sporte | February 16, 2008I love the way you show me secret things.
All I do is type: Select * from name_of_a_table
And you share everything with me.
Without you, my vision is obscured, and all I see is the display on the page.
In fact, this was the push that finally made me decide to learn SQL.
In our bacterial metagenomics experiment, I realized that my students could use FinchTV to enter their blast results into our iFinch database.
That was cool, but with the web interface, we could only view one result at a time.
On the other hand, if we use the right SQL query in the iFinch query window, we can see…
sporte | February 14, 2008They could have used the data from my serial killer survey, but no, being scientists or science-related, the ScienceBlogs overseers want to find out for themselves.
Plus the chance of winning and iPod is higher than the chance of winning the lottery and you don't even have to buy a ticket.
Take the survey, maybe even win. I wonder if they have the pink Valentine iPods?
sporte | February 14, 2008Believe it or not, this is a DNA kiss.
Have a loverly Valentine's DNA!
(And just in case you're wondering, yes, I did put it on a coffee mug.)
sporte | February 13, 2008Confused about terms like "autonomy" and "beneficance" and their relationship to biomedical research?
The Northwest Association for Biomedical Research (NWABR) is offering a short course at the University of Washington, Feb. 29th and March 1st, on Ethics in Science.
Registration details and a description are below.
An Ethics Shortcourse
February 29, 2008, 4-8pm and March 1, 10am-4pm Waterfront Activities
Center, University of Washington
Registration Deadline: February 15, 2008 To apply online, please visit:
http://www.nwabr.org/education/esc.htm
$25 with credit card or $20 with check.…
sporte | February 12, 2008Well, probably getting a stipend to help you do it.
And, the really cool thing is that's part of the deal!
Hustle, hustle the deadline is March 7th, and all the contact info is below.
The NSF Research Experience for Undergraduates program in Environmental Microbiology at UNLV is accepting applications.
This grant provides students with the opportunity to work on a research project for a 10 week period with a faculty mentor. Students receive a $4000 stipend, round trip airfare, and housing in a UNLV dormitory.
Mentors have projects in the following areas:
⢠Adaptation of…
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 11, 2008One of my chief joys in life, often to dismay of others, is working with data. Some members of my family (who shall remain nameless) would characterize this fixation as bordering on obsessive, others just call me a "geek" and leave it at that.
I don't care.
Give me a data set and I can play happily for hours. The sky gets dark. The dog entreats me over and over to please throw her sopping toy so she can go chase it. The cats walk between my hands and the keyboard and rub their bodies against my face.
But I don't see any of that when there's a computer screen in front of me and columns…
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,…
sporte | February 9, 2008A 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 decided a few…
sporte | January 14, 2008is coming home and flying into Seattle. I took these pictures with my phone (in Airplane Mode, of course).
In the first shot, you get to see Mt. St. Helen's and all the interesting geology around it.
Can you tell which way the volcano blew?
Mt. Rainier is in the background
The second shot is downtown Seattle.
sporte | January 11, 2008Yesterday, I posted a memorial for Ron Mardigian, an enthusiastic champion of science education at Bio-Rad. Today, I scanned RPM's blog and what do I see?
A choir! Bio-Rad has produced a really funny music video. It reminds me of the music video from "We are the World," except some members of the choir are holding PCR machines and singing about the wonders of PCR!
Scientists for Better PCR is a really cute video, with a catchy tune, and it's fun to watch. If you're teaching about PCR, I highly recommend showing it to your class.
sporte | January 10, 2008We often see memorials written about famous scientists, but we rarely see them about the people who work in the background to help people learn the science in the first place. Ron was one of those people whose work inspired teachers and helped spark excitement in science students throughout the world.
I just learned last week that Ron passed away and I'm still in a state of shock.
I met Ron ten years ago at the first BIO teachers' conference. I was a conference volunteer, working on the teachers' program planning committee and representing Bio-Link. BIO 99 was the first time that the…
sporte | January 9, 2008The New England Journal of Medicine published a study yesterday showing that small changes in the DNA in the long arm of chromosome 16 are associated with autism.
I met a teenager with autism last summer, when I attended family night at the Seattle Park and Rec summer camp program for kids with special needs. It's a fantastic program. The kids spend a week or more at summer camp and the parents get some much needed time off.
I sat down on a log and my daughter (one of the counselors) introduced to me a boy in her cabin and told me that he's interested in trains. Since I rode a train for…
sporte | January 2, 2008When in doubt, turn to the internet.
In a couple of weeks, I'm going to start teaching my first on-line course. So far, I've been preparing by:
learning how to use Blackboard
getting a subscription to iFinch so we can do bioinformatics in style, and share data and other files
getting a microphone and some software for making video podcasts
But, since this is brand new and I'm used to seeing students face-to-face, I have a queasy feeling in the pit of my stomach. I do not want to be one of those people who simply puts lecture notes on a web site.
So, I'm turning to you for advice dear…
sporte | December 28, 2007If you look below the fold, you can see two molecules locked in a tight embrace. These molecules or their closely related cousins can be found in any cell because their ability to evolve is slowed by their need to interact with each other in the right way.
In an earlier post, I asked:
Who are they?
One partner is a small bit of 16S ribosomal RNA, about 56 nucleotides to be precise. The other partner is S15, one the proteins in the ribosome.
If we could look inside the bacteria that made these, we would see lots of other proteins binding to these two partners within a molecular machine.…
sporte | December 26, 2007Genetics textbooks abound with stories of European royalty and the hazards of having children after you've married one of your cousins. It struck me as an interesting parallel that the lion is such a popular symbol in so many royal coats of arms. Like the royal families of Europe, certain lion populations have also suffered from a few too many copies of certain recessive genes.
I first read about the Florida panthers a few years ago while researching material for a class that I teach on using bioinformatics. It wasn't my first encounter with big cats and their DNA. Years before, while…
sporte | December 24, 2007This wasn't in the lab, but it was an accident, and it was funny later on.
Normally, I wouldn't think twice about storing bacterial cultures in a refrigerator. After all, bacteria on a petri plate, inside of a plastic bag, are kind of stuck. They can't get out of the plates, and even if they did, they certainly can't crawl out of a plastic bag.
I thought soil bacteria, on agar plates, were mostly harmless.
I was wrong.
When my husband was finishing graduate school, he brought home some agar plates that he had streaked, with different Streptomyces species, so that he could photograph them…
sporte | December 23, 2007You're not likely to see the Twisted Chipmunk Christmas Song on the big screen this weekend.
But, if you liked White Trash Christmas, you'll enjoy this irreverent holiday video.
From the Seattle animators, formerly known as ToonedIn, now Global Wonder Entertainment.
sporte | December 22, 2007White Trash Christmas.
This is the perfect antidote to the Frosty, Rudolph, and The Little Drummer Boy overdose.
From the Seattle animators, formerly known as ToonedIn, now Global Wonder Entertainment.
sporte | December 20, 2007You can get a jump on the Darwin Day festivities.
Once again the Alliance for Science is sponsoring an essay contest for Darwin Day. If you download their suggestions for good essay writing, you can get your essay done over winter break and have a good crack at winning on those cash prizes!
The Alliance for Science is pleased to announce our second annual National High School Essay Contest. We invite interested students to submit essays of up to 1,000 words on one of two topics -- Climate and Evolution or Agriculture and Evolution. Click on the topic names for some possible ideas to explore…