In fact, it’s not the only online bibliography of research into comic books. There are three more which are linked to from that site: ComicsResearch.org, comics research bibliography, and Sekundärliteratur zum Comic (German). To my knowledge, nothing similar even exists for quantum computing.

In a related note, the University of Waterloo once offered a course, ENGLISH 760, called “American Comics and Graphic Novels”. The course description is as follows:

In this course we’ll read and study contemporary American “juxtaposed pictorial and other images in deliberate sequence, intended to convey information and/or produce and aesthetic response in the viewer” (McCloud), i.e., comics. We’ll take a look at the history of American comics — and comics in general — and think about the structure, function, and rhetorical potency of this genre of literature, which relies (usually) on an especially rich correlation of text and image. To help understand that correlation, we’ll draw on the work of visual language theorists, social semioticians, and comic artists themselves, such as Scott McClud [sic] and Will Eisner. Among the comic artists we’ll likely study are Lynda Barry, Charles Burns, Daniel Clowes, R. Crumb, Frank Miller, Joe Sacco, Art Speigelman, and Chris Ware. Course work will include a presentation, an essay, and a short comic (no drawing skills required). For more information, please follow this link: http://www.arts.uwaterloo.ca/~amcmurry/comicgradcourse.pdf

Students in the class don’t even have to draw! I actually sat in on a few lectures.

Incidentally, Scott McCloud, the author of “Understanding Comics”, gave a talk on comic books at TED 2005, which is worth watching if you’re both a scientist and a fan of the medium.

It’s because of things like this that I sometimes question whether I was in the right academic field for my graduate studies.

– davinci 11781

Related posts:

1. Writing my Ph.D. Research Proposal live

The plug-in is rather simple, but since a web search turned up nothing similar (which is kind of surprising), and someone might find it useful, I thought I’d post it here.

Here is the code for “wikindx.php”:

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<?php
/* 
Plugin Name: Wikindx
Plugin URL: http://stargrads.net/blogs/davinci/2009/09/wikindx-macro-plug-in-for-wordpress
Description: Adds a macro to WordPress to insert bibliography information from Wikindx.
Author: D. L. Yonge-Mallo
Version: 1.0
Author URI: http://stargrads.net/blogs/davinci/
*/
 
function parse_wikindx($content) {
    $WikindxPath="http://path.to/wikindx/";
 
    preg_match_all('#<wikindx( resource="([ \w]+)")?(>(.*)</wikindx>| ?/>)#Usi', $content, $wikindxs, PREG_SET_ORDER);
 
    if ( count($wikindxs) > 0 ) {
        foreach ( (array) $wikindxs as $wikindx ) {
            if( empty($wikindx[2]) ) {
                $output = "ERROR: WIKINDX MISSING RESOURCE ARGUMENT";
            } else {
                $resourceId = $wikindx[2];
                $string = file_get_contents("{$WikindxPath}cmsprint.php?action=getResource&id={$resourceId}");
                if($string) {
                    $array = unserialize(base64_decode($string));
                    $output = $array[$resourceId] . " ([{$WikindxPath}index.php?action=resourceView&id={$resourceId} details])";
 
                } else {
                    $output = "ERROR: WIKINDX RESOURCE ".$resourceId." NOT FOUND";
                }
            }
            $content = str_replace($wikindx[0], $output, $content);
        }
    }
 
    return $content;
}
add_filter('the_content', 'parse_wikindx', 2);
?>

Replace “http://path.to/wikindx/” in the above with the URL to your installation of Wikindx, obviously. For example, mine is “http://stargrads.net/bibliography/”.

Put the file into the “plugins” directory on WordPress, or if you are using WordPress^μ, then into its “mu-plugins” directory.

The plug-in creates a new macro “wikindx” with one parameter “resource”, which can be used inside WordPress posts like this:

<wikindx resource="68" />

Replace “68″ in the example with the resource ID of the bibliography entry whose information you want. (This ID can be found in the URL of the resource’s page on Wikindx.) The result is that the macro is replaced by the bibliographical information for that resource. For the above example, this would be:

R. Cleve, D. Gavinsky, and D. L. Yonge-Mallo, “Quantum Algorithms for Evaluating Min-Max Trees,” in Proc. TQC 2008, Tokyo, Japan, 2008, (details)

This plug-in can be used to good effect with Rob Miller’s Footnotes plug-in for WordPress, like this:

<ref name="CGMSY08"><wikindx resource="206" /></ref>

The result^[1] can be seen in the footnote below.

– davinci 11780

Update (Sept. 15, 2009): I’ve added the plug-in to the WordPress Plugin Directory.

Related posts:

1. Using the Ajaxified Expand Post Now plug-in with Rob Miller’s Footnotes plug-in
2. Annotate With Jarnal Plug-In Module for Wikindx
3. Using jsMath with WordPress, bbPress, and Wikindx

Because I’m using Jarnal to annotate these papers, I wanted to integrate the ability to launch Jarnal into Wikindx itself, and also to store the annotations in Wikindx along with the attached documents.

I wrote the Annotate With Jarnal plug-in module for Wikindx initially for my private use, so it’s not very polished. But it gets the job done.

The module adds an “Annotate With Jarnal” menu item to the “Resources” menu in Wikindx. To use it, copy the URL of an attached PDF file, and paste it into the module’s input box. The module then generates a Jarnal Meta File which (if everything is set up correctly) launches Jarnal with the PDF file as the background.

Here is a series of screen shots showing the module in action:

The result of the above sequence of steps is that Jarnal fetches the PDF file from Wikindx, and displays it for annotation:

The annotations can be saved using Jarnal’s “Network Save” feature. This writes the Jarnal file back to the “attachments” subdirectory in the Wikindx directory on the web server, with a file name created from appending the “.jaj” extension to the hash code of the annotated file. The next time the PDF file is opened through the module, the annotations will be loaded along with the PDF file.

A user must be logged in to Wikindx to use the module. However, beyond that, there is currently not a lot of security. Furthermore, the interface is not very easy to use. Ideally, there would be an “annotate” button or link next to each attached PDF file, so that the user does not have to bother with copying the URL and pasting it. Right now, there’s nothing to stop the user from entering a malformed or nonsense URL, but in most cases the module will respond by displaying an error message or doing nothing.

The module can also be used with the Macro Expander plug-in for WordPress, to provide a link to directly annotate a PDF file from a WordPress blog entry. I kept my research notes in a private WordPress blog on my laptop, and this feature allowed me to link to and annotate the relevant papers directly from my research notes.

For more information, and the source files, see the module’s web site on launchpad.net.

– davinci 11779

Related posts:

1. Wikindx macro plug-in for WordPress
2. Converting DigiMemo files to Jarnal format
3. Using the Ajaxified Expand Post Now plug-in with Rob Miller’s Footnotes plug-in

Essentially, you just need to add the following code in the header of your web site (where “path.to” should be replaced with the URL to your installation of jsMath):

<script type="text/javascript" src="http://path.to/jsMath/easy/load.js"></script>

For this web site, the above line was added to the headers of each of the template files of the component software packages.

One minor trick to getting jsMath to work with Wikindx is that all special characters have to be escaped properly\(\). For example, to get the title of Mario Szegedy’s paper^[1] on quantum walks to display correctly, as seen here, I had to enter the title as:

Spectra of Quantized Walks and a \$\sqrt{{}\delta\epsilon{}}\$-Rule

That is, where the LaTeX math syntax requires a left curly bracket, you enter “{{}”, and where it requires a right curly bracket, you enter “{}}”. The title then appears as in the footnote below.

I have created a setup help page on the wiki to record details such as these. Also, see this forum post for some macros defined for use on this site.

– davinci

Related posts:

1. Wikindx macro plug-in for WordPress
2. Using the Ajaxified Expand Post Now plug-in with Rob Miller’s Footnotes plug-in
3. Annotate With Jarnal Plug-In Module for Wikindx

I have decided to write my research proposal live and online. Besides being a way to test out theories about electronic publishing as well as an excuse to experiment with the relevant technologies, I have a more personal reason for doing this.

Over the years, I have acquired a number of absolutely horrendous academic habits due to the necessity of hiding my studies from my parents, such as keeping a low profile and limiting my publishing. I would usually not even begin a project unless I believed that there was a chance I could complete it without being discovered, and would reveal it only after it was already a fait accompli which my parents could do nothing about. Often I would destroy my own work. These are of course habits which are impossible to maintain at the postgraduate level, and I have to break them.

The task of writing online immediately raises a number of questions. For example, what about copyright and other legal issues? Which tools would I need or should I use?

I have set up a wiki for the purpose of writing the proposal, with the goal of using it for future academic writings also. The MediaWiki software (the wiki engine originally created for Wikipedia) keeps a history of edits, which dissuades me from continually deleting the contents of the document and restarting from scratch. The jsMath extension allows me to render LaTeX formulas in the wiki. I have also been keeping a bibliography using WIKINDX, from which I can insert citations into the wiki. I haven’t yet figured out what to use for figures and diagrams, but most of the major tools necessary for writing a scientific paper seem to be covered.

I don’t want to dwell on the legal issues, except that the proposal should have the same legal status as if I had written it using more traditional means and submitted it on paper. I have put the entire wiki under a Creative Commons Attribution-Noncommercial-No Derivative Works license.

The research proposal is here. It’s far from complete, but that’s exactly the point.

– davinci

Related posts:

1. Overcoming my writer’s block, part 3: science writing in high school
2. Why and for whom am I writing this?
3. My depression in Waterloo, part 8: disguising my research

To begin with, I didn’t find any ready-made projects which exactly suited my needs. The most impressive, and the one which came the closest to what I was looking for, is OpenWetWare, but its focus is on biology and biological engineering. Chemists have also gotten into the act with UsefulChem, which is hosted on wikispaces.

I did not locate any project of a similar scope or scale for physics or, perhaps ironically, computer science. The physics community is actually an early adopter of electronic scientific publishing, with its embrace of the arXiv since 1991. And the quantum community has not just one but two — count ‘em, two — whole wikis to itself: Quantiki and Qwiki. Michael Nielsen (the Mike of Mike and Ike, which is widely considered the standard text for quantum computation) has written an extensive post about the opening up of scientific culture.

Another reason for building the site myself, instead of relying on a ready-made solution, is the degree of control I would have over its customization. For a biologist or chemist, communications technologies such as blogs and wikis are only tools. But for a computer scientist, these technologies are themselves objects of study.

Following OpenWetWare’s example, I have installed MediaWiki (for wikis) and WordPress (for blogs), and I have also added bbPress (for bulletin boards) and WIKINDX (for bibliography management) into the mix.

Despite the fact that the name ★grads.net, which came to me in a fit of inspiration, suggests multiple grad(uate student)s, for now this experiment in open notebook science is mine alone.

– davinci

No related posts.