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Saturday, 27 September 2008

Boycott Thomson Research

My work currently depends upon Thomson Research’s EndNote. However, because Thomson is currently in the process of suing George Mason University for developing open-source Zotero, I will begin the process of looking for a replacement for EndNote. I recommend all educators to do the same, especially if they are in a position to make site-wide purchasing decisions. I will myself begin looking for a piece of software that can replace EndNote. In the meantime, of course, I will not upgrade my license and I recommend that all students and educators not purchase new licenses from Thomson.

I make this recommendation despite that I depend on Thomson Research’s EndNote for a substantial portion of my research and teaching. Using EndNote, I have built up a relatively complex and feature-rich custom export template. In addition to a two-month period where I generated the basic export template, the template has absorbed about a year and an half incremental changes. In short, my work absolutely depends upon EndNote. However, I use EndNote only as a go-between academic databases and Tinderbox.

Regarding the series of screencasts I have begun producing to describe how I use software and digital media in my research and teaching, it will take me some time to find a suitable replacement for EndNote in my workflow. My screencasts will continue as planned and I will abstract as much as possible the role EndNote occupies in my workflow with an eye toward eliminating it from my process entirely. For the immediate future, however, I will use my current version of EndNote.

The first version of EndNote I purchased a license for was EndNote 8. I did not actively use EndNote, however, until 2005 at which point I upgraded to EndNote X. Several months ago (back in May I believe), I upgraded to EndNote X1. Based on the EndNote product alone, I believed Thomson Research to be a very retrograde company. EndNote has a poorly designed database template mechanism and a virtually unusable database field editor. With regard to their maintenance of the program code, Thomson has stopped releasing bug fixes as of EndNote X1, choosing instead to charge licensed users $100 for upgrades.

While EndNote works reasonably well, the market for bibliography management software has a number of capable competitors. Papers, RefWorks, BibDesk, and Zotero are notable examples. I have been aware that Thomson has released EndNote X2 but have decided not to upgrade because the new software offers little for the price and fails to provide features which should have been included from the very first version. For example, in-place editing, unlimited display fields, and unlimited custom fields are not possible in EndNote. Shameful, really.

What I find particularly troubling about Thomson’s decision to sue George Mason University is that Zotero is publicly-developed open-source software that is highly regarded by many University librarians and academic researchers. To litigate against such a project is to be on the dishonorable side of the battle. The fate of the suit, should it reach the courts, will depend on whether Thomson can prove GMU is in breach of contract for enabling Zotero to produce EndNote-compatible documents.

My best guess is that GMU has technically and unwittingly violated the terms of use for EndNote. However, Thomson's lawsuit will only draw attention to open-source Zotero whose source code has, by now, been downloaded thousands of times. In fact, Thomson's suit advertises Zotero to the very people who would purchase EndNote licenses. But most importantly, if Thomson somehow manages to win their suit, research universities will begin scrutinizing license agreements for clauses which prevent them from producing intellectual property. This, of course, would be good news for academic researchers and bad news for software companies.

Reading between the lines, Thomson has probably recently seen its sales of EndNote licenses drop and they are attacking what they perceive the easiest (or most deserving) target. The problem with such thinking is that attacking open source projects is really just about the most foolish thing any company can do.

I wish Thomson Research as swift and painless an end as they deserve. end of article

Monday, 22 September 2008

Dynamic Anchors using Javascript and Tinderbox

This entry is a very brief introdcution to one of the ways in which I use Tinderbox to enhance my teaching. Tinderbox is an unusual program in that it provides so a high degree of flexibility that at first (and second) glance it isn't clear how one might even use such software. Tinderbox in many way resembles a database program, but deeper experience with the program reveals the limitations and inaccuracy of such a comparison.

In the spring of 2006, I began seriously exploring Tinderbox's capabilities and what I found was a program that could, among other things, help me organize my research, engineer and customize data objects, establish relationships between those data objects, and provide a modular toolset for constructing websites. All of my websites are based on Tinderbox documents, including this blog.

In the winter of 2008, I overhauled the Tinderbox document I use to adminster my course website. For the first year of my getting to know Tinderbox, I produced a document as a container for a series of notes each representing a discrete HTML page. In January of this year, I rebuilt the Tinderbox document so that larger HTML structures--such as divs, tables, and unordered lists--were represented by notes and subelements--such as rows, cells, and list items--were represented by notes nested inside the notes representing the larger, block-level HTML elements. I develped export templates for the required block elements as well as many subelements. As a result, building and modifying my course websites involves little, if any, tinkering at the level of HTML. I can focus on the overall document I'm editing and not worry so much about formatting. This is especially important when working with so detailed an object as, for example, the daily syllabus for the theory course I am presently teaching.

A few things I would like to point out about the current syllabus for the theory course is that the coding of typographer's quotes around articles, last-name orientation for authors, page ranges for assigments, in-line URLs for downloadable materials, content for the RSS feed, the cell formatting to identify the next meeting, and many other style and structural elements are accomplished by my Tinderbox document.

What's more, the fundamental unit of an assignment on my daily syllabus originates from a bibliographic entry produced by EndNote. First, I select references in EndNote for export. I run a PERL transformation on those exported items which produces a Tinderbox document. I then import these Tinderbox objects into my course Tinderbox document, rearranging and tagging the objects until I have a workable syllabus.

This process is nearly identical to the one I use in my own research. In the next month or so, I will be building a new Tinderbox document to deliver a multimedia object (set of interrelated data) which examines the cultural significance of postmodern zombie cinema, a web-accessible project which will be closely related to a scholarly article whose working title is "Planet Zombie.

In the following video, I explain how using Tinderbox enables me to enhance my teaching using the web. Unlike paper syllabus, a web-accessible syllabus can accommodate additions, in this case, additions to help students understand difficult material covered in class. More importantly, unlike many pedagogical devices which provide students with more information about course readings, this process requires almost no additional effort.

In particular, I use an open-source tool called Skim (without question the best tool for annotating PDFs I have ever used). I use Skim to take notes on the readings and, when I'm done, export those notes to a text file. I then use a PERL script to transform those notes into a Tinderbox document and add the resulting objects to my course's Tinderbox document. I tag these objects and re-export the daily syllabus to the web when I'm finished. The notes I rank three or higher are then published under their respective assignments in initially hidden divs.

Here is the video which explains just a few of the benefits of providing such materials for my students.

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Saturday, 20 September 2008


This morning, I finished reading "Those Who Write, Teach” by David Gessner, an assistant professor at the University of North Carolina Wilmington, who discusses the effect of academic teaching (Creative Writing) on writers. In addition to being an excellent read, the article speaks to and for me, especially this (the last) sentence:

After all, what would that part, my inner monomaniac, like more than to tear off his collar and sabotage the job that keeps him from running wild?"

My reaction to those words is complicated, especially in light of my decision not to pursue tenure at my current institution. My reasons for not seeking tenure are multiple and, let me be clear on this, none of them have to do with my happiness with the job. I love my job and the people with whom it brings me into contact. In this regard, the job has been (and continues to be) more than I ever hoped for.

The main reason I have decided not to seek tenure at Ohio University is that my project is not near enough to completion.

Of course, there are other professional and personal reasons that have figured into my decision, not to mention situational realities the disclosure of which would provide information about my feelings regarding the future of my academic career. This blog is not the place for such information, not yet anyway. What I can say, however, is that none of the reasons informing and circumstances shaping my decision—a 2-year process which culminated in June and whose result I communicated to my colleagues in July—is as significant as the fact that, as much progress as I have made in the last three years, I am not yet done writing.

And like Gessner, I don’t just tolerate or endure teaching. I love it. end of article

Works Cited

Dibbell, Julian. "Those Who Write, Teach." The New York Times Magazine 19 September 2008.

Sunday, 14 September 2008


I was going to wait to write something about David Foster Wallace’s death, but after reading Kathleen Fitzpatrick’s comment about him in the New York Times I understood that I have something to say now. She had said that DFW’s Infinite Jestwas ironic, but at the same time it was attempting to take emotional risk [. . .] A lot of contemporary literature uses irony as a self-protective gesture, but he never did that. He was like a lot of postmodern novelists, but braver” (Williams).

I read David Foster Wallace’s Infinite Jest in the Winter of 1998, two years after my brother’s death and twenty-six after my father’s.1 I was, at the time, separated from myself and others to such an extent that I was having conversations without being in them. I remember, for example, one time standing on the street on a late summer Charlottesville’s afternoon talking to my friend Michele. My emotional state was such that I was nodding and responding in all the appropriate places, saying things relevant to the conversation. The problem, as I recall it, was that I would have no recollection of the conversation that had transpired even thirty seconds previous. I was losing the conversation even as I was having it. My two reigning emotions of that time period were horror and devastation.

With my dissertation more like a primal intuitiion than a considered thesis—a would-be discursus on how the shift from Freudian to Lacanian psychoanalytic discourse was pardigmatic of the shift from Modernism to Postmodernism—I decided I was going to get back to the roots of my first love, literature, to figure out what I was going to write about. I took DFW’s second novel from my shelf and read it for the first time. In five days. In an epoch of my life that seemed built of despair, DFW’s novel reminded me that thinking and compassion, together combined, still could matter. I fell in love with nearly every character in the novel and hadn’t been so moved by a work of art in years, then or since.

I wish David Foster Wallace had not had to make the decision to exit this life when he did. There is so much yet I cannot say. end of article

1 By suicide.
Works Cited
Wallace, David Foster. Infinite Jest: A Novel. Boston: Back Bay Books, 1996.
Wallace, David Foster. Oblivion: Stories. New York: Little, Brown and Company, 2004.
Williams, Timothy. "Postmodern Writer Is Found Dead at Home." The New York Times 14 September 2008.

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