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Professional | Jeffrey D. Allen


Simple Java REST Framework

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

qTip Library with WordPress 3

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 (978).


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.

MBCB On Bioconductor

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.

Pressure-Sensitive Keystroke Dynamics Dataset

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.

Read more

MBCB Package Submission

Our Model-Based Background Correction (MBCB) R package (publication previously discussed here) has finally been submitted to Bioconductor.

MBCB is a software package aimed at background-correcting Illumina microarrays using model-based statistics. These methods include a Bayesian Method, MLE, Non-Parametric, Robust Multi-Array Average, and GMLE. Various normalization methods are also offered for post-processing.

Hopefully it will be available within the coming weeks. In the mean time, the current versions of the software are available here:

Update: MBCB is now included in Bioconductor 2.7. More detailed instructions are available here.

Sample data files: Signal.txt (912), Negative Control (1019)

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