Sat, 20 Jun 2009 13:01:38 -0500

For those of you who may have been wondering where I've been, these past few weeks have seen me grading final projects, writing a chapter on analyzing Next Gen DNA sequencing data for the Current Protocols series, and flying back and forth between Seattle and various meetings elsewhere in the U.S. It will probably take years of bike commuting to make up for my carbon credits, but most meetings I attend don't have viable alternatives in venues like Second Life or World of Warcraft. Anyway, as I sit writing on an airplane, I think I could revise the title for Dr. Seuss' famous book to "Oh the places I've been."

Inside the tropical house at the Missouri Botanical Garden

Fri, 08 May 2009 08:00:18 -0500

One of the interesting things I learned today was that many people are calling for the genome sequences of the chimps and Macaques to be finished.

This is especially amusing because the human genome isn't quite done. We're primates, too! Why not finish our genome?

Wed, 06 May 2009 08:00:04 -0500

We always enjoy home science experiments and it was fun the other night to learn about a new experiment we could try with our teenage daughter and an iPhone.

As it turned out, the joke was on us.

Tue, 05 May 2009 13:32:15 -0500

Warfarin, a commonly used anti-clotting drug, sold under the brand name of Coumadin, has a been a poster child for the promise of pharmacogenomics and personalized medicine.

The excitement has come from the idea that knowing a patient's genotype, in this case for the VKORC1 and CYP2C9 genes, would allow physicians to tailor the dose of the drug and get patients the correct dose more quickly.

And it seems obvious that a test that would allow doctors to predict your ability to metabolize warfarin, would be a great thing, right?

Sat, 02 May 2009 19:00:12 -0500

Nick's post on Amantadine resistance in swine flu was so interesting, I had to look at the protein structures myself.

I couldn't find any structures with the S31N mutation that Nick discussed, but I did find some structures with the M2 protein and Amantadine. Not only are these structures beautiful, but you can look at them and see how the protein works and how the drug prevents the protein from functioning.

Fri, 01 May 2009 16:23:30 -0500

No more delays! BLAST away!

Thu, 30 Apr 2009 23:00:44 -0500

We'll have a blast, I promise! But there's one little thing we need to discuss first...

Thu, 30 Apr 2009 22:00:41 -0500

We had a great discussion in the comments yesterday after I published my NJ trees from some of the flu sequences.

If I list all the wonderful pieces of advice that readers shared, I wouldn't have any time to do the searches, but there are a few that I want to mention before getting down to work and posting my BLAST results.

Thu, 30 Apr 2009 21:01:10 -0500

We were joking about this a couple of hours ago, but I just picked up the phone and learned that two middle schools will be closed for the week.

Aki Kurose and Stevens middle schools are closed from tomorrow to May 8th. Yikes!

Thu, 30 Apr 2009 11:55:36 -0500

Last night, the phone rang at 9:22 pm. I quickly glanced at the caller ID. Hmmm. Why is the Seattle School district calling us at this time of night?

Apparently the swine flu has come to Seattle and the school district thought we should know.

Those messages are helpful if you're a parent, but they don't tell much about the rest of the world.

Health Map is a really wonderful, user-friendly, resource for following the epidemic.

Wed, 29 Apr 2009 18:03:10 -0500

I'm teaching an on-line bioinformatics course this semester for Austin Community College. They are in Texas of course, but I am in Seattle. This presents a few interesting challenges and some minor moments of amusement.

Today, the school sent all the faculty emails telling us to stay home if we're sick.

Got it. If I think I have flu, I will not fly to Texas.

Instead, I'll stay home and watch videos on coughing without contaminating others.

Watch "Why don't we do it in our sleeves?" and find out how you rank on the safe coughing scale.

Wed, 29 Apr 2009 11:21:54 -0500

What tells us that this new form of H1N1 is swine flu and not regular old human flu or avian flu?

If we had a lab, we might use antibodies, but when you're a digital biologist, you use a computer.

Activity 4. Picking influenza sequences and comparing them with phylogenetic trees

Tue, 28 Apr 2009 22:01:20 -0500

This afternoon, I was working on educational activities and suddenly realized that the H1N1 strain that caused the California outbreak might be the same strain that caused an outbreak in 2007 at an Ohio country fair.

UPDATE: I'm not so certain anymore that the strains are the same. I'm doing some work with nucleic acid sequences to look further at similarity.

Here's the data.

Tue, 28 Apr 2009 18:16:10 -0500

I was pretty impressed to find the swine flu genome sequences, from the cases in California and Texas, already for viewing at the NCBI.

You can get them and work them, too. It's pretty easy. Tomorrow, we'll align sequences and make trees.

Activity 3: Getting the swine flu sequence data

Tue, 28 Apr 2009 12:38:24 -0500

I'm a big of learning from data. There are many things we can learn about swine flu and other kinds of flu by using public databases.

In digital biology activity 1, we learned about the kinds of creatures that can get flu. Personally, I'm a little skeptical about the blowfly, but...

Now, you might wonder, what kinds of flu do these different creatures get? Are they all getting H1N1, or do they get different variations? What are H and N anyway?

We can discuss all of these, but for now, lets see what kinds of flu strains infect different kinds of creatures.

Activity 2. What flu infects who?