Sandra Porter
sporte
Posts by this author
May 1, 2008
Yesterday morning I was sitting at conference table, downing coffee to keep my eyes open, when I heard someone say that it's springtime now and the snakes are waking up. Well, those kinds of statements at the breakfast table do have a way of getting my attention.
I turned sideways and realized the…
May 1, 2008
APRIL was so much fun, that I thought I should find a molecule for May. I searched both the Gene database, the structure database, everywhere, without any luck.
Finally, I decided to change the search and use the date instead of the name of the month. And here we have it, straight from PubChem. A…
April 27, 2008
A potential link between lung cancer and human papilloma virus may make parents even more glad about vaccinating their children with Gardasil®. Not only are the children protected against viruses that commonly cause cervical cancer, they may be protected against some forms of lung cancer as well.…
April 26, 2008
Over 2600 genetic diseases have been found where a change in a single gene is linked to the disease. One of the questions we might ask is how those mutations change the shape and possibly the function of a protein?
If the structures of the mutant and wild type (normal) proteins have been solved…
April 24, 2008
Bill Gates, Eric Lander, Maynard Olson, Leena Peltonen, and George Church fielded questions last night at a fascinating panel discussion on personal genomics at the University of Washington.
We were fortunate to be in the audience. I'll share some of the questions and answers, in some cases…
April 22, 2008
One of my favorite web 2.0 technologies is the webinar. When you work at a company and not a University, with constant seminars, it gets a bit harder to hop on a bus and travel across town to learn about new things. Webinars are a good way to fill that gap. I grab my coffee cup, put on my…
April 17, 2008
In the class that I'm teaching, we found that several PCR products, amplified from the 16S ribosomal RNA genes from bacterial isolates, contain a mixed base in one or more positions.
We picked samples where the mixed bases were located in high quality regions of the sequence (Q >40), and…
April 16, 2008
Ribosomes are molecular machines that build new proteins. This process of synthesizing a protein is also known as translation.
Many antibiotics prevent translation by binding to ribosomal RNA. In the class that I'm teaching, we're going to be looking at ribosome structures to see if the…
April 11, 2008
I know some of you enjoy looking at data and seeing if you can figure out what's going on.
For this Friday's puzzler, I'm going to send you to FinchTalk, our company blog, to take a look at lots of data from a resequencing experiment that was done to look for SNPs and count alleles. The graph is…
April 9, 2008
You can find out. Blaine Bettinger, the Genetic Genealogist has a fun little quiz.
April 8, 2008
I 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…
April 4, 2008
This morning I had a banana genome, an orange genome, two chicken genomes (haploid, of course), and some fried pig genome, on the side. Later today, I will consume genomes from different kinds of green plants and perhaps even a cow or fish genome. I probably drank a bit of coffee DNA too, but didn'…
April 3, 2008
Goodbye desktop, we're off to see the web.
Both my students and I have been challenged this semester by the diversity of computer platforms, software versions, and unexpected bugs. Naturally, I turned to the world and my readers for help and suggestions. Some readers have suggested we could solve…
April 2, 2008
A few months ago I posed some questions about the regulations that might oversee personal genomics companies (Who's your Daddy? and Step right up, get your very own DNA profile).
Why?
Because I am biased. At Geospiza, where I work, we make software products that help our customers, who do DNA…
April 1, 2008
I added the spring colors.
April 1, 2008
Is it real or is it April Fools?
The March 21st issue of Science has an interesting news article by Elizabeth Pennisi and a letter to the editor about a proposal to wikify GenBank. Currently, the NCBI holds the original authors responsible for editing or correcting entries and this does cause…
March 31, 2008
We used to love watching him blow stuff up on TV.
But things are different now....
GrrlScientist has the movie.
March 29, 2008
Our new Scibling, Jane, is a real life computer scientist. If you've ever wondered what computer scientists really do during the day, Jane will set you straight (I guess they're not playing Nintendo. Darn! Another illusion shattered, just like that.)
Jane has also promised to explain why computer…
March 27, 2008
If you're old enough or you've taken microbiology, there's a chance that sometime in your life you heard of Legionaire's disease.
This disease was caused a bacteria that inhabited the air conditioners in a hotel where several veterans held a conference. Naturally, it was the microbiologists who…
March 27, 2008
I made this video (below the fold) to illustrate the steps involved in making a phylogenetic tree. The basic steps are to:
Build a data set
Align the sequences
Make a tree
In the class that I'm teaching, we're making these trees in order to compare sequences from our metagenomics experiment with…
March 20, 2008
Believe it or not, there is the remote possibility that I may get to have some influence in getting a web application built, that I can use in teaching, that will do something that I want.
Unfortunately, I know very little about the relative merits of AJAX/JavaScript vs. Flash vs. a custom C++…
March 19, 2008
Have you ever wondered how to view and annotate molecular structures? At least digital versions?
It's surprisingly easy and lots of fun.
Here's a movie I made that demonstrates how you can use Cn3D, a free structure-viewing program from the NCBI. Luckily, Cn3D behaves almost the same way on…
March 19, 2008
The University of Virginia does.
They survey students every year to find out what they're up to tech-wise. Apparently 99% of their first year students own computers.
And, a large majority of those computers are laptops (3058/3113 or 98%).
And, what's on those laptops? Let's have a drum roll:…
March 17, 2008
Bio-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…
March 17, 2008
One of my colleagues has a two part series on FinchTalk (starting today) that discusses uncertainty in measurement and what that uncertainty means for the present and Next Generation DNA sequencing technologies.
I've been running into this uncertainty myself lately.
I have always known that DNA…
March 16, 2008
Things move off of our entry page pretty quick sometimes. If you missed this post from Bioephemera, go take a look.
She has great pictures and a fascinating story about one Seattle's favorite places.
March 16, 2008
Conflicts between predators like cougars and coyotes and human companions like pets and small children are becoming more common as people move into areas that used to be wildlife habitat.
The Seattle Times has a great story this morning about biologists in Washington who are studying cougars to…
March 14, 2008
It's a good thing my 13 yr old doesn't read my blog.
Why? Because I'm on to her. Being a biologist, well, acronyms are my life. And, for a long time, I've been able to interpret some of the lingo that she uses on AIM. Lately, we've certainly been having our little talks about cell phone…
March 14, 2008
I'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…
March 13, 2008
I think all of us; me, the students the OO advocates, a thoughtful group of commenters, some instructors; I think many of us learned some things that we didn't anticipate the other day and got some interesting glimpses into the ways that other people view and interact with their computers.
Some of…