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
We have lots of DNA samples from bacteria that were isolated from dirt. Now it's time to our own metagenomics project and figure out what they are. Our class project is on a much smaller scale than the honeybee metagenomics project that I wrote about yesterday, but we're using many of the same principles.
The general process is this:
1. We sort the chromatogram data to identify good data and separate it from bad data. Informatics can help you determine if data is
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
Welcome Bio256 students!
This quarter, we're going to do some very cool things. We are going to use bioinformatics resources and tools to investigate some biological questions. My goal, is for you to remember that these resources exist and hopefully, be able to use them when you're out working in the biotech world. I don't believe that bioinformatics is a subject that you can really grasp without getting your fingers dirty. So, this course will include a lot of hands-on work.
My friend and collaborator at Johns Hopkins University has given me data sets from the past three years and ... Read more
This morning Bora and I both gave talks in Second Life. Since this was a pretty new experience for me, I thought I'd share my thoughts on it.
Ever since the days when I watched cartoons on Saturday mornings, I thought it might be fun to be in one. But when I tried it this morning, truthfully, it was a bit scary. I haven't experienced stage fright like that for quite awhile. Perhaps it was the setting. I was really nervous and I hadn't practiced with Second Life enough to know what to do.
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
Biology as a second-language: the immersion method
Language teachers say the best way to learn a language is by total immersion and even better, spending time in the country where it's spoken conversing with native speakers.
See it, hear it, speak it, use it!
Put yourself in a position where you must do these four things to survive (or at least find the restroom) and you will learn more rapidly than by any other method.
Graduate school serves a similar purpose for scientists. You go from an environment where your fellow ... Read more
Two protein structures from an avian influenza virus are shown below. One form of the protein makes influenza virus resistant to Oseltamivir (Tamiflu®)
Don't worry, these proteins aren't from H5N1, but they do come from a related influenza virus that also infects birds.
One protein structure is from a strain that is sensitive to an anti-viral drug called "Tamiflu®". The other structure is from the same virus, except there's a slight difference. A single base change in the viral RNA changed the codon that tells the translation ... Read more