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Jeffrey D. Allen Professional and Personal Updates 2012-10-24T22:09:35Z http://jdadesign.net/feed/atom/ WordPress jeffreya http://jdadesign.net <![CDATA[Simple Java REST Framework]]> http://jdadesign.net/?p=116 2012-10-24T22:09:35Z 2012-10-24T22:09:35Z I just wrapped up the scaffolding for a simple Java REST web service framework. We used Maven to handle all dependencies and requirements, Spring for Dependency Injection, Hibernate for ORM, and RESTEasy for the web service/REST portion.

The source code’s available on GitHub for those interested: https://github.com/QBRC/Resprirnate

jeffreya http://jdadesign.net <![CDATA[Install RGL in Ubuntu]]> http://jdadesign.net/?p=113 2012-10-14T15:10:58Z 2012-10-14T15:10:58Z I had a few hurdles to get through when trying to install the “rgl” R package in Ubuntu. In summary, here was my solution:

From the terminal:

sudo apt-get install r-cran-dev xorg-dev libglu1-mesa-dev

Then from R:


 Detailed Log

The first snag I hit was the following implying I was missing some necessary X code:

checking for X... no
configure: error: X11 not found but required, configure aborted.
ERROR: configuration failed for package ‘rgl’

You’ll need the `xorg-dev` package to get around this issue. I then hit an error regarding a `GL` library:

checking for X... libraries , headers
checking GL/gl.h usability... no
checking GL/gl.h presence... no
checking for GL/gl.h... no
checking GL/glu.h usability... no
checking GL/glu.h presence... no
checking for GL/glu.h... no
configure: error: missing required header GL/gl.h
ERROR: configuration failed for package ‘rgl’

A quick Google showed that the `libglu1-mesa-dev` package contained these headers. Once I had installed those package, the install process went smoothly!

Note, too, that there may be a precompiled package may be available for your distribution under the name r-cran-rgl. In my case, I needed a more recent version of the package than was offered there, hence this exploration.

jeffreya http://jdadesign.net <![CDATA[Dogs]]> http://jdadesign.net/?p=109 2010-12-27T23:52:49Z 2010-12-27T23:52:44Z
jeffreya http://jdadesign.net <![CDATA[South Dallas]]> http://jdadesign.net/?p=108 2010-12-27T23:52:59Z 2010-12-10T23:51:33Z A few pictures from South Dallas

jeffreya http://jdadesign.net <![CDATA[qTip Library with WordPress 3]]> http://jdadesign.net/?p=107 2010-11-16T22:54:50Z 2010-11-16T22:54:50Z I like using the qTip library to handle dynamic tooltips in my sites. I also use WordPress as my CMS-of-choice. Unfortunately, I found that they don’t, by default, play very nicely together.

I’ve attached my modified version of the qTip library (based on v.1.0.0-rc3 — current at the time of writing) which solves these issues.


Here’s what I had to fix in order to make this compatible:

  1. There’s a bug in qTip that is still lingering. It only becomes an issue when using a recent version of jQuery. I had to make the modifications described in the link mentioned previously.
  2. WordPress can’t give jQuery exclusive usage of the “$” variable, so all “$” references must be changed to “jQuery.” This script has been updated to reflect those changes.


As promised, the modified Javascript file is available here: Wordpress-Friendly qTip Library (979).


To use this (or any) Javascript file in WordPress, you’ll need to add a few lines to the “functions.php” file of your active theme.

//make sure we've loaded jQuery

* Adds the qTip javascript library.
function addQtip() {
 wp_enqueue_script('qtip',get_bloginfo('template_directory') . '/js/jquery.qtip-1.0.0-rc3.min.js');
add_action('init', 'addQtip');

This script assumes that you’ve uploaded the attached Javascript file in the “js” directory of your active theme. If you have it elsewhere, you’ll need to adjust the reference in the “wp_enque_script” line.

And that’s it! You should now be able to use qTip within WordPress.

jeffreya http://jdadesign.net <![CDATA[MBCB On Bioconductor]]> http://jdadesign.net/?p=105 2010-11-17T15:13:49Z 2010-08-03T18:08:44Z The Model-Based Background Correction (MBCB) R package is now included in “under-development” Bioconductor version (currently v. 2.7). There are two ways to use the version of MBCB included on Bioconductor:

1. Use R 2.12 (under development, at the time of writing) and execute the following two commands:


2. Manually install the packages into older R version available here.

Sample data files are still available in the previous announcement.

jeffreya http://jdadesign.net <![CDATA[Washington, DC]]> http://jdadesign.net/?p=104 2010-07-31T15:07:57Z 2010-07-31T15:07:57Z Pictures taken on a trip to Washington, DC.

jeffreya http://jdadesign.net <![CDATA[Grand Cayman]]> http://jdadesign.net/?p=102 2010-06-20T15:49:01Z 2010-06-07T23:21:13Z Pictures from a trip to the Caymans.

Photos #7, 8 taken by Dave Allen.

jeffreya http://jdadesign.net <![CDATA[Genetic Engineering from a Christian Perspective]]> http://jdadesign.net/?p=101 2010-05-06T14:57:18Z 2010-05-06T14:57:08Z I wrote a paper dealing with the issue of Genetic Engineering from a Christian standpoint for a Bioethics course. I argue that genetic therapy is licit but genetic enhancement and eugenics are not.

Complete paper available here: Genetic Engineering from a Christian Perspective (3268)

jeffreya http://jdadesign.net <![CDATA[Pressure-Sensitive Keystroke Dynamics Dataset]]> http://jdadesign.net/2010/04/pressure-sensitive-keystroke-dynamics-dataset/ 2010-05-13T14:49:52Z 2010-04-17T00:52:54Z As a part of my thesis in Keystroke Dynamics, I collected quite a bit of data on users typing a handful of passwords. I’ve decided to make this data available publicly for two main reasons:

  1. It could lower the entry barrier to the field. Individuals interested in developing an algorithm but without the means to collect a significant amount of data will be able to use this data to experiment. Also, most researchers don’t have access to pressure-sensitive keyboards when developing their algorithms. This data will allow researchers to test their algorithms and consider this extra dimension of typing data.
  2. I hope that this dataset could become a standard for the field of keystroke dynamics. One thing which I felt was substantially lacking in my literature review was any basis of comparison when analyzing different approaches. My hope is that researchers can, after developing an algorithm, measure their results on this dataset as a way to objectively compare performance.

The data is currently available in two formats, with a third in the works.

A MySQL database dump is available here: Public Keystroke Dynamics SQL (20838). The structure of the database is depicted in the figure to the left.

The same data is also available is a series of Comma-Separated-Value (CSV) files and can be downloaded here: Public Keystroke Dynamics CSV (9077). The same structure and relationships apply, though they’re obviously not enforced in CSV files.

The data was collected over a period of a few months in 2009-2010 on over 104 different users. “Extensive” data was collected on 7 of these users – who entered between 89 and 504 entries total.

The rest of the users just entered each password between 3 and 15 times to provide a substantial amount of “impostor” data on each password.

Three different passwords were tested to try to cover the range of different approaches in KD:

  1. pr7q1z – a password of gibberish meant to test the performance of Pressure-Sensitive KD on modern “strong” passwords.
  2. jeffrey allen – the use of personal information (such as a name) has been recommended in KD before. By using my own name and recording my typing habits on it, the performance of using personal information can be measured.
  3. drizzle – a word meant to test the use of normal dictionary words which likely have no personal significance to any user.

In total, 2,739 entries were collected — over 900 on each password.

Please feel free to use this dataset for any non-commercial purposes. I do ask that you let me know if you use this dataset and please use the following citation (for now):
Allen, Jeffrey D., An Analysis of Pressure-Based Keystroke Dynamics Algorithms, Computer Science and Engineering, Southern Methodist University, 2010.

If you’re interested in contributing more data (pressure-sensitive or not), please contact me as well; I’d love to incorporate more datasets into this one.

Another dataset is available at http://www.cs.cmu.edu/~keystroke/