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teaching

Category archives for 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…

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…

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,…

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…

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,…

A few weeks ago I attended a education conference at Pacific Science Center entitled, “A Conversation that Can Change the World.”

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…

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…

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…

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.