TheSpicyChicken » Science

The Science of Hearing – We need you!

Spicy — Tue, 26 May 2009 18:42:00 +0000

A friend of mine, and neuroscience graduate student at Case Western Reserve University are conducting a study into the genetic basis of hearing the following sound:

http://tinyurl.com/2wjoxy

NPR recently did a story that teenagers have been using the above sound as a ring tone to evade the prying eyes ears of adults.

So we started a little investigation of our own, and we need your help! Just click on that sound file, play it, and respond in the comments with your age, gender, and if you can hear it or not.

SCIENCE!

Finally… back to Science.

Spicy — Fri, 07 Nov 2008 18:39:01 +0000

With the election behind and a collective sigh of relief from the science community we can get back to the good stuff– throwing some fuel into the engine we call SCIENCE! For my part, I got some much needed time to learn about and implement some simple algorithms utilizing CUDA. CUDA is a c-extension from Nvidia for leveraging the massive computational power in your GPU. In my case my GeForce 8600M graphics card in my MacBook Pro.

I have to give some serious props to the devs of CUDA because it is very straight forward and makes programming for the GPU rather intuitive. I have been able to implement the Lloyd’s Algorithm for the K-Means problem in just a few days. The speed increase is graphically represented in the following graph.

In green is the time in seconds required to compute the kmeans solution using the CPU and in red is the time required for the GPU. The variance in the times comes from the nature of Lloyd’s algorithm which, depding on the input, can take a variable amount of time. The GPU times are also varied but it is difficult to see in the figure.

These results are just from running the application on my MBP. If you have a machine with many graphics processors (or many machines each with their own GPU) then you can parallelize this even more and massively boost your computational power. In my opinion the GPU architecture is the future of scientific computing as so many of our computational challenges can be addressed using parallelization.

For those that are interested I will be writing up some CUDA tutorials covering Installation/Set Up, A “Hello World” example, and the full K-Means implementation over at MacResearch.org.

Chem(o)informatics

Spicy — Wed, 29 Oct 2008 18:02:57 +0000

As a PhD student you start out by doing rotations, quarter-long research projects, in various Professor’s lab. In my rotation I am attempting to learn all there is to know about Chem(o)informatics. I write it that way because there is an apparent dispute as to what exactly to call this field of study (Cheminformatics versus Chemoinformatics). As I do with many problems, I turned to Google for the answer. A quick search revealed that the term Cheminformatics is more prominent. “Ah ha!” I exclaimed. For the all knowing Google could not be wrong and so it must be. However, an itch in the back of my mind made me do a search using Google Scholar. Alas, to my dismay, it showed the opposite. In an attempt to break the tie and resolve this conflict I attempted another search in PubMed. Surely that would settle things. The results of my studies are below.

(Perhaps definatively, my spellcheck says there both wrong.)

Journal 1.2

Spicy — Wed, 29 Oct 2008 03:07:44 +0000

Once again I find myself faced with the need for journaling software. Last time I scoured the internets looking for good (and hopefully free) software for writing down and organizing my scientific studies (and other tasks) in a journaling program. However, I was disappointed in what I discovered. This led to the birth of Journal, a dead-simple Cocoa application for just that.

Journal is not without its limitations however and I again was seeking out an alternative for my work. I have had slightly higher success and probably my favorite app is VoodooPad, which is a native cocoa wiki. Alas, however, the structure of a wiki may not be the best for organizing a linear progression of work (and yet has lots of advantages as well) but compounded by the $40 price tag I was put off. I turned back to my app, Journal, and decided it really wouldn’t take too much work to make Journal a whole lot better. So I quickly implemented some extra features (rich-text editing and image/pdf incorporation) and turned out the next release of this software. My hope is again that some will enjoy it.

You can download Journal 1.2 here.