Bioinformatics

A friend of mine; serial entrepreneur, and former president of Genetic Systems; Joe Ashley, told me once that starting a business is an unnatural act.

Now that I've done it, I agree. Even with my multiple back-up plans, possible grants, and part-time activities, my stomach still hurts and my mind is racing. My new company has "spun out" of another. Spinning out of control until you fall down from exhaustion. It's a great metaphor all right.

Sure, there's excitement and adventure. I love my new shiny business cards and my new shiny web site! It's fun ... Read more

Have you ever wondered how to find things in the NCBI databases? Maybe you tried to find something but didn't know how it was spelled. Or maybe you tried to use a common name like "pig" or "deer" to find information in a database, not knowing that all the organism names are in Latin. Or perhaps you're wondering just what kind of information is stored for different kinds of records and if you could search for this information. I wrote a book that covered this topic quite thoroughly, a couple of years ago, for the NCBI structure database ... Read more

I suppose I should have expected this. I thought it might be fun to see what the databases had to say about turkeys. So, I queried the NCBI databases, found a taxonomy reference, and started clicking related links to see pictures of the different species. Why? Because it would be great to see what the different species of turkies look like and compare them. Here's a species of wild turkey that I didn't expect to find.

I just love this title! It's nerdy and cute, all at the same time. I read about this in www.researchblogging.org and had to check out the paper and blog write up from The Beagle Project (BTW: some of you may be interested in knowing that The Beagle Project is not a blog about dogs.) The paper describes a class where students from Marseilles University investigate the function of unidentified genes from a ... Read more

Ebola virus has impressed me as creepy ever since I read "The Hot Zone: A Terrifying True Story some years back by Richard Preston. (I guess he has a new book, too, ... Read more

I'm sure everyone else thinks the big news today is the announcement by the Washington State Health department requiring hospitals to report MRSA cases to the state. I think the cool news is their on-line database. We'll get to that a bit later. What is MRSA? MRSA stands for methicillin-resistant Staphylococcus aureus. It's a serious pathogen that causes skin infections and greater damage if it enters the body. The Seattle Times report - a quick summary For the past three days the Seattle Times has been ... Read more

Want to learn more about Parkinson's disease? See why a single nucleotide mutation messes up the function of a protein? I have a short activity that uses Cn3D (a molecular viewing program from the NCBI) to look at a protein that seems to be involved in a rare form of Parkinson's disease and I could sure use beta testers. If you'd like to do this, I need you to follow the directions below and afterwards, go to a web form and answer a few questions. Don't worry about getting the wrong answers. I won't know who ... Read more

HealthMap is a great site that could be an excellent resource when teaching a biology, microbiology, or health class. Not to mention, I can picture people using it before they travel somewhere or even just for fun. I learned about HealthMap awhile ago from Mike the Mad Biologist, but I didn't get time to play with the site until today. Here's an example to see how it works. How do I use HealthMap? ... Read more

Let's play anomaly! Most of this week, I've written about the fun time I had playing around with NCBI's Blink database and finding evidence that at least one mosquito, Aedes aegypti, seems to have been infected at some point with a plant paramyxovirus and that the paramyxovirus left one of its genes behind, stuck in the mosquito genome. During this process, I realized that the method I used works with other viruses, too. I tried it with a few random viruses and sure enough, I found some interesting things. You've got a week to give it a try. Let's see ... Read more

Lots of bloggers in the DNA network have been busy these past few days writing about Google's co-founder Sergey Brin, his blog, his wife's company (23andme), and his mutation in the LRRK2 gene. I was a little surprised to see that while other bloggers (here, here, ... Read more