Wednesday, November 15, 2006

Virtual Reality Used to Cure Phantom Limb Pain

Today, slashdot.org had a post concerning the use of Virtual Reality (VR) technology to cure phantom limb pain (PLP). PLP is the sensation one may feel after the loss of a limb via amputation. For example lets say a person's left leg is amputated due to diabetes but they still feel pain in their left foot even though they no longer have that limb; this is PLP. The Virtual Reality comes into play by tricking the amputee's brain into believing they still have the limb and therefore reduces pain felt in PLP.

Some may differ in this opinion but I consider this to be bioinformatics related since its the use of computer science techniques to address a biological or clinical problem. What does everyone else think?

Tuesday, November 14, 2006

Ruby Programming Language

I decided to attend a Ruby user group today and figured I needed to get up to date with Ruby as fast as possible. The following are the links I found most useful:



Does anyone have additional suggestions on how to quickly get started with Ruby?

Artificial Intelligence

I realized that yesterday I kept on mentioning artificial intelligence without even explaining the general concept of it. Kind of defeats the whole theme ("simplifying bioinformatics") of my site, huh? Well here is a quick briefing on the concept of artificial intelligence.


According to netdictionary, artificial intelligence is "a branch of computer science that studies how to endow computers with capabilities of human intelligence." Now lets not get crazy and think of highly intelligent system such as Data from Star Trek (seen on the left). These capabilities of human intelligence can be basic concepts such as the ability to classify objects. For instance how we classify an shape to be a circle versus a square.



The idea is to provide the computer with enough information so that it can use an algorithm to make these classifications. For instance in the case of shapes one may provide the computer with the number of lines. Well of course the square has four lines while the circle has none or one depending on how you define a line. Remember this is an oversimplified case.

These classifications can get quite advance such as the typical logistic credit application problem. In most beginning AI courses students are presented with credit application data and are charged with the task of programming the computer to decide whether an application should be approved or not. Another example is Dr. Brooks's classification algorithm to distinguish between different structures of sarcoma tumor beds, covered yesterday.

Well thats as simplified as I can put it, what does everyone else think?

Monday, November 13, 2006

Artificial Intelligence and Cancer Research

I attended a talk today, concerning the use of artificial intelligence (AI) in cancer research.  Dr. Paul Brooks discussed his research using AI to study a particular treatment of sarcoma, a cancer in the supportive tissues of the body (i.e. blood vessels, bones, muscles, etc).

He described the need to use computer algorithms to improve brachytherapy, a method that can be applied post removal of a tumor.  What brachytherapy does is insert sealed sources of radiotherapy around the the area from where the tumor was removed to treat the leftover diseased tissue.  In the abstract of his publiction Dr. Brooks describes the current practice of determining the area for brachytherapy treatment to be a "tedious manual process". 

What his research entailed was using AI to automatically classify the contours of how the radiotherapy sources were to be placed.  The AI would be able to distinguish between various structures of sarcoma tumour beds and suggest the best placement for the radiotherapy treatment.

I'm not sure about any other bioinformaticians out there but its pretty exciting to see computer science and biology merged together for actual clinical application.

Dr. Brooks's abstract can be found here via PubMed.

Tuesday, November 7, 2006

Hooray for Bioinformatics!

The BBC news had a report last week on a UK Scientist winning a large international prize with his work in E. Coli. What was supposed special about his work is that he used computers to model a part of the biological system of E. Coli. Its nice to see Bioinformatics (or Computational Biology) recognized internationally. If you want to know more you can read the article here.