Nearly two years ago, I ran this series on a bunch of reference managers available in both commercial and open source models. Some things have changed since then, and others have not. OpenOffice.org Bibliographic has pretty much stagnated, Bibus has undergone incremental improvements, and Zotero has leap-frogged ahead to a function-rich 2.0 beta and survived a lawsuit from the makers of Endnote (which remains the commercial standard for reference management).
Today, a post at Bora Zivkovic's Blog Around the Clock higlights yet another new bibliographic offering, Mendeley. It is free, but not open source, and still in the beta stage, but it looks like it might offer some interface improvements over programs like Zotero and Endnote. Definitely worth following - do any of you readers have experience with Mendeley?
Showing posts with label zotero. Show all posts
Showing posts with label zotero. Show all posts
Wednesday, September 2, 2009
Friday, June 5, 2009
Good News for Zotero
Sunday, October 19, 2008
Zotero in the news. . .
And this time, because of a lawsuit from Thomson Reuters. Here's hoping this turns out for the best! Thanks to Mike Taylor for pointing out this news item (also here on Nature).
The basic gist of the lawsuit, apparently, is that the latest beta version of Zotero imports the Endnote style files, an alleged violation of the Endnote user agreement, among other things. Thomson Reuters alleges that the "reverse engineering" of their files (and allegedly, part of the software) is illegal. . .we'll see how this pans out, but I am not sure if I see the difference between what Zotero did and the file format translation capabilities of programs like Microsoft Office, etc.
The basic gist of the lawsuit, apparently, is that the latest beta version of Zotero imports the Endnote style files, an alleged violation of the Endnote user agreement, among other things. Thomson Reuters alleges that the "reverse engineering" of their files (and allegedly, part of the software) is illegal. . .we'll see how this pans out, but I am not sure if I see the difference between what Zotero did and the file format translation capabilities of programs like Microsoft Office, etc.
Wednesday, June 18, 2008
JVP - Zotero Style!
In a previous post, I lamented how difficult it is to create custom style files in the program Zotero. As a brief recap, this reference manager does a fantastic job of downloading references from the web and creating citations and bibliographies in Word or OpenOffice.org Writer. But, if you want to venture beyond the default style library (which is steadily expanding with a number of add-ons), you have a little style-file writing to do.
Creating a Zotero style file is not for the faint-of-heart. These are written in an XML scripting language called "CSL" (for "Citation Style Language"). As I was writing my dissertation, I needed to format one of my chapters with the format for Journal of Vertebrate Paleontology. Of course, Zotero didn't have a style available for this, and I wasn't in any mood to format everything by hand. So, I decided to invest an afternoon in learning enough CSL to be dangerous.
In actuality, I didn't learn much CSL at all. I took an existing style (American Psychological Association) and retrofit it for JVP. The APA style was close enough to start, and I had to tweak author orders, abbreviations, etc. The result is uploaded here. Caveat emptor!!! As you will find, my work is nowhere near perfect - I got the citation styles down pretty well for journals and edited volumes, and beyond that things might be a little wonky. Anyone who wishes to do their own tweaking is welcome to do so - and I would appreciate it, in fact!
Because I'm not a real code-head, I had to rely on a few "crutches" to limp through modifying the style file. First, a style preview tool, written by Dan Stillman, was invaluable. Follow the directions here in order to use that. Second, I relied on the CSL schema, which was the final authority on what various parameters meant. After that, it was tweak, test, re-tweak, and re-test, until I got something I could live with. It took a few hours of time, but was well worth it.
Good luck! Anyone else have their own style files they've written?
Creating a Zotero style file is not for the faint-of-heart. These are written in an XML scripting language called "CSL" (for "Citation Style Language"). As I was writing my dissertation, I needed to format one of my chapters with the format for Journal of Vertebrate Paleontology. Of course, Zotero didn't have a style available for this, and I wasn't in any mood to format everything by hand. So, I decided to invest an afternoon in learning enough CSL to be dangerous.
In actuality, I didn't learn much CSL at all. I took an existing style (American Psychological Association) and retrofit it for JVP. The APA style was close enough to start, and I had to tweak author orders, abbreviations, etc. The result is uploaded here. Caveat emptor!!! As you will find, my work is nowhere near perfect - I got the citation styles down pretty well for journals and edited volumes, and beyond that things might be a little wonky. Anyone who wishes to do their own tweaking is welcome to do so - and I would appreciate it, in fact!
Because I'm not a real code-head, I had to rely on a few "crutches" to limp through modifying the style file. First, a style preview tool, written by Dan Stillman, was invaluable. Follow the directions here in order to use that. Second, I relied on the CSL schema, which was the final authority on what various parameters meant. After that, it was tweak, test, re-tweak, and re-test, until I got something I could live with. It took a few hours of time, but was well worth it.
Good luck! Anyone else have their own style files they've written?
Friday, May 23, 2008
The Open Source Dissertation
My university has done a wonderful thing, in accepting only PDF files for deposition of a thesis or dissertation with the graduate school. Gone are the days of printing 5 copies of a 300-page document on acid-free paper that costs 20 cents a page (and then finding out that one of the margins is 0.1" too wide, so please correct and resubmit before the deadline in three hours). The transition is a wonderful step forward, and also means that it is much easier to distribute the dissertation.
As a proponent of free and open source software (having made the big switch about a year ago), I wanted to do as much as I could within the realms of that universe. This posting summarizes the software I used, with the hope of inspiring others to follow a similar path (whether in whole or in part).
Data visualization: I processed all of my CT scan data in 3D Slicer. For segmenting structures, generating surfaces, and measuring volumes, look no further! [I still need to do a more complete post on this one.] Additional analysis was done in ImageJ.
Data analysis: Initial data entry in OpenOffice.org's Calc, with analysis primarily in R and an occasional venture to PAST.
Figures: Raster image editing was done in the GIMP, and line drawings or composite figures were assembled in Inkscape.
Word processing: All done in OpenOffice.org's Writer. The PDF output function was very nice for sending drafts to committee members and advisors, and the software's Microsoft Office compatibility is such that I could also send and receive marked-up documents (in .doc format) pretty easily. For the final document, I exported each chapter in PDF format.
Referencing: All of my references were sorted, organized, and rendered as bibliographies with Zotero. Along the way, I created custom styles for Journal of Vertebrate Paleontology and Zoological Journal of the Linnean Society. More on this process in another post.
Document assembly: To assemble all of my dissertation's chapters into a single PDF document, I used Ghostscript. The output was quite pleasing, and easily accomplished through the command line in a matter of seconds.
Presentations: For my oral dissertation defense, I created my presentation using OpenOffice.org's Impress.
As a proponent of free and open source software (having made the big switch about a year ago), I wanted to do as much as I could within the realms of that universe. This posting summarizes the software I used, with the hope of inspiring others to follow a similar path (whether in whole or in part).
Data visualization: I processed all of my CT scan data in 3D Slicer. For segmenting structures, generating surfaces, and measuring volumes, look no further! [I still need to do a more complete post on this one.] Additional analysis was done in ImageJ.
Data analysis: Initial data entry in OpenOffice.org's Calc, with analysis primarily in R and an occasional venture to PAST.
Figures: Raster image editing was done in the GIMP, and line drawings or composite figures were assembled in Inkscape.
Word processing: All done in OpenOffice.org's Writer. The PDF output function was very nice for sending drafts to committee members and advisors, and the software's Microsoft Office compatibility is such that I could also send and receive marked-up documents (in .doc format) pretty easily. For the final document, I exported each chapter in PDF format.
Referencing: All of my references were sorted, organized, and rendered as bibliographies with Zotero. Along the way, I created custom styles for Journal of Vertebrate Paleontology and Zoological Journal of the Linnean Society. More on this process in another post.
Document assembly: To assemble all of my dissertation's chapters into a single PDF document, I used Ghostscript. The output was quite pleasing, and easily accomplished through the command line in a matter of seconds.
Presentations: For my oral dissertation defense, I created my presentation using OpenOffice.org's Impress.
Saturday, February 2, 2008
Zotero 1.0.3 now available
Some readers may remember my endorsement of the Firefox plug-in Zotero as one of the best open source options for reference management. You will be pleased to know that a nice little upgrade - from 1.0.3 from 1.0.2 - is now available. It includes some added functional support for downloading references from some major sites, such as PubMed, updated output styles, and some handy fixes for a few bugs in word processor integration. Zotero 1.0.3 is a must-have release for anyone who uses this program (and is worth a look for those who don't use it yet!).
Thursday, December 20, 2007
Reference Managers on Parade - Part III
Zotero
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 OpenOffice.org 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.
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 OpenOffice.org 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.
Subscribe to:
Posts (Atom)