June 20, 2009
Category: Bioinformatics • Plant biology • Science education
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
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Posted by Sandra Porter at 1:01 PM • 2 Comments
May 8, 2009
Category: Genome • Genomics
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?
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Posted by Sandra Porter at 8:00 AM • 16 Comments
May 6, 2009
Category: Biology (Macroscopic ) • Computers and software • Neurobiology • Science education • iphones • technologies for teaching
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.
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Posted by Sandra Porter at 8:00 AM • 14 Comments
May 5, 2009
Category: Databases • Genomics • PharmGKB
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?
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Posted by Sandra Porter at 1:32 PM • 2 Comments • 0 TrackBacks
May 2, 2009
Category: Cn3D • Influenza resources • Science education • molecular structures • viruses
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.
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Posted by Sandra Porter at 7:00 PM • 4 Comments
May 1, 2009
April 30, 2009
Category: Bioinformatics • Genome • Influenza resources • Science education • classroom activities • sequence analysis • web resources
We'll have a blast, I promise! But there's one little thing we need to discuss first...
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Posted by Sandra Porter at 11:00 PM • 0 Comments
Category: Bioinformatics • Genetics & Molecular Biology • Genomics • Influenza resources • Microbiology • Science education • biotechnology • classroom activities • sequence analysis • viruses
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.
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Posted by Sandra Porter at 10:00 PM • 4 Comments
Category: Influenza resources • Seattle
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!
Posted by Sandra Porter at 9:01 PM • 1 Comments
Category: Databases • Influenza resources • Science education • classroom activities • technologies for teaching • web resources
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.
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Posted by Sandra Porter at 11:55 AM • 4 Comments
I am a microbiologist and molecular biologist turned tenured biotech faculty turned bioinformatics scientist turned entrepreneur. My passion is developing instructional materials for 21st century biology (
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