Whatever happened to Bill Nye the Science Guy?
Category: Humor
We used to love watching him blow stuff up on TV. But things are different now.... GrrlScientist has the movie....
Posted by Sandra Porter at 11:54 AM • 4 Comments •
My thoughts on biology, teaching, life, and exploring the living world via the digital one. Only my opinions are represented by these postings, they do not represent the viewpoints of any funding agency or Geospiza, Inc.
I am a microbiologist and molecular biologist turned tenured biotech faculty turned bioinformatics scientist turned entrepreneur. My passion is developing instructional materials for 21st century biology (Geospiza Education).
e-mail digitalbio at gmail.com
March 31, 2008
Category: Humor
We used to love watching him blow stuff up on TV. But things are different now.... GrrlScientist has the movie....
Posted by Sandra Porter at 11:54 AM • 4 Comments •
March 29, 2008
Category: Science education
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.)...
Posted by Sandra Porter at 11:10 AM • 0 Comments •
March 28, 2008
Category: Microbiology
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 collected samples of the bacteria and figured out what was going on. Now,...
Posted by Sandra Porter at 12:12 AM • 1 Comments •
March 27, 2008
Category: phylogeny
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 the multiple copies of 16S ribosomal RNA (rRNA)...
Posted by Sandra Porter at 9:11 AM • 22 Comments •
March 20, 2008
Category: Computers and software
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++ plug-in, that does something with WX Windows...
Posted by Sandra Porter at 9:10 AM • 12 Comments •
March 19, 2008
Category: molecular structures
A video tutorial on molecular structures.
Posted by Sandra Porter at 5:37 PM • 1 Comments •
Category: Science education
It's not Linux.
Posted by Sandra Porter at 5:23 PM • 6 Comments •
March 17, 2008
Category: Science education
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 structures and drug resistance, but if you have topic requests, feel free to submit them in the comments....
Posted by Sandra Porter at 6:13 PM • 0 Comments •
Category: Bioinformatics
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....
Posted by Sandra Porter at 2:05 PM • 3 Comments •
March 16, 2008
Category: Science Art
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....
Posted by Sandra Porter at 6:20 PM • 2 Comments •
Category: Cats
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 learn if cougars and people can coexist. The biologists think most of...
Posted by Sandra Porter at 11:42 AM • 0 Comments •
March 14, 2008
Category: Humor
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 bills for texting and...
Posted by Sandra Porter at 9:29 PM • 0 Comments •
Category: Computers and software
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 something new, since Office 2004 on Mac OS 10.5...
Posted by Sandra Porter at 2:31 PM • 21 Comments •
March 13, 2008
Category: Bioinformatics
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 the people who participated in the challenge found...
Posted by Sandra Porter at 6:42 PM • 0 Comments •
Category: Bioinformatics
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 people who are interested in Next Generation DNA...
Posted by Sandra Porter at 12:28 PM • 0 Comments •
March 12, 2008
Category: Computers and software
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 students turned...
Posted by Sandra Porter at 12:50 PM • 35 Comments •
March 11, 2008
Category: Microbiology
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 positions of ribosomal RNA...
Posted by Sandra Porter at 12:00 PM • 6 Comments •
Category: Biology (Macroscopic )
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 and Canada. Images from the Ikonos satellite tell us though, that future migrating butterflies are...
Posted by Sandra Porter at 10:04 AM • 5 Comments •
Category: teaching
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 should have...
Posted by Sandra Porter at 8:00 AM • 33 Comments •
March 10, 2008
Category: Bioinformatics
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 the EOS satellites delivers a terabyte or more of data...
Posted by Sandra Porter at 9:31 AM • 0 Comments •
Category: teaching
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, Yellow Dog Linux, Vine, Turbo, Slackware, etc.. It...
Posted by Sandra Porter at 8:09 AM • 12 Comments •
March 9, 2008
Category: Humor
Happy Birthday! Is it PZ Myers or Captain Barbosa in disguise?...
Posted by Sandra Porter at 1:50 PM • 2 Comments •
March 7, 2008
Category: sequence analysis
Here's a fun puzzler for you to figure out. The blast graph is here:...
Posted by Sandra Porter at 12:28 PM • 2 Comments •
