Sandra Porter
sporte
Posts by this author
It's a Solexa data directory.
I've held off on blogging about Next Generation Sequencing here, but now that one of my colleagues has started blogging about it, it seems like a good time to write a little about FinchTalk, our company blog.
We've decided that we can serve an educational role for…
Okay 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…
I read about this in Bio-IT World and had to go check it out. It's called the Genome Projector and it has to be the coolest genome browser I've ever seen.
They have 320 bacterial genomes to play with. Naturally, I chose our friend E. coli. The little red pins in the picture below mark the…
Your canopy is disappearing, you're likely to freeze.
NASA's Earth Observatory reports that over 1,110 acres of forest were illegally logged, during the past four years, in the Monarch Butterfly Biosphere Reserve in central Mexico.
Monarch butterflies travel here from all over the United States…
The 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…
The NASA Earth Observing System is an incredible resource for both science and education. One of the amazing things about it is all the different kinds and quantities of data are assembled together into pictures that even grade school kids can immediately comprehend.
How do they do it?
Each of…
Three (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,…
Happy Birthday!
Is it PZ Myers or Captain Barbosa in disguise?
Here's a fun puzzler for you to figure out.
The blast graph is here:
The table with scores is here, click the table to see a bigger image:
And here is the puzzling part: Why is the total score so high?
If you want to repeat this for yourself, go here.
You can use this sequence as a query (it…
Do different kinds of biomes (forest vs. creek) support different kinds of bacteria?
Or do we find the same amounts of each genus wherever we look?
Those are the questions that we'll answer in this last video. We're going to use pivot tables and count all the genera that live in each biome. Then…
This is third video in our series on analyzing the DNA sequences that came from bacteria on the JHU campus.
In this video, we use a pivot table to count all the different types of bacteria that students found in 2004 and we make a pie graph to visualize the different numbers of each genus.
The…
What do you do after you've used DNA sequencing to identify the bacteria, viruses, or other organisms in the environment?
What's the next step?
This four part video series covers those next steps. In this part, we learn that a surprisingly large portion of bioinformatics, or any type of…
For 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…
Bora had an enjoyable post yesterday on obsolete lab skills. I can empathize because I have a pretty good collection of obsolete lab skills myself. These days I'm rarely (okay, never) called upon to do rocket immunoelectrophoresis, take blood from a rat's tail, culture tumor cells in the anterior…
Long ago, I worked in a large lab that was divided into several small rooms. For part of that time, I shared one of the small rooms with a graduate student from Taiwan. She was a wonderful person who taught me that many cultural norms are not normal in other cultures.
One moment stands out.
She…
I 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…
They 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…
Believe 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.)
Confused 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…
Well, 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…
yep, 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…
One 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…
A 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…
A 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…
is 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…
Yesterday, 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…
We 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…
The 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…
When 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…
If 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…