Monday, December 24, 2007

Reference Managers on Parade - The Conclusion

Other Options
My wife, a physics graduate student, is constantly puzzled by the fact that the paleontology community hasn't adopted LaTeX. Odds are that most of you reading this (someone does read this blog, right?) have never heard of LaTeX. It's somewhat akin to HTML, in that it's essentially a markup language for scientists. Thus, it's a little scary for those who have never ventured beyond the confines of their word processor. But. . .it's incredibly powerful. There are a whole host of bibliography management tools for LaTeX - JabRef is one example. The main reason LaTeX hasn't entered my sphere is because I collaborate with a lot of people who don't use it - so, there isn't a lot of incentive for me to learn it. Maybe one day, though. . .

Closing Thoughts
There isn't really a "perfect" open source reference manager out there yet. All of the packages have significant strengths, but also sometimes significant weaknesses. I think that the next year will experience major gains in open source reference managers, and hopefully by this time next year there will be several extremely good options. For the time being, I recommend experimenting to find one that works for you. Zotero is my current reference manager of choice - its integration with Firefox and capability to easily dump formatted references into a word processor move it to the top of the pack.

Saturday, December 22, 2007

Reference Managers on Parade - Part IV Bibliographic (OOoBib)
First, a disclaimer: This software doesn't exist yet. But, I've included it here just to generate a little excitement for what could be a great addition to
Pros: According to the project website, this will greatly augment the bibliographic features for OOo Writer. We'll have to see what this entails in the long run.
Cons: Microsoft Office users are probably out of luck here. Switch to if you want to give it a spin! And the biggest current downside: this program isn't functional yet.
The Bottom Line: Look for this to appear sometime in the second half of 2008.

Thursday, December 20, 2007

Reference Managers on Parade - Part III

Zotero is a very nifty little plug-in for Firefox that has very, very quickly become my reference manager of choice. It is in quite active development, and has a very promising future ahead of it, I think.
Pros: Web integration is insanely good! So you find the webpage for the latest article in Nature. A little icon appears in the browser's navigation bar. You click the icon, and all of the article's information - authors, abstract, direct URL, etc. - is dumped into your database. Zotero also accepts the standard "reference export" option, for sites that don't yet support direct export. Also, Zotero has two very functional plug-ins that allow users to "cite while you write" in Microsoft Word and Writer, and it functions in any operating system that supports Firefox. You don't have to be connected to the internet to use Zotero, either (because all files are stored locally).
Cons: The two biggest downsides that I've run into are 1) it is insanely difficult and not at all intuitive for the average user to create output styles in the current version, and the available output styles are quite limited (although they promise to correct this in the near future); and 2) character formatting (italics, underlining, etc.) is not an option within the database. Some journal homepages (notably JVP's BioOne page) aren't yet supported for direct linking. But. . .you can still import references using the standard "reference export" option (exactly as you do in Endnote).
Note: If you export from the BioOne website, use the Procite or Reference Manager format - the Endnote format doesn't seem to capture all relevant data. And BioOne, if you're listening, it's really, really annoying that you force the titles and author names of your reference exports into all caps. No journal on earth uses this format!
The Bottom Line: Zotero is *the* open source option for reference management, and it's only going to get better.

Tuesday, December 18, 2007

Reference Managers on Parade - Part II

Bibus is one of the more functional open source bibliographic managers. Based on an SQL backend, it will run in Linux, Mac, and Windows OSes.
Pros: The interface is pretty intuitive, and it is easy to create style files for output in specific journal formats. Bibus also includes a feature akin to "Cite While You Write," compatible with both Microsoft Word and Writer. Manual input of references is pretty easy.
Cons: The Bibus development team is quite small, and it can be a looooong time between updates. There is no support for character formatting in the database either (italics, underlining, etc.), which is quite annoying if your references have scientific names in them. Additionally, it's not entirely straightforward (although certainly possible) to import bibliographic information from journal websites. In the current version of Ubuntu Linux, lots of folks are having trouble getting it to link in with This is the main reason I abandoned Bibus for the package discussed in my next post. . .
The Bottom Line: Bibus is pretty functional, but has its quirks. It's a good choice for Windows and some Linux users, but requires a little effort sometimes.

Sunday, December 16, 2007

Reference Managers on Parade - Part I

Everyone has a massive reference library, but few know how to manage it. Ideally, you want an application that will let you record all of your papers and import formatted citations into a document. In the upcoming series of posts, I'm going to review some reference managers, both open source and commercial.

This program is the classic reference management program, and probably one of the most widely supported by publishers. It has been around for years now, and it shows the polish and feature richness that you would expect for a mature program. This is not an open source or free program, but I include it here just as a standard of comparison.
Pros: The Cite-While-You-Write feature is quite handy; this tool allows you to build your paper's reference list automatically while you type the paper (hence the name for this feature!). Also, Endnote has a very broad output styles database, and it is quite easy to build reference styles (JVP even has a style available from the journal website). You can format italics within each bibliographic entry. It is quite easy to import references from journal websites, too. Available for both Windows and the Mac OS.
Cons: It's expensive - $250 to download, and $300 (oops, I mean $299.95) to have a physical copy shipped to you. Also, there are occasional functionality issues if you try to run the program under WINE (and Cite-While-You-Write doesn't work in No native Linux version is available.
The Bottom Line: If you can afford it, Endnote is the way to go. It has polish and pizazz, and it is widely supported. Linux users are better off looking elsewhere, though.

Saturday, December 15, 2007

Books on the Job Hunt

Now it's time for a post about something not computer related - the job hunt! As some who know me may know, I am in the middle of my job search. This has its ups and downs - there are stressful moments, entertaining moments, and moments of pure confusion. I've gotten a lot of really great advice from many friends, colleagues, and advisors, which has made things infinitely easier (and probably infinitely more successful, in the long run). But what do I do when my advisor doesn't want 20 phone calls a day about how to get started on writing this or that? A selection of handy books have been a real life-saver in this regard!

In this blog post, I'm going to discuss two books (and a website) that I've found especially handy in guiding my job search. They each have their pros and cons, and unique styles. Word of advice to fellow grad students: Read these books sooner rather than later - preferably at least six months in advance of when you plan your own search.

The Chicago Guide to Landing a Job in Academic Biology. By C. R. Chandler, L. M. Wolfe, and D. E. L. Promislow.
This book came out earlier this year. I first spotted it at the U of Chicago Press table at the SICB meetings, and knew I had to have it. Although the title says "Biology," it really would be of interest to most any paleontologist aiming for a job in higher education. The authors of this book lay out a nice and tidy sequence of events - both from the perspective of the applicant as well as from the perspective of the hiring department. As I've read through it, I've found myself nodding my head in agreement with most everything they have to say. The writing style is informal, like you're having a conversation over a beer after hours, and the book is filled with anecdotes laying out the do's and don'ts of the job search from people who have been at both sides of the equation. The example CV's and letters are generally quite helpful, although it might be nice to see a few more samples. Also, they bring up many points about interviewing skills, applications, etc., that I never would have thought of and never had thought to ask about. Two gaps in the books coverage might reduce its usefulness for some folks. First, it doesn't really cover academic jobs outside of the university system - i.e., museum curatorships and the like. Also, it probably won't be that helpful for people aiming for positions as collections managers or preparators. I don't know of any source, beyond chatting over a beer at SVP, that really offers this sort of advice. Second, much of it is geared for people in the North American system - I would be curious to learn from my non-North American colleagues how things work! Despite these gaps, if you buy only one book on the job hunt, "Finding a Job in Academic Biology" would be it.

The Academic Job Search Handbook (3rd Edition). By M. M. Heiberger and J. M. Vick.
This book, now in its third edition, is really intended to address all folks seeking work in academia - whether they're philosophers, paleontologists, or specialists in late 16th century Algerian literature. As such, there are many aspects of the book that aren't all that useful or relevant. The several pages of sample C.V.'s in the humanities and social sciences are usually just flipped through when I'm utilizing this. It has roughly the same content as the Chicago Guide, but offers more detail in certain areas (such as potential questions during an interview). The authors take themselves a little more seriously than the authors of the Chicago Guide, but that's ok too! The Academic Job Search Handbook is a good choice to round out your job hunting book collection.

Chronicle Careers
This website, from Chronicle of Higher Education, has some really nice forums and advice columns, which have been particularly helpful for me. They also have a yearly "CV Doctor," in which people send in their CV's for evaluation and comment. Of course, it covers all fields of academia (and all stages, from grad school to emeritus), but there really are some good things on this site. Ms. Mentor is always good for a chuckle, too.