The Dream Project

I just found this cool DREAM Project Challenge where teams compete in deriving a gene network and predicting its output.

Cyberinfrastructure

I thought that this article provided a good overview of how biologists view cyberinfrastructure needs. I think that most of the current infrastructure has been designed with too much complexity and too little thought as to how researchers could use the tools. We need to get the users together with the developers more.

Next Generation Sequencing

We have just purchased a 454 machine at BYU. It is capable of sequencing a whole human genome in 3 days for around $20,000.
I wonder what impact this will have on biological research. We now should be able to gather statistically significant samples of DNA from groups impacted by different phenotypes (like cancer) and should then be able to apply bioinformatics to sort through the deluge of data that will be available. One machine can produce 1TB per day and the algorithms to sort everything out are really lacking.

Chemalign

I just attended a PhD Defense for Hyrum Carroll.  He presented his work on a new alignment algorithm that uses biochemical properties instead of sequence identity to fill in the Needleman-Wunsch matrix.  He found that if you use different chemical properties for each secondary structure that you get a significant increase in accuracy.  Chemalign is part of the psoda package at dna.cs.byu.edu.

Introduction

I have noticed that many bioinformatics sites are written from a biology perspective.  I have noticed a big difference between the way biologists and Computer Scientists think.  This blog will focus on the state of bioinformatics from a Computer Science Perspective.