DNA sequence traces are often used in cases where:
  1. We want to identify the source of the nucleic acid.
  2. We want to detect drug-resistant variants of human immune deficiency virus.
  3. We want to know which base is located at which position, especially where we might be able to diagnose a human disease or determine the best dose of a therapeutic drug.
In the future, these assays will likely rely more on automation. Currently, (at least outside of genome centers) many of these results are assessed by human technicians in clinical research labs, or DNA testing ... Read more
The Wired Campus has an interesting article on nursing students at Tacoma Community College. In John Miller's class, the students practice interviewing patients in Second Life. This sort of activity, of course, is one that could be carried out in a classroom, but I can see the advantages of having student interview other "people" who are for the most part, strangers. It will be a different and valuable experience. Read more
I had some strange notions when I made the jump from working at the lab bench to teaching at the white board. I thought good teaching meant interesting lectures. And I was completely unaware that people actually conducted research in science education. If I had been asked about education research, I would have replied that it was largely anecdotal, probably limited to sociologists and primary grades, and as far as I was concerned, useless.

And, honestly, to me it was useless.

I never saw any of science education articles or journals. No other ... Read more

Last year I wrote about an experiment where I compared a human mitochondrial DNA sequence to primate sequences in the GenBank. Since I wanted to know about the differences between humans, gorillas, and chimps, I used the Entrez query 'Great Apes' to limit my search to a set of sequences in the PopSet database that contained gorillas, bonobos, chimps, and human DNA. A week ago, I tried to repeat this experiment and...

It didn't work.

All I saw were human ... Read more

Metagenomics is a field where people interrogate the living world by isolating and sequencing nucleic acids. Since all living things have DNA, and viruses have either DNA or RNA, we can identify who's around by looking at bits of their genome. Researchers are using this approach to find the culprit that's killing the honeybees. We're also trying to find out who else shares our bodies, and lives in our skin, in our stomachs, and other places where the sun doesn't shine. Craig Venter used ... Read more
The simple fact is this: some DNA sequences are more believable than others. The problem is, that many students and researchers never see any of the metrics that we use for evaluating whether a sequence is "good" and whether a sequence is "bad." All they see are the base calls and sequences: ATAGATAGACGAGTAG, without any supporting information to help them evaluate if the sequence is correct. If DNA sequencing and personalized genetic testing are to become commonplace, the practice of ignoring data quality is (in my opinion) simply unacceptable. So, for awhile anyway, I'm ... Read more
Would you like to have some fun playing with chromatograms and helping our class identify bacteria in the dirt? This quarter, my bioinformatics class, at Shoreline Community College, will be working with chromatograms that were obtained by students at Johns Hopkins University, and graciously made available by Dr. Rebecca Pearlman. (See see "Sequencing the campus at the Johns Hopkins University" for more background.) We are going to do a bit of metagenomics by using FinchTV and ... Read more
It's hard to teach bioinformatics when schools work so hard to keep us from using computers. Anecdotes from the past Back in my days as a full-time instructor, I fought many battles with our IT department. Like many colleges, we had a few centralized computer labs, tightly controlled by IT (aka the IT nazis), where students were supposed to go to do their computing. Instructors also had a centralized computer lab, but over the years, we gained the right to have computers in our offices. Our major battle was whether or not we'd be allowed to use Macs ... Read more
If like me, you were a little disoriented and confused when you visited Second Life and traveled through orientation island, then you may like this. The Wired Campus (from The Chronicle for Higher Education) led me to an interesting post from the New Media Consortium and a new place to visit once I get a bit of time to do so. The NMC has set up a special orientation island for educators. From the photos, this island looks like a unusually clean and artistic ... Read more
I've been reading quite a bit lately about Universities setting up virtual classrooms in Second Life, so when Bertalan Meskó from ScienceRoll invited me to come give a poster, I decided it was time to take the plunge. Besides, I'm going to be teaching an on-line bioinformatics course this spring for Austin Community College, so this seemed like a good time to find out what the fuss is all about. Tomorrow, Bora Zivkovic (A Blog Around ... Read more

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