teaching

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 in assignment results with nonsensical pie graphs. So, I asked what other instructors do with software that behaves differently on different computing platforms. I never did hear from ... Read more

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 my students install an entirely different operating system and download OpenOffice to do something that looks a whole lot harder in Open Office than it is in Microsoft Excel ... Read more

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 quickly gets to be too exponential.) Nope, sorry, three versions of Microsoft Office on three different operating systems are bad enough. This semester, I'm teaching an on-line for the first time ever. The subject isn't new to me. I've taught ... Read more

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 year, I collect the data from her students' experiments. Then, in the bioinformatics classes I teach, we work with the chromatograms and other data to see what we can find. This is the first part of a four part video series ... Read more

yep, I've become a videoblogger, at least sometimes. See the first video below. Be kind in the comments, this is a new thing for me. This video introduces the different blast programs, discusses word size, and how blastn works, the blastn score and the E value. The treatment is light and not too in depth, but as I said, it's an introduction.

A few weeks ago I attended a education conference at Pacific Science Center entitled, "A Conversation that Can Change the World." It was interesting.  Everyone was pretty enthusiastic at the meeting and there was a lot of positive energy.

• We got to see Theresa Britschgi from Seattle Biomedical Research Institute make Jack Faris, President of the Washington Biotechnology and Biomedical Association, get dressed up in a biohazard protection suit.
• We heard from Dennis
... Read more

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 of database these days and I've discovered that it's really helpful to know something about SQL. Even a tiny bit of SQL, like "SELECT * from table" goes a long, long way. This revelation didn't happen overnight and when I ... Read more

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 plots that I refer to are ... Read more

Since DNA diagnostics companies seem to be sprouting like mushrooms after the rain, it seemed like a good time to talk about how DNA testing companies decipher meaning from the tests they perform. Last week, I wrote about interpreting DNA sequence traces and the kind of work that a data analyst or bioinformatics technician does in a DNA diagnostics company. As you might imagine, looking at every single DNA sample by eye gets rather tiring. One of the things that informatics companies ( ... Read more

As many of you know, I'm a big fan of do-it-yourself biology. Digital biology, the field that I write about, is particularly well-suited to this kind of fun and exploration. Last week, I wrote some instructions for making a phylogenetic tree from mitochondrial genomes. This week, we'll continue our analysis. I wrote this activity, in part, because of this awful handout that my oldest daughter brought home last year. She presented me with an overly photocopied paper that showed ... Read more