS agnostic.
Also, Arikia is an excellent writer AND quite a blast to hang out with. :)
Posted by: Michelle Gill | November 8, 2009 12:14 PM
I use LaTeX for writing papers unless a journal requires MS Word, because I find LaTeX easier to use and more reliable for texts longer than four pages. (I have been known to refuse to submit to certain journals because they only have MS Word submission templates.) I use BiBDesk for Mac to store references. No easy export from Web of Science, but many other cool features. For shared libraries, I am in the process of moving to CiteULike. This allows people to download references in BiBTeX or RIS format (for import into EndNote and Reference Manager etc.) - so collaborators aren't forced to use the same software.
(I hate being forced to use MS Word, but when I do need to edit a Word document, I try to use the original software instead of Pages or OpenOffice. With Word, there's always a piece of formatting to be buggered up.)
Posted by: perceval | November 8, 2009 12:15 PM
In attempt to avoid anything Microsoft, I started off using a combination of LaTeX, BibTex and JabRef (does roughly the same things as EndNote), which are all free, cross-platform and make typing special characters as well as in-text citations less of a nuisance. With Word, you have to manually remove and retype the author's name if you want to write "So and so et al. (1721), whereas with LaTeX et al., it's just a matter of typing \citet{soandso} or \citep{soandso}. Did I mention it's free? Unfortunately, my co-author (read, PI) didn't approve, so EndNote it is. Shockingly enough (...) Word likes to mess up the table numbering and inserts line breaks all over the place, but people still seem reluctant to move away from it despite knowing all this. I just switched my PDF manager from Papers to Mendeley though.
Posted by: C | November 8, 2009 12:59 PM
Zotero is my reference manager of choice--mainly because it's free and platform-independent.
Posted by: Jonny Dover | November 8, 2009 1:00 PM
The question here is not which ref manager to use. The question is wtf incompetent advising program is letting some poor schmuck type out refs by hand in (checks cal) 2009!!!
Posted by: DrugMonkey | November 8, 2009 1:06 PM
I use RefWorks. I like it mainly because you can create your library online and access from any computer you wish. And it has an add-on for MS Word (and it is also easy to export citations to LaTeX).
Posted by: Change | November 8, 2009 1:07 PM
One who doesn't give two fucks about telling his student that reference programs exist?
Posted by: Isis the Scientist | November 8, 2009 1:07 PM
I made my choice of reference software over 15 years ago. At that time, reference manager was the only network-installable multiuser platform, so I went with that. I don't know about the other ones; I'm happy enough with RM to not bother looking. With RM, we pay for a network license, and there's only one master reference library. If somebody downloads a PDF of a paper, we have a file naming convention (FirstAuthor Year Journal - short title) and we link the RM entry to the PDF in a shared folder.
As for duck-shaped waffles, allow me to share on of my few excellent innovations in parenting. Make up pancake batter a little thinner than usual. Put it in a sport waterbottle (the squeeze kind with a popup lid). Heat some oil in your pan. Using the batter-bottle, draw out your shape (letters, planets, dinosaurs, names, cartoon characters). Let it cook for about 1 minute. Then surround the shape with more batter to make a round pancake. or a custom shape pancake. Finish cooking. When you flip, the pancake has a dark part in your shape, and a light part.
Posted by: David | November 8, 2009 1:22 PM
I use a combination of bookends and papers.
Papers is an application that allows you to keep all your journal articles organized and easily retrievable. It also interfaces directly with various databases, so the pdfs and citation information are automatically added as you grab them via whatever database you are currently using.
When I am writing a paper or a grant, I create a collection of articles in Papers. I then export the collection to Bookends, which I then use to create the bibliography. It works nicely with most word processing software, including latex, so I am happy.
I realize this process sounds a little complicated, but it nicely separates the functions of gathering and reading information, writing the paper/grant, and formatting.
Posted by: laserboy | November 8, 2009 1:37 PM
I use Refworks and RefGrab-It add on. I have a Mac but it works on PCs as well. I think your institution may need to subscribe to RefWorks, or you have to purchase it. RefWorks is much like EndNote, but it's web-based. It also has a Write-N-Cite option, although I haven't figured it out yet. I like the RefGrab-It add-on because you can be surfing the web or using a search engine (like Web of Science) and RefGrab-It will search your page for citations. You can then click on the citations you want and it will import them into your RefWorks account.
Posted by: EcolEvolGrad | November 8, 2009 1:42 PM
@DM- advising program or advisor?
My advisor still types everything out by hand. Particularly funny since he doesn't type properly (more of a hunt and peck style; albeit a relatively rapid one). He's got most of the standard schtick references memorized, I think. I offered to help him set up endnote, but he was having none of it.
Actually, I wouldn't be shocked if everyone in my lab does it by hand, except me. There was much ado about changing reference formats for a manuscript, like it would take a non-trivial amount of time.
If you meant advising program, well our library services and IT web education programs both offer endnote help, but my specific grad program certainly didn't mention any such thing.
Posted by: becca | November 8, 2009 2:22 PM
I vote for Endnote. I'm an Endnote fanatic and have had fantastic experiences with it =]
Posted by: HennaHonu | November 8, 2009 2:27 PM
I have a Mac and use BibDesk---a bibtex manager. It is free and powerful. There is a cross platform software called JabRef that seems to do same thing. Another mac only solution is Paper's, which is lovely. But Papers costs $40 bucks and doesn't yet have very good bibtex integration. I think that is coming, so once they get decent bibtex integration I will likely switch. People also seem to like Mendeley and Zotero.
I like bibtex because I mostly write papers in latex. Also it is free and easy, no complex formatting drama as with endnote. If something is giving you trouble, you can always just open up the text file and change it. Simple. Occasionally I word in a word processor, there are tools out there to integrate Pages and Bibdesk or Word and Bibdesk.
Hot tip: Google scholar will give you a link for bibtex or endnote data. If you go to google scholar settings, scroll to the bottom, there will be an option to for provide bibliographic data. Once you change this setting, every google scholar result will have a link to the data file. This is very, very useful.
Posted by: yolio | November 8, 2009 2:28 PM
Your university's library system provides an on line bibliographic data base that interfaces with most client side software including Endnote, and processes information from searches on the libary's web site.
Posted by: Shhhh | November 8, 2009 2:56 PM
I use Zotero which works on my mac and also PC. It's free. It also has a "group" feature which is useful for a lab.
Posted by: las | November 8, 2009 2:57 PM
I'm only a student, so I have no money, and Zotero's the only thing I've tried. That being said, I quite like Zotero's ability to recognize various types of pages and come up with whatever format I need, since I use references other than publications for my non-science classes.
Posted by: curiousgeorgie | November 8, 2009 3:06 PM
I use Endnote as well, but have pondered switching on occasion. Whenever my thoughts turn to greener pastures of reference management, I consult the Wikipedia page comparing all of the different reference manager software out there. It's delightfully comprehensive, and covers all of the free stuff, to boot!
Posted by: jebyrnes | November 8, 2009 4:10 PM
I use Endnote, which is easy to use with Web of Science, but I recommend keeping a copy of your document without the cite-while-you-write tags, as they once threatened to destroy my thesis two days before it was due.
My supervisor told me to type my references out by hand, but laziness won over obedience.
Posted by: Em | November 8, 2009 4:27 PM
Because I write all my publications in Latex, I keep all my references in a Bibtex file. There are excellent environments available for using latex / bibtex / revtex on all operating systems; Windows, Mac and Linux. You can re-use it for your posters and presentations as well.
Posted by: Angela | November 8, 2009 6:23 PM
p.s. all of the above are also free :)
Posted by: Angela | November 8, 2009 6:24 PM
I'm in the middle of writing my PhD thesis. I'm using LaTex on a mac (so TexShop) and using Bibdesk for reference mgmt. The overall workflow is still imperfect. Most of my papers come from pubmed searches. From there, i use a bookmarklet to post it to CiteULike. In citeulike, I type in a few tags and press Enter. Now the citation info is in Citeulike. Meanwhile, back at the pubmed page, I click the link to the paper and download that. I open Bibdesk, click on my External Folder link that syncs with Citeulike, click "import" on the entry I just added, switch to the "Last added" folder, and drag the downloaded file onto the entry there. I have a friend who tried to automate storing a citation and automatically retrieving the file, but the publisher links to PDFs are inconsistent as to make the whole thing time-consuming and fragile. Trying to automate it myself (for a smaller set of journals) is one of the few procrastination projects I haven't attempted. Yet.
In Bibdesk, to create a reference in your documuent, you just drag the entry to your latex (or whatever) document, and it inserts in a default format that works for me, but can be tweaked as needed. When you typeset the document, and tell it to generate the bibliography, voila! Automagic.
The most annoying part of this process is that journal titles sometimes get imported in a never-used form, e.g. "The Journal of neuroscience : the official journal of the Society for Neuroscience" which is invariably referred to as "The Journal of neuroscience" or something shorter. I'm not actually sure that those are from the pubmed input to citeulike, but I am sure that they are extremely annoying. The can be fixed by editing the record in Bibdesk or with some fancy perl/regex procrastinatory goodness.
Whatever you do, backup backup backup, and preferably use a versioning system too.
Posted by: Rhileigh Almgren | November 8, 2009 7:15 PM
I started with EndNote way back when in the days when I still used a Mac. It was the first one that seemed to work well on that platform with Word. I have never changed, even after I switched to a PC. I mean, once you have ~250 refs entered, who wants to change?
I gave both of my kids EndNote as soon as they took a research paper course in high school. I SO wish they had had this stuff when I started out...
Posted by: Pascale | November 8, 2009 10:30 PM
I use Zotero for managing papers and references. It's not perfect - no software I've tried is - but it's more than good enough. I normally use LaTeX for writing papers, which means BibTex for reference lists, which Zotero supports just fine. It supports Word and OpenOffice too if you're unlucky enough to have to write a paper in Word-format, though I've yet to use it enough to give a definite opinion of that.
Posted by: Janne | November 9, 2009 2:07 AM
Almgren: "I have a friend who tried to automate storing a citation and automatically retrieving the file, but the publisher links to PDFs are inconsistent as to make the whole thing time-consuming and fragile. Trying to automate it myself (for a smaller set of journals) is one of the few procrastination projects I haven't attempted. Yet."
This is one thing that Zotero does really well, especially since it lives as a plugin in your browser. It has patterns for a large number of journal websites, paper collections and citation databases and knows how to extract biographical data and pdf's. So when you find a paper online - in PubMed or wherever - you can usually just click on a small "paper icon" that appears in your bowser address field and Zotero automagically creates an entry for that paper with abstract and bibliographical details, and downloads and stores the pdf if available. Very, very nifty.
Posted by: Jann | November 9, 2009 2:13 AM
Mendeley - the answer to all my bibliographic problems! Like many, I guess, I started with Endnote, but my bibliographies were getting so long I wanted to start tagging papers in different categories and found that Endnote will only allow one tag per paper. Much frustration followed to the point that I started an Access file so that I could make my own tags and notes about papers.
Within five minutes of using Mendeley I'd transferred all my Endnote libraries and it was happily reading in all the information in my PDFs (ok, it's not 100% accurate, but mostly pretty good). I can now tag and annotate to my heart's content.
Posted by: Martyn | November 9, 2009 4:33 AM
I alpha tested Mendeley and was very positively impressed as a way of managing PDF's ... at that time it was not a reference manager but that functionality was planned. Anyone who has not looked at it might give it a glance.
Posted by: Greg Laden | November 9, 2009 7:54 AM
Sci started with EndNote, but then came back to it a few months later, and without someone to show her the ropes, was totally lost. Switched to Reference Manager, and I've been really happy. OTOH, both of them I had to have SHOWN to me (the instructions vanish on these things so fast). Reference Manager has all the stuff Endnote does with being able to cite as you write and update your ref lists, etc. We do not have a global citation index in the lab, due to the truly vast number of almost entirely unrelated projects, but that seems like an AWFULLY good idea.
Posted by: Scicurious | November 9, 2009 10:23 AM
One option that people seemed to have left out is that several programs can scan a PDF file, locate the DOI (with varying reliability), look up the citation on the 'net, then file it for you.
I'll probably put out a short blog on my thoughts on improving this sometime.
Posted by: Grant | November 9, 2009 1:21 PM
I used EndNote for over 10 years, using it for reference list and pdf manager (a poor one). Well, originally it managed my photocopies of articles, but that day is long over. I think I have about 1900 articles in my main library. But the addition of yearly updates after Thomson Reuters took over drove me away.
So now I've been using Mendeley for pdf manager. The ability to tag things and keep notes attached to the pdf file is key.
Still used EndNote to include the references in my last paper though. I'll try Mendeley for the next one, but it's not clear how well that will work.
Posted by: Nat | November 9, 2009 2:11 PM
They are trying to get everyone to go to RefWorks here. Would it be worth my time to go to a training session or will I be able to figure it out myself?
Posted by: katydid13 | November 9, 2009 2:23 PM
It's up now, see: http://sciblogs.co.nz/code-for-life/2009/11/10/bibliographies-why-cant-research-papers-self-document-what-they-are/
Key thing is I wish research documents would self-document what they are. It'd make maintaining bibliographies a lot easier...! :-)
Posted by: Grant | November 9, 2009 3:46 PM
Aigaion and Zotero are both fabulous and free.
@yolio : Thank you so much for the google scholar bibtex tip. You've just made my life a million times easier!
Posted by: Laurel | November 9, 2009 6:06 PM
I use EndNote because it's basic and makes sense to me. I'm still back on v.9 but it allows me to attach both the pdf and an extra document of notes to each entry, plus I can do custom keywords. I tried Zotero and although it looks cool, it was causing problems with Firefox, plus all my data was already in EndNote and the transition was daunting. I tried Mendeley but it was so godawful slow and buggy I bailed. I also add notes directly onto pdfs in FoxPro, my pdf reader. Now I just need to take all this information and somehow turn it into a dissertation...
Posted by: Diane | November 9, 2009 10:18 PM
I currently work for RefWorks, and I have seen how RefWorks has benefited users first hand. RefWorks & EndNote are in fact quite different in several ways:
-RefWorks has NO limit to the amount of records you can store, while EN Web has a limit of 10k.
- RefWorks supports formating (italics, bold, etc.), EN Web does not.
- You can store any type of data in RefWorks, while EN Web does not allow you to attach files to be stored.
- RefWorks has 1,900 import filters while EN Web has 700
- RefWorks has a built in RSS feed reader & a mobile interface for smart phones and PDAs (RefMobile).
- RefWorks has Accucite, and online style guide, while EN Web does not.
- RefShare allows users to share a folder or an entire database with another RW user or NON-User (including attachments, notes, comments, etc), while EN Web only lets you share with other ENweb users,not even an EndNote desk-top user.
While I respect that everyone is entitled to choose whatever service they prefer, I have included a link to a comparative analysis of RefWorks & EndNote to offer an additional perspective: http://ow.ly/q0ud.
Thanks.
Posted by: Devin | November 12, 2009 12:06 PM
Devin, the link doesn't seem to work (even after removing the final period from the hyperlink). Do you have a more direct URL?
Posted by: Jason | November 12, 2009 1:52 PM
The only one I've used is RefWorks with Write-n-Cite, but I found it easy to use and had no problem importing references or formatting. Furthermore, it is supported by both Mac and Windows, and I had no trouble working on my paper on either type of computer.
Posted by: JaneHerriot | November 15, 2009 4:32 PM
OMG!!!!!! I have a fan! Aw you're the best.
Posted by: Arikia | November 28, 2009 5:56 AM