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Archives for April, 2009

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

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…

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!

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…

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…

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

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…

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

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,…

Genome sequences from California and Texas isolates of the H1N1 swine flu are already available for exploration at the NCBI. Let’s do a bit of digital biology and see what we can learn. Activity 1. What kinds of animals get the flu?