Stephen Lynch

Ok, I’m probably the last person to hear about him, but I was listening to pandora the other day, and decided to create a “Flight of the Conchords” channel, and pandora played a couple of songs by Stephen Lynch.  I liked those songs, so I picked up one of his CDs from amazon, and it arrived yesterday.  I’m really enjoying it.

To give you an idea, here is a youtube video of the song D&D off the CD (Superhero):

That video is PG…most of the other stuff on the CD is rated R…not that I mind, but fair warning.

Breaking CAPTCHA

I always figured there were ways spammers could get around CAPTCHA (Completely Automated Turing Test To Tell Computers and Humans Apart), but I’d never seen it discussed.  For those that might not be familiar with the name, a CAPTCHA is one of those weird text challenges where you have to type in some cryptic text to register on a site:

CAPTCHA Sample

I stumbled across an article describing a trojan that presents voyeurs with a woman doing a strip tease – each successful CAPTCHA entry removes another article of clothing.  One such trojan (HotLan) has been used to create more than 500,000 accounts on popular e-mail sites.

It struck me as a bit ironic that clicking on the “Discuss this article” link on that website prompted me with a registration form that included a CAPTCHA challenge.

The CAPTCHA web site acknowledges the issue, but deems it “not a concern”:

While it might be the case that some spammers use porn sites to attack CAPTCHAs, the amount of damage this can inflict is tiny (so tiny that we haven’t even noticed a dent!).

In spite of all this, I don’t see much of an alternative, and I’m sure I’ll continue to use CAPTCHAs on sites.  At least it makes it a lot harder for spammers…

Cardiac Physiology and Action Potential Movies

In Physiology class today, we talked about cardiac physiology and the action potentials for heart contraction.  it was a lot of information to soak up, so I went looking for some additional sources.  I found a handful of movies by Walid Aziz (aka hyperhighs) on youtube that are simple, but he has a knack for explaining things.  I’ve collected the links here that are relevant to my class, but he has posted many more videos on physiology and anatomy.

• Heart Physiology (Ventricular filling: part 1/6)
• Heart Physiology (Cardiac pressure-time curve: part 2/6)
• Heart Physiology (Cardiac output: part 3/6)
• Heart Physiology (Starling law: part 4/6)
• Heart Physiology (Length-tension plot: part 5/6)
• Heart Physiology (Dynamic heart plot: part 6/6)

• Cardiac Action Potential (Pulse propagation: part 1/6)
• Cardiac Action Potential (Pacemaker AP: part 2/6)
• Cardiac Action Potential (Autonomic effect: part 3/6)
• Cardiac Action Potential (Cardiomyocyte AP: part 4/6)
• Cardiac Action Potential (Electro-mechanics: part 5/6)
• Cardiac Action Potential (Sarcomere: part 6/6)

First BioSharp App – RestrictionFinder

I’ve started work on my first application that uses BioSharp.  It is called RestrictionFinder, and its purpose is to help find a pair of restriction enzymes that give distinct cleavage patterns when an insert is present in a plasmid in the forward direction, reverse direction, or absent.  It also has the ability to limit the search to pairs of enzymes with compatible buffers.

Here is a screen shot of the sequence entry form:

Sequence Entry Form

If the sequence contains uppercase and lowercase, the lowercase is assumed to be the insert, and the start/end positions are set automatically.

As part of the solution, I needed a small database (just a file, really) of enzymes and their buffers.  I could not find a readily available file for this, so I wrote a small console app that extracts the data from the REBASE web site.

This is still a work in progress, but the source code is checked into the BioSharp SVN repository.