sporte | July 27, 2007I've had some requests for some more molecular puzzles since the last one that I posted (see A DNA puzzle ). One person liked it so much he even blogged about it.
So, here's one for you to chew on over the weekend.
This puzzle is a variation of an activity in Exploring DNA Structure, a CD/lab book that I made (with funding from the NSF) and used for some educational research.
tags: DNA structure, DNA , molecular structure, biochemistry
Any ideas?
sporte | July 25, 2007Not content with his recent exploits in human experimentation and cavorting with Plosites in San Francisco, Professor Steve Steve jetted across the country once again, last week, hitting both both Blacksburg, VA and Seattle, WA, and creating pandemonium wherever he went.
And raising the question - how does he get back and forth across the coast so quickly?
Will you find out below? Will you ever find out? Who knows what you'll find out when you see- oh no! what's he doing? Steve! You'll get sunburned! Noooooooo!
Steve! Not in front of photographers!
Professor Steve Steve bears it all…
sporte | July 24, 2007What do people do in bioinformatics software companies?
tags: biotechnology careers, biotechnology, career+descriptions,bioinformatics
In our old conference room, in our last office, we used to have this little card on a stand, entitled "Sun's universe of stars." Over the years, we watched several of those stars blink out, one by one. The card disappeared, too. Maybe we got tired of marking off the companies as they went, maybe we just lost the card when we moved to our present office. No matter. Over time, the bioinformatics universe got a little smaller and colder each time another…
sporte | July 23, 2007Last week I found a bug in the new NCBI BLAST interface.
Of course, I reported it to the NCBI help desk so it will probably get fixed sometime soon. But it occurred to me, especially after seeing people joke about whether computer science is really a science or not, that it might surprise people to learn how much of the scientific method goes into testing software and doing digital biology.
tags: blast, software testing, scientific method, science education
What happens when the scientific method isn't used?
I wrote earlier in January about applying scientific principles from the wet…
sporte | July 18, 2007If you missed reading some of the comments on yesterday's post, I highly recommend that you go back and catch up.
I especially want you all to pay close attention to the comments from Deepak and Keith Robison. Like me, they work in industry and not in an ivory tower. Unlike me, they actually work in the biotech industry, while I work with people who slave away building the picks and shovels (picture a Greta Garbo sigh, for dramatic effect).
Their words ring true to me and match the kinds of things that I've seen and experienced. If you're interested in bioinformatics as a career or how…
sporte | July 17, 2007I had an enlightening experience recently, after I wrote some bioinformatics activities, under contract, for a community college. At the end of the project, the person at the college asked me if the activities were anything like the things that a "bioinformatics technician" would do on the job.
tags: biotechnology careers, biotechnology, career+descriptions,bioinformatics
Well no, I said, and added that I'd never heard of a bioinformatics technician before and I really didn't know what they would do. I thought that the people most likely to use our activities on-the-job would be research…
sporte | July 16, 2007BLAST is a collection of programs that are used to compare sequences (DNA, RNA, or protein) to larger collections of sequences that are stored in databases. I've used BLAST as a teaching tool for many years, partly because it's become a standard tool for biological work and partly because it's very good at illustrating evolutionary relationships on a molecular level.
A few months ago, the NCBI changed the web interface for doing BLAST searches at their site. I wrote earlier about changes that I made to our animated tutorial in response to the new BLAST. Now, I want to mention some of the…
sporte | July 15, 2007At the Seattle Art Museum's new sculpture garden, we can read all the signs.
The artworks are easily offended.
The unsanctioned baby eaglets have disappeared.
The grass won't grow without your help.
We pay attention to the grass.
sporte | July 15, 2007Professor Steve Steve, recently accused of consorting with a certain Washington madam came clean today with an alibi that he claims, proves the allegations are nothing more than malicious lies.
Dr. Steve insists that he was at the Fred Hutchinson Cancer Research Center doing experiments with teachers! And he has the photos to prove it!
Professor Steve Steve, the only panda with a Myspace page does seem to hit more locations in a night than our friend Santa Claus.
He also travels more frequently.
Some of you may remember the incidents of last winter, when Dr. Steve "got down" with a few low…
sporte | July 13, 2007Although, I didn't believe it when I first saw it. With all the years that I've heard (or taught) that all DNA is antiparallel, it was hard to believe my eyes.
Yet here is parallel DNA, with both strands oriented in the same direction, right here on your monitor. And the commenters were correct.
tags: DNA structure, DNA , molecular structure, biochemistry
The image that I posted a couple of days ago was made from part of this same structure. In that image, I hid the rest of the bases to make it easier to see why this structure is so strange.
Here are two images that show the landmarks a…
sporte | July 12, 2007By now, many of you have probably seen the the new BLAST web interface at the NCBI. There are many good things that I can say about it, but there are a few others that caught me by surprise during my last couple of classes.
tags: blast, BLAST tutorial, science education
Because of these changes, and because I'm giving a workshop for teachers on BLAST at the Fralin Biotechnology Conference in Blacksburg, VA, next week, it seemed like a good time to update our animated BLAST tutorial at Geospiza Education and save myself some trouble.
I originally created the BLAST for beginners tutorial to…
sporte | July 11, 2007What do people in biotechnology do on the job?
What can students do with a science degree once they've finished college? Some answers can be found at the "Life Sciences Central web site. Created by the Workforce Development Council of Seattle-King County, this is a wonderful resource for anyone who's considering biotechnology for a potential career.
My favorite part of the site is the series of short video interviews from people in the biotech industry, describing what they do on the job and how they got there.
tags: biotechnology careers, biotechnology, career+descriptions
Ten interviews…
sporte | July 10, 2007Okay, all of you biochemists and molecular biology types. I have a puzzle for you that I found by accident during a lecture. Yes, I was the one lecturing and the notes will be posted soon.
In the meantime, here's your puzzle: What's unusual about this pair of bases?
tags: DNA structure, DNA , molecular structure, biochemistry
(Those of you who attended our Chautauqua course - I know you probably know the answer - but don't answer, okay?)
sporte | July 9, 2007It was only a couple of weeks ago but it seems like years. I had spent a month learning how to use most of the features on my shiny new phone and we were in Alaska using Google maps to find our way around Fairbanks.
My thumbs were getting sore, but so what? I could a give a slide show on my phone, I could read my Gmail messages, and we could find a friend's house in the Google map satellite view and amaze our older relatives with the thrill of technology.
I'm not even a materialistic, gadgety sort of person, but I was in love.
And now, well, maybe you guessed it.
tags: chromatograms,…
sporte | June 28, 2007When we make primer sequences for an assay, two characteristics we're concerned with are the specificity of the primers and the sensitivity.
We can use blastn to evaluate whether or not our primers are likely to work.
Specificity: The specificity of a primer set is related to whether the primers are binding only to the sequences that we want to detect or to additional sequences. If our primers bind to lots of sequences - or even unrelated sequences- then they are probably not specific enough. If we made primers that were complementary to a polyA addition site or to an Alu sequence, we would…
sporte | June 28, 2007X71396, U37840, AF242849, Z11977, K03291, AY568721, NM_113475, NM_001056982, NM_001048464, NM_001060543, NM_001060540, NM_001061783, NM_129923, NM_129922, NM_001067252, NM_001056384, NM_001053908, NM_001058687, NM_001059721, NM_001062013, NM_111344, NM_115302, NM_001056908, NM_112085
sporte | June 26, 2007I'm seeing these things everywhere. Well, okay, maybe not everywhere. But I have seen lots of these in both Fairbanks and Anchorage.
Is this a coincidence?
This is a hand-sanitizer, with instructions on how to cough safely.
sporte | June 22, 2007What happens when a biologist tries to talk with the IT group? Needless to say, they don't speak the same language.
Reposted from the archives.
Imagine this. You've been sequencing DNA for a few years now, perhaps ESTs, or something else, and storing files on your local network. Your system administrator makes backup files for you and all is well.
But one day you learn about interesting results that other people are getting by assembling sequence data themselves and you decide to try it, too.
Watch out! You are about to descend into bioinformatics hell.
Soon you learn that the assembly…
sporte | June 21, 2007If we asked any biologist to pick the five most important techniques in biology, that list would certainly include PCR.
PCR stands for Polymerase Chain Reaction. It's used everywhere. We use it to amplify DNA for cloning, we use it for diagnostic tests, for DNA sequencing, for identifying pathogens, for identifying our long-lost relatives (and sometimes parents), and in forensics. If there's a technique that involves DNA, PCR is probably involved somewhere, too.
Since PCR is such an important technique, and we're going to be using PCR in our course, it's worth checking out a few…
sporte | June 20, 2007Quoth Dr. Stemwedel, from Adventures in Science and Ethics.
In the case of Universities and four-yr colleges, I completely agree. If you're looking for job training, go to a community college.
This post is in response to one of the comments from the other day. This commenter expressed frustration at having a completed a bioinformatics training program that left him/her with a certificate but without the right skills to find a job.
tags: bioinformatics, education
He/she suggested that "the government must select candidates for teaching from industry"
This post is my answer.
In the U.S.,…