teaching:
Bio-Link is accepting applications for this year's National Summer Fellows forum, June 2-6th, in Berkeley, CA. You can get an application at www.bio-link.org I'll be there, doing some kind of bioinformatics workshop. I'll probably be talking about either metagenomics or comparing protein structures and drug resistance, but if you have topic requests, feel free to submit them in the comments....
Posted on March 17, 2008 6:13 PM • 0 Comments •
I've been writing quite a bit this week about my search for a cross platform spread sheet program that would support pivot tables and make pie graphs correctly. This all started because of a bug that my students encountered in Microsoft Excel, on Windows. I'm not personally motivated to look for something new, since Office 2004 on Mac OS 10.5...
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Posted on March 14, 2008 2:31 PM • 21 Comments •
Okay OpenOffice fans, show me what you can do. Earlier this week, I wrote about my challenges with a bug in Microsoft Excel that only appears on Windows computers. Since I use a Mac, I didn't know about the bug when I wrote the assignment and I only found out about it after all but one of my students turned...
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Posted on March 12, 2008 12:50 PM • 35 Comments •
The other day, I wrote that I wanted to make things easier for my students by using the kinds of software that they were likely to have on their computers and the kinds that they are likely to see in the business and biotech world when they graduate from college. More than one person told me that I should have...
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Posted on March 11, 2008 8:00 AM • 33 Comments •
Three (or more) operating systems times three (or more) versions of software with bugs unique to one or systems (that I don't have) means too many systems for me to manage teaching. Thank the FSM they're not using Linux, too. (Let me see that would be Ubuntu Linux, RedHat Linux, Debian Linux, Yellow Dog Linux, Vine, Turbo, Slackware, etc.. It...
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Posted on March 10, 2008 8:09 AM • 12 Comments •
For the past few years, I've been collaborating with a friend, Dr. Rebecca Pearlman, who teaches introductory biology at the Johns Hopkins University. Her students isolate bacteria from different environments on campus, use PCR to amplify the 16S ribosomal RNA genes, send the samples to the JHU core lab for sequencing, and use blastn to identify what they found. Every...
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Posted on February 26, 2008 10:14 AM • 0 Comments •
A quick video introduction to BLAST.
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Posted on February 12, 2008 8:14 AM • 13 Comments •
A few weeks ago I attended a education conference at Pacific Science Center entitled, "A Conversation that Can Change the World."...
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Posted on February 10, 2008 12:17 PM • 6 Comments •
A long standing debate in my field is whether or not biologists, who work with computers, need to learn how to program. I usually say "no." Let the programmers program, the biologists interpret the results, and let everyone can benefit from each other's expertise. Well, I've changed my mind in one respect. Most biologists need to work with some kind...
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Posted on February 9, 2008 5:55 PM • 21 Comments •
Which read(s): 1. contain either a SNP (a single nucleotide polymorphism) or a position where different members of a multi-gene family have a different base? C 2. doesn't have any DNA? B 3. is a PCR product? A, B, and C. All of three reads were obtained by sequencing PCR products, generated with the same set of primers. The quality...
Posted on November 20, 2007 3:20 PM • 0 Comments •
Kind of like reading tea leaves, but more meaningful.
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Posted on November 19, 2007 10:10 AM • 10 Comments •
You too, can compare chimp and human DNA.
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Posted on November 16, 2007 8:51 AM • 0 Comments •
Can you do it? This is what bioinformatics technicians or data analysts do in diagnostic labs.
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Posted on November 15, 2007 9:09 AM • 4 Comments •
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,...
Posted on November 13, 2007 4:53 PM • 3 Comments •
Open access to educational research would benefit us all.
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Posted on November 12, 2007 8:29 AM • 11 Comments •
An evolution activity for the classroom.
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Posted on November 9, 2007 3:47 PM • 0 Comments •
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...
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Posted on October 28, 2007 2:24 PM • 0 Comments •
Sequencing the dirt: see how it's done
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Posted on October 27, 2007 7:00 PM • 0 Comments •
Would you like to have some fun playing with chromatograms and helping our class identify bacteria in the dirt?...
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Posted on October 24, 2007 4:05 PM • 0 Comments •
It's hard to teach bioinformatics when schools work so hard to keep us from using computers....
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Posted on October 23, 2007 2:04 PM • 14 Comments •
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....
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Posted on October 17, 2007 9:50 AM • 0 Comments •
Bora and I are giving posters in Second Life. Here's how you can attend.
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Posted on October 14, 2007 10:38 PM • 21 Comments •
For the record: Chlamydia is NOT a virus. I am bummed. I like the little MicrobeWorld radio broadcasts, and the video podcasts are even more fun. But I was perusing the archives and I found this:...
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Posted on September 26, 2007 11:42 AM • 7 Comments •
Why I love Nature podcasts
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Posted on September 25, 2007 12:53 PM • 14 Comments •
Developing "biological intuition" through case studies
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Posted on August 17, 2007 1:53 PM • 0 Comments •
Software testing and the scientific method.
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Posted on July 23, 2007 3:46 PM • 0 Comments •
Do course evaluations have to be a popularity contest? Or can they be useful tools for improving a class? tags: teaching, student evaluations A few days ago, evolgen lamented that his students weren't giving him useful information on their end-of-course evaluations. I'm not surprised. When I first started teaching, I was a given a copy of the standard-teacher-evaluation-form-that-everyone-used....
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Posted on June 4, 2007 8:00 AM • 8 Comments •
Science labs are not for all people.
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Posted on March 31, 2007 7:44 PM • 7 Comments •
I received a mysterious file last week, via e-mail from one of my students. According the e-mail, the file contained the answers to an assignment....
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Posted on February 13, 2007 8:50 PM • 9 Comments •
The bioinformatics classes that I teach use web services and web sites as much as possible, but I still find that it's helpful to have programs on our classroom computers. Here is a list of my favorite desktop programs for those of you who might want to add some bioinformatics activities to your biology courses....
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Posted on January 12, 2007 1:37 PM • 10 Comments •
I was frantically getting ready for class when I happened to glance out the window. What did I see? Big fluffy white flakes rapidly falling from above. You can't say we weren't warned. The newspapers have been predicting snow since Monday. It's just, well, unusual. And Seattle is never prepared to deal with it. Even the kids aren't looking too...
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Posted on January 10, 2007 11:21 PM • 4 Comments •
There's nothing like the first day of class to make you appreciate the difference between the equipment you end up using at schools and the equipment that you get to use on the job. For the month of January, I'm teaching a night class in bioinformatics at a local community college. We're introducing lots of web-based programs, and databases, and...
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Posted on January 9, 2007 12:11 PM • 3 Comments •
We need lab movies of people doing things wrong.
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Posted on November 6, 2006 9:04 AM • 3 Comments •
Like sex education in a religious household, lab technique must sometimes be learned from your friends.
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Posted on November 1, 2006 8:00 AM • 7 Comments •
typing that is.
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Posted on October 9, 2006 11:00 AM • 1 Comments •
The blood typing lab, part I. What went wrong? and why? Blood typing part II. Can this laboratory be saved? Those wacky non-major Zoo students are at it again! And this time they drew blood! Mike's undergraduate students learned about blood typing, a common tool of detectives and real crime TV. They did the classic blood typing lab, and by...
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Posted on October 7, 2006 1:36 PM • 2 Comments •
Why not use a scientific approach to teaching?
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Posted on October 6, 2006 11:42 AM • 4 Comments •
Students don't leave science because it's too hard, or too easy, students leave science because of the way that it's taught.
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Posted on September 27, 2006 1:16 PM • 6 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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