teaching
sporte | May 27, 2008Students, teachers and scientists converge tommorrow morning from all around the Puget Sound region and elsewhere in Washington to share their experiences and talk about science. The students will present posters, science-themed music, art, drama, and many different types of projects that involved first-hand research and investigation. Scientists from the local biotech companies and research institutions talk with the students and judge the projects.
The public viewing time is tomorrow, May 28th, between 9 am-12 noon at the Meydenbauer Center. More information can be found here.
This…
esiegel | May 23, 2008We need one of those propaganda videos, like the Marines had when I was a kid:
Seriously, I remember watching that and actually thinking it would be awesome to be a Marine! (And for those of you who don't know me that well, I loathe armed conflict.)
Well, I'm a scientist. Can't we do anything cool to attract people to be interested in it, or help support it? Baby steps, folks, baby steps. And Duncan Forbes at Swinburne in Australia (where I almost moved when I was offered a position with them last February) has composed a how-to guide entitled:
So You Want To Be A Professional Astronomer!
It…
pontiff | May 10, 2008For a second straight year, the winner of the U.S. Teacher of the Year, is a University of Washington graduate. Of course I'm not supposed to say that, as not bragging is an sacred northwest tradition. (Did you know that the University of Washington receives the second most federal research funding of any institute in the United States?)
The teacher who won the award is Michael Geisen, who teaches in Prineville, Oregon, wish is just north and east of Bend, OR. Dude, not only is he an awesome science teacher, but he also gets to live in a sweet locale. Bend is an outdoor enthusiasts…
jane | April 28, 2008If you read almost any academic blog, or Rate Your Students, or really any site that academics frequent, you'll encounter discussion, debate, and general bitching about students' lack of ability to (a) properly cite sources and (b) avoid plagiarism. Discussions with my academic friends in more writing-intensive disciplines bear out what cyberspace illustrates: students don't, or can't, or won't, properly cite sources.
This carries over into computer science, too, though, and that's something that's been on my mind lately: How do we teach students how to properly "cite", and avoid…
pontiff | April 11, 2008Last week, in the class I'm teaching, we talked about the basics of deterministic finite automata. In week two we moved on to more interesting and slightly less basic material. In particular we introduced the notion of a nondeterministic finite automata and, by the end of the week, had showed that the class of languages accepted by deterministic finite automata is exactly the same class of languages accepted by nondeterministic finite automata.
What I love about this basic material is that you take a seemingly crazy idea: machines that can follow multiple computational paths at the same…
sporte | April 8, 2008I love using molecular structures as teaching tools. They're beautiful, they're easy to obtain, and working with them is fun.
But working with molecular structures as an educators can present some challenges. The biggest problem is that many of the articles describing the structures are not accessible, particularly those published by the ACS (American Chemical Society). I'm hoping that the new NIH Open Access policy will include legacy publications and increase access to lots of publications about structures.
It would also be great if other funding agencies, like the National Science…
pontiff | April 5, 2008This quarter I am teaching CSE 322: Introduction to Formal Models in Computer Science. Good fun. As part of my teaching I am LaTeXing up lecture notes from the class, which follow closely the book we are using, Sipser's "Introduction to the Theory of Computation." Here are the first three lectures for those with nothing better to do during their weekend:
Lecture 1: Welcome and Introduction
Lecture 2: Formal Definition of Deterministic Finite Automata
Lecture 3: Regular Operations on Languages
The notes are certainly full of many typos and such, but maybe there is a young teenager who isn…
purepedantry | April 4, 2008I didn't have much to do this afternoon, so I played hookie and went down to the FIRST Robotics Competition. The competition pits bands of high school students (and their engineer/mentors) in a contest to see who can build the best robot for an assigned task. At the moment the local competition (the national competition is in Georgia, I think) is going on in the Javits center in Manhattan.
This convention is a true festivus of geekiness. I kid you not: I have never seen such a raucous bunch of robotics nerds in my life. It was like the party scene from Real Genius. At one point the…
sciencewoman | March 31, 2008First, note the time stamp on this post. I have just now succeeded in getting Minnow to sleep and have sat down with a cup of tea and tomorrow's lecture to prepare. It's going to be a long short night. And I'm already tired.
I'm tired because for some inexplicable reason, Minnow couldn't sleep last night between 3:15 am and >5 am. And when Minnow can't sleep, neither do I. This afternoon as I tried to start writing tomorrow's lecture and preparing this week's lab, I was overcome by exhaustion and I broke down and bought a bottle of Coke. It seemed like a good idea at the time, but in…
pontiff | March 31, 2008...realizing that the class you are teaching for the first time this quarter ends on the half hour, not the hour, and therefore the fact that you are rushing through the material must seem extremely amusing to the students who know the class ends at 20 minutes after. Doh. Doh. Doh!
sporte | March 17, 2008Bio-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.
sporte | March 14, 2008I'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 doesn't seem to have the same bugs that appear on Windows. However, I would like things to work for my students. Since I don't want to have to write instructions for every software system on the planet, Google Docs would be my ideal answer, if it…
sporte | March 12, 2008Okay 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 any other instructors, but I did hear from lots of Linux fans. And, lots of other people kindly…
sporte | March 11, 2008The 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.
I guess they missed the part where I said that I wanted to make the students work a little easier.
Before I go…
jane | March 10, 2008On an intellectual level (and a good friend reminded me of this a few days ago), I realize that when students plagiarize or otherwise cheat in a course, it has nothing to do with me.
On an emotional level, it still stings. It's hard to dissociate the action/intent from the personal.
I'm currently dealing with a particularly tricky and trying case. Bright kid, tons of potential, can definitely do the work and excel at the work, but ... repeat offender.
I can't help but think, "why?"
On a practical level: why did the student go to the lengths she (I'm just going to use "she" for simplicity)…
sporte | March 10, 2008Three (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…
sporte | February 26, 2008For 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…
sciencewoman | February 21, 2008From the email files:
To: Science Woman (science.woman@mystery.edu)
From: sillyname@yahoo.com
Subject: Hey
can u tell me how to do number 4 on the problem set. i no u went over it in class but i have had a VERY LONG week lol tests ha ha ha and i lost my notes. pleeease help
Stu
Dear Stu,
The notes are available on the class website, but you can also solve #4 by ... We'll also be working more examples in class tomorrow. Please see me during office hours if you need more help.
Sincerely,
Dr. Science
I am *so* sick of correspondence like that - and that's from a typical student in my upper-level…
sporte | February 12, 2008yep, 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 quick introduction to BLAST from Sandra Porter on Vimeo.
sporte | February 10, 2008A 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 Schatz about the Pacfic Science Center's outreach programs.
We had our required moment of technical failure when Ran Hinrichs,…