Sandra Porter
sporte
Posts by this author
May 5, 2009
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…
May 2, 2009
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…
May 1, 2009
No more delays! BLAST away!
Time to blast. Let's see what it means for sequences to be similar.
First, we'll plan our experiment. When I think about digital biology experiments, I organize the steps in the following way:
A. Defining the question
B. Making the data sets…
April 30, 2009
We'll have a blast, I promise! But there's one little thing we need to discuss first...
I want to explain why I'm going to use nucleotide sequences for the blast search. (I used protein the other day). It's not just because someone told me too, there is a solid rational reason for this.
The…
April 30, 2009
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…
April 30, 2009
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!
April 30, 2009
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…
April 29, 2009
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…
April 29, 2009
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
We can get the…
April 28, 2009
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…
April 28, 2009
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
1. Go…
April 28, 2009
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…
April 28, 2009
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?
For the past few years we've been worrying about avian (bird).…
April 23, 2009
Usually, I'm kind of a hermit, but I heard there would be Bacon and so, I'm going to leave the house next Weds, night and attend a science blogging event at the University of Washington.
I think it will be fun. Not only will there be Bacon, there will be pizza and other bloggers, who may or may…
April 23, 2009
A couple of years ago, I answered a reader's question about the cost of genome sequencing. One of my readers had asked why the cost of sequencing a human genome was so high. At that time, I used some of the prices advertised by core labs on the web and the reported coverage to estimate the cost…
April 22, 2009
That's how new life forms are created every day in the wild, folks. Human researchers of course have added a few twists on the theme. If we can't induce bacteria or animal cells to collect new bits of DNA on their own, we turn to electroshock therapy. With plants.... aw heck, we just shoot them…
April 21, 2009
This is a video that a friend made that shows, very clearly, how to pour an agarose gel, load the samples and run it. I especially like the way he used a bit of time lapse photography to show the dyes separating as the gel ran.
April 15, 2009
"Yo, you regulate it's genes"
The English makes me cringe, but I love the idea. Tom McFadden, an associate instructor at Stanford, has made a series of Biology rap videos and posted them on YouTube.
Yo, check it out.
April 2, 2009
We saw it this morning while walking the dog.
Figure 1. A sign nearby claims this is a "Seagle."
Figure 2. The ducks must think swimming is safe.
March 30, 2009
If you haven't seen these, check out Jake Young's collection of videos showing T cells getting infected by HIV. The best one is at the bottom of the post.
March 30, 2009
A few weeks ago I heard a story from a friend in Oklahoma. She works with high school science teachers, helping them learn how to add biotechnology to their courses.
One teacher, in particular, has taken the new science activities to heart. Her students did so well, they won a science competition…
March 30, 2009
Watching the chIPs roll in,
then I watch them roll away again,
I'm just sitting on the DNA,
wasting time
(sung to the tune of "Sitting on the dock of the bay" by Otis Redding)
Hesselberth et.al. recently published a paper about digital genomic
footprinting that blew me away because it has so much…
March 27, 2009
The NIH has some extra money to fund summer research for students and teachers.
Check it out!
The NIH and grantee partner institutions have a unique opportunity to support summer research experiences for high school and college students, as well as elementary, middle, and secondary school…
March 26, 2009
I don't usually publish press releases, but I'm making an exception for this one, since your's truly is one of the Co-PI's. If you're a teacher within commuting distance of Seattle, the schedule and sign up information is here.
NSF AWARDS $1.3 MILLION TO NWABR FOR BIOINFORMATICS EDUCATION…
March 26, 2009
In which we identify unknown human proteins.
Yesterday, I wrote about using the BLOSUM 62 matrix to calculate a score for matches between two proteins. Those scores give us a good start on understanding how blastp determines whether two sequences are matching by chance or because they're more…
March 25, 2009
In which we search for Elvis, using blastp, and find out how old we would have to be to see Elvis in a Las Vegas club.
Introduction Once you're acquainted with proteins, amino acids, and the kinds of bonds that hold proteins together, we can talk about using this information to evaluate the…
March 24, 2009
For the past few months, the shake-up that began with Next Generation DNA Sequencing has been forcing me to adjust to a whole new view of things going on inside of a cell. We've been learning things these past two years that are completely changing our understanding of the genome and how it works…
March 22, 2009
What do the missing Romanov children, genetically engineered humans, financial risk taking, and poop have in common?
You can read about all these topics from this month's Gene Genie carnival at Mary Meets Dolly.
Who would have thought that mutations could be so much fun?
March 21, 2009
Cofactor Genomics is offering to sequence a genome for a few classes for free using Next Generation DNA Sequencing technology (either Illumina GA or via AB SOLiD).
Quoting from their site:
Cofactor will ask course organizers for a 1 page description of how their ~700Mb sequencing project could be…
March 16, 2009
I guess I put my foot in it when I wrote that Genome Technology article on DIY Bio. I've already gotten a couple of e-mails today and I can see on the Google groups DIY bio section, that I managed to offend some people by suggesting doing biotechnology successfully at home might mean that you…