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 ... Read more
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. My husband is an enthusiastic fan of the iPhone store. Last night, he downloaded this application called "Army Knife." This application has, I kid you not, the following nine items:
  • unit converter - these are always helpful, especially if you travel
  • ultrasonic whistle
  • protractor
  • Heart (beats per minute) counter
  • measuring tape
  • ... Read more

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.

As Nick mentions, the M2 protein from influenza ... Read more

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

           C.  Analyzing the data sets

D.  Interpreting the results

I'm going intersperse my results with a few instructions so ... Read more

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 reason is the redundancy in the genetic code.

Okay, that probably didn't make any sense to those of you who didn't already know the answer. Here it is. ... Read more

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. Here were some of the great suggestions and pieces of advice; 1. Do a BLAST search. Right! I can't believe I didn't do that first thing, I think the ... Read more

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.


... Read more

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. ... Read more

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 genome sequences, piece by piece, as I described in earlier, but the NCBI has other tools that are useful, too.

The Influenza Virus Resource will let us pick sequences, align them, and make trees so we can quickly compare the sequences to ... Read more

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. Once I realized that the genome sequences from the H1N1 swine flu were in the NCBI's virus genome resources database, I had to take a look. And, like eating potato chips, making ... Read more

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