sporte | April 22, 2008One 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 headphones, and I get to listen to someone tell me about their work for an hour and show slides over the web. It's nice.
Our company is even going to be involved in two webinars in the next two months. One of us is giving an Illumina webinar tomorrow on managing Next Generation Sequencing data. A…
sporte | April 17, 2008In 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 determined that the mixed bases mostly likely come from different ribosomal RNA genes. Many species of bacteria have multiple copies of 16S ribosomal RNA genes and the copies can differ from each other within a single genome and between genomes.
Now, in one of our last projects we are determining where…
sporte | April 16, 2008Ribosomes 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 polymorphisms that we find in the sequences of 16S ribosomal RNA are related antibiotic resistance.
This is related to our metagenomics project where we investigate the polymorphisms we find in 16S ribosomal RNAs.
This 6 minute video introduces ribosomes, discusses where they're found, what they're made of,…
sporte | April 11, 2008I 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 at the end of the post.
The graph shows data from 4608 reads (sequenced from both strands, forward and reverse). And there are some interesting patterns. Can you figure them out?
sporte | April 9, 2008You can find out. Blaine Bettinger, the Genetic Genealogist has a fun little quiz.
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…
sporte | April 4, 2008This 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't consume a complete coffee genome since my grinder isn't that powerful and much of the DNA would be trapped inside the ground up beans.
Of course, microbes have genomes, too. But I do my best to cook those first.
So, what is a genome? Is it a chromosome? Is it one of those DNA fragments or…
sporte | April 3, 2008Goodbye 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 everything by using Linux. Others have convincingly demonstrated that Open Office is a reasonable alternative.
But, now there's something new and cool on the web.
Okay, it's still in the beta stages, and apparently it can only be used by a limited number of people at a time, but it's certainly…
sporte | April 2, 2008A 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 testing, meet FDA and CLIA regulations. Since some of our customers do DNA testing for diagnostics and clinical studies, we are well aware of the regulatory issues that concern DNA sequencing and DNA sequence data. Most DNA diagnostics labs are regulated by CLIA, the Clinical Laboratory Improvement…
sporte | April 1, 2008Is 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 problems when those authors fail to return to the scene and fix what they've submitted. Some researchers are suggesting that third parties be allowed to fix some of those mistakes or at least add comments to records, to warn the unwary.
There are some good arguments on both sides and it's certainly…
sporte | March 31, 2008We used to love watching him blow stuff up on TV.
But things are different now....
GrrlScientist has the movie.
sporte | March 29, 2008Our 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 science is a science and not engineering.
That part hasn't happened yet, but I work with software engineers and I have written a bit about the mysterious things that they do. Databases need to vacuumed? Who knew?
I'm looking forward to hearing Jane describe answer the question from the…
sporte | March 27, 2008If 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 collected samples of the bacteria and figured out what was going on.
Now, there's something else going on and I'm thankful to Mike for letting us know.
In a strange twist of fate, those archives have been destroyed. And those weren't the only valuable samples.
Why? For what reason? I usually…
sporte | March 27, 2008I 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 the multiple copies of 16S ribosomal RNA (rRNA) genes that we can find in single bacterial genomes. Bacteria contain between 2 to 13 copies of 16S rRNA genes and we're interested in knowing how much they differ from each other. Later, we'll compare the 16S ribosomal RNA genes from multiple species of…
sporte | March 20, 2008Believe 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++ plug-in, that does something with WX Windows or QT.
What do you think?
sporte | March 19, 2008Have 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 both Windows and Mac OS X.
Introduction to Cn3D from Sandra Porter on Vimeo.
sporte | March 19, 2008The 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:
60% have Windows VISTA
26% have Mac OS X
12% have Windows XP
and, 2% or less have something else - like Linux.
This is why I really, really, want good web-based applications.
Just for the record, I don't care what operating systems students use. My concern how to help them use those computers to do…
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 17, 2008One 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 sequencing errors occur. This is why people build tools for measuring the error rate and why quality measurements are so useful for determining which data to use and which data to believe. But, some of the downstream consequences didn't really hit home for me until a recent project. This project…