## Archive for the ‘Featured’ Category

## On SSL/TLS and HTTPS — Briefings for my Computer Security class

** Brief:** This is a technical briefing I made for fellow students in a Computer Security class (Winter 2011) about Secure Socket Layer [SSL] (now Transport Layer Security [TLS]). These briefings fit in nicely since it came after Dr. Obimbo explained the number theory behind RSA (modulus prime exponentiation). I went to the primary source on this topic to write this document: thanks to the Internet Engineering Task Force. I’ve posted this document as a consumable reference for anyone who needs it.

>>> **Download:** A Network Security Spotlight on SSL/TLS and HTTPS (pdf) <<<

*Figure $_: A Schematic of the SSL/TLS Handshaking Procedure.*

*This document is licensed under Creative Commons Attribution 3.0 Unported. The enclosed figures are further released into the public domain.*

## Fuzzy c-means for greylevel image segmentation

Here’s a script I threw together to do grey-level segmentation using fuzzy c-means. This appeared as a small part of a project in the image processing course I took. The algorithm deployed was really a proof of concept meant to replicate and verify the results of another author — as such, I don’t recommend ever using fuzzy c-means for this task as it’s pretty inefficient. This software will handle any number of grey-level-segments you desire, but I recommend eight as a maximum.

*The code and course project paper are originally dated April 20th, 2011.*

>>> **Download:** FCMProjectPaper.pdf | FCMProject.tgz <<<

( *Requires* pypng — *Python PNG encoder/decoder* )

Here are the examples included in the above archive. I like pictures.

Sunny in 8-bit greyscale, 3-bit greyscale, 2-bit greyscale.

Auryo in 8-bit greyscale, 3-bit greyscale, 2-bit greyscale.

Enjoy 😀

## My talk at Barcode of Life, Adelaide (2011)

I’ve just finished my presentation in Adelaide. This is the first real biology-heavy conference I’ve been to. Sujeevan has brought me along with the BOLD team from BIO in order to present my work — and more importantly — to acquire some resolution about the barcoding culture and its biological significance. The Consortium for The Barcode of Life (CBOL) co-hosted this event with many biodiversity parties in Australia. Another huge group present was the International Barcode of Life (iBOL) project. The Barcode of Life Conference is held every other year and is attended by researchers interested in the concerted international barcoding effort. I presented my preliminary findings with a data analysis session and had excellent feedback — it’s pretty clear where to go next with my thesis! My talk describes the first steps to automating barcode (contig-like) assembly from ab1 sequencer trace files. This talk describes the present need for automation, trends that we can readily detect in currently assembled data and most importantly — detectable patterns in how human experts perform manual barcode assembly.

The full name of the conference is *Fourth International Barcode of Life Conference*.

>>> **Download:** ( pdf: EddieMaBOL2011Adelaide.pdf | zip: EddieMaBOL2011Adelaide.pdf.zip ) <<<

Slides 6, 16, 24 from my presentation — The need for automation; Compositional bias and human edits [null hypothesis]; Where are human edits occurring [in Lepidoptera]?

This has been a very enjoyable conference 😀

## My talk at Complex Adaptive Systems, Chicago (2011)

I’ve just returned from the Complex Adaptive Systems conference on Wednesday after an eight hour drive — well, most of the driving was done by Dr. Obimbo and Haochen. I presented my paper *An evolutionary computation attack on one-round TEA*. This paper is built on top of my course project in Computer Security (University of Guelph, Winter 2011). This is my first cryptanalysis paper, and is an aside to the bioinformatics focus of my thesis.

My slides introduce Tiny Encryption Algorithm (TEA) pretty well, along with Genetic Algorithm (GA) and Harmony Search (HS). The slides detailing the results aren’t quite as self-explanatory, but are bearable since the theme is fairly easy to establish: *simpler keys are easier to break than more complicated ones*.

>>> **Download: **CAS2011Chicago.pdf — my presentation from Chicago. <<<

I *might* look at cryptanalysis again in future — but I’ll certainly use Evolutionary Computation (EC) again. It’s just too readily available in my toolkit, and is far too easy to deploy. One of the major lessons of this project that became very clear through during discussion with the audience is that the operators that are part of an EC algorithm should reflect the kind of problem we’re trying to solve. This might seem obvious at first, but I think it’s more subtle than that. For this project, HS enabled the EC to probe a keyspace with many repetitions — something that GA operators alone didn’t provide us.

In general however, the solution space is lumpy enough that using ECs against stronger encryption schemes is just not viable — unless the EC had some magic to overcome the linearly inseparable lumps. I haven’t yet met such an operator and am not convinced one way or another about its existence. I’ll certainly introduce you if I ever do bump into it 😛

## Partial Derivatives for Residuals of the Gaussian Function

I needed to get the partial derivatives for the residuals of the Gaussian Function this week. This is needed for a curve fit I’ll use later. I completely forgot about Maxima, which can do this automatically — so I did it by hand (Maxima is like Maple, but it’s free). I’ve included my work in this post for future reference. If you want a quick refresh on calculus or a step-by-step for this particular function, enjoy :D. The math below is rendered with MathJax.

The Gaussian Function is given by …

$$ f(x) = ae^{-\frac{(x-b)^2}{2c^2}} $$

*a*,*b*,*c*are the curve parameters with respect to which we differentiate the residual function*e*is Euler’s number

Given a set of coordinates I’d like to fit (x_{i}, y_{i}), i ∈ [1, m], the residuals are given by …

$$ r_i = y_i – ae^{-\frac{(x_i-b)^2}{2c^2}} $$

We want to get …

$$ \frac{\partial{r}}{\partial{a}}, \frac{\partial{r}}{\partial{b}}, \frac{\partial{r}}{\partial{c}} $$

## Exposing MATLAB data with JFrame & JTextArea

Today, I’ll describe my first foray into MATLAB. My task is simple — there’s already a GUI developed as a toolbox. The user inputs a bunch of data, and it crunches it away and provides a graph and displays a dialogue box about the moments of the data. The issue here is that we’d like to know more about the data — particularly, we’d like to retrieve the ordered pairs corresponding to each of the plotted points in the graph.

In this exercise, I’ll show you how to use JFrame & JTextArea to display the coordinates of a graph in an already existing MATLAB GUI toolbox or plugin.

*The reason why I’ve decided on this approach rather than outputting directly to the MATLAB console is because I eventually want to add additional functions to reshape and reformat the text, and also to save the text that appears in its own window using additional Java swing components. But that’s a story for another day.*

**The Quick How-To … ( ***3 steps*** )**

Choose the toolbox or plugin you’d like to modify and open up its “.m” file. This is where you’ll want to add your custom code. There are three parts to this exercise — first, we need to get a few classes from Java; then, we need to store the data we want to display; finally, we make the display appear.

In this example, I’ll import the bare minimal amount of Java classes — you can extend this functionality by adding more swing classes if you like. I’ve arbitrarily prefixed my Java variables above with the prefix “expose”.

import javax.swing.JFrame; import javax.swing.JTextArea; import javax.swing.JScrollPane; // Scrollbars -- optional. exposeReport = JFrame('Data Report'); exposeTa = JTextArea(24, 80); exposeScroll = JScrollPane(exposeTa); exposeScroll.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_ALWAYS); exposePane = exposeReport.getContentPane(); exposePane.add(exposeScroll); exposeReport.pack();

*I’m not exactly sure why MATLAB doesn’t include scrollbars automatically.*

Of the above, there are only two variables which we’ll need to refer to again later — “exposeReport” and “exposePane”.

The next step is to use your JTextArea as an output terminal. Just append strings to it as the graph is being built — you’ll have to look at your specific plugin to figure out the logic behind the graph — in general, you’ll be looking for a for-loop and a function that alters the graph.

// Look for a 'for' loop with a line that adds data to the graph. // Here, I've used the variable SomeX for a point's x-coordinate, // and SomeY for a point's y-coordinate. exposeTa.append(sprintf('%d\t%d\n', SomeX, SomeY));

The loop spins around and incrementally adds all of the points. Note that I’ve used “%d” as a conversion to numbers expressed in base-ten (including floating point values). This is different from the conversion character in C where “%d” indicates only integers.

We add the final code after the loop exits. This next code makes your data report window visible — just as you’d expect from Java.

exposeReport.setVisible(1);

I opted to put this line after the code that reveals the toolbox’s original summary window — this causes my report to appear on top.

That’s all there is to it! Enjoy 😀

**MATLAB from a CS student perspective**

MATLAB has always been a bit of an oddball language for me. It’s dynamically typed but also exposes Java’s classes if you ask nicely. It’s C-looking and provides functions that the C-programmer would be happy accepting such as *strcat* and *sprintf*, but again — putting on the dynamic spin by returning the constructed string rather than modifying the contents of a buffer. All in all, the design choices do a good job of making MATLAB do what it’s intended to do; it gives scientists and engineers a way to succinctly express math to a machine without having to take too many computer science courses.